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Chloropicrin is widely used to control ginger wilt in China, which have an enormous impact on soil microbial diversity. However, little is known on the possible legacy effects on soil microbial community composition with continuous fumigation over different years. In this report, we used high throughput Illumina sequencing and Biolog ECO microplates to determine the bacterial community and microbial metabolic activity in ginger harvest fields of non-fumigation (NF), chloropicrin-fumigation for 1 year (F_1) and continuous chloropicrin-fumigation for 3 years (F_3). The results showed that microbial richness and diversity in F_3 were the lowest, while the metabolic activity had no significant difference. With the increase of fumigation years, the incidence of bacterial wilt was decreased, the relative abundance of  Actinobacteria  and  Saccharibacteria  were gradually increased. Using LEfSe analyses, we found that  Saccharibacteria  was the most prominent biomarker in F_3. Eight genera associated with antibiotic production in F_3 were screened out, of which seven belonged to  Actinobacteria , and one belonged to  Bacteroidetes.  The study indicated that with the increase of fumigation years, soil antibacterial capacity may be increased (possible reason for reduced the incidence of bacterial wilt), and  Saccharibacteria  played a potential role in evaluating the biological effects of continuous fumigation.   Electronic supplementary material  The online version of this article (doi:10.1186/s13568-017-0475-1) contains supplementary material, which is available to authorized users.

Legacy effects of continuous chloropicrin-fumigation for 3-years on soil microbial community composition and metabolic activity