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Background  Representatives of the genus  Bacillus  are increasingly used in agriculture to promote plant growth and to protect against plant pathogens. Unfortunately, hitherto the impact of  Bacillus  inoculants on the indigenous plant microbiota has been investigated exclusively for the species  Bacillus amyloliquefaciens  and was limited to prokaryotes, whilst eukaryotic member of this community, e.g. fungi, were not considered.    Results  The root-colonizing  Bacillus subtilis  PTS-394 supported growth of tomato plants and suppressed soil-borne diseases. Roche 454 pyrosequencing revealed that PTS-394 has only a transient impact on the microbiota community of the tomato rhizosphere. The impact on eukaryota could last up to 14 days, while that on bacterial communities lasted for 3 days only.    Conclusions  Ecological adaptation and microbial community-preserving capacity are important criteria when assessing suitability of bio-inoculants for commercial development. As shown here,  B. subtilis  PTS-394 is acting as an environmentally compatible plant protective agent without permanent effects on rhizosphere microbial community.    Electronic supplementary material  The online version of this article (doi:10.1186/s12866-017-1039-x) contains supplementary material, which is available to authorized users.

Addition of plant-growth-promoting Bacillus subtilis PTS-394 on tomato rhizosphere has no durable impact on composition of root microbiome