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Background   Bacillus thuringiensis  ( Bt ) crops have been cultivated at a large scale over the past several decades, which have raised concern about unintended effects on natural environments. Microbial communities typically contain numerous rare taxa that make up the majority of community populations. However, the response of dominant and rare taxa for fungal diversity to the different root environments of  Bt  plants remains unclear.    Results  We quantified fungal population sizes and community composition via quantitative PCR of ITS genes and 18S rRNA gene sequencing of, respectively, that were associated with  Bt  and conventional cotton variety rhizosphere soils from different plant growth stages. qPCR analyses indicated that fungal abundances reached their peak at the seedling stage and that the taproots and lateral root rhizospheres of the  Bt  cotton SGK321 were significantly different. However, no significant differences in population sizes were detected between the same root zones from  Bt  and the conventional cotton varieties. The overall patterns of fungal genera abundances followed that of the dominant genera, whereas overall patterns of fungal genera richness followed those of the rare genera. These results suggest that the dominant and rare taxa play different roles in the maintenance of rhizosphere microhabitat ecosystems. Cluster analyses indicated a separation of fungal communities based on the lateral roots or taproots from the three cotton varieties at the seedling stage, suggesting that root microhabitats had marked effects on fungal community composition. Redundancy analyses indicated that pH was more correlated to soil fungal community composition than Bt protein content.    Conclusions  In conclusion, these results indicate that dominant and rare fungal taxa differentially contribute to community dynamics in different root microhabitats of both  Bt  and conventional cotton varieties. Moreover, these results showed that the rhizosphere fungal community of  Bt  cotton did not respond significantly to the presence of Bt protein when compared to the two conventional cotton varieties.    Electronic supplementary material  The online version of this article (10.1186/s40168-018-0570-9) contains supplementary material, which is available to authorized users.

microbiome

The response of dominant and rare taxa for fungal diversity within different root environments to the cultivation of Bt and conventional cotton varieties