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Background  Important industrial traits have been linked to plasmids in  Lactococcus lactis .    Results  The dairy isolate  L. lactis  subsp.  lactis  biovar diacetylactis FM03P was sequenced revealing the biggest plasmidome of all completely sequenced and published  L. lactis  strains up till now. The 12 plasmids that were identified are: pLd1 (8277 bp), pLd2 (15,218 bp), pLd3 (4242 bp), pLd4 (12,005 bp), pLd5 (7521 bp), pLd6 (3363 bp), pLd7 (30,274 bp), pLd8 (47,015 bp), pLd9 (15,313 bp), pLd10 (39,563 bp), pLd11 (9833 bp) and pLd12 (3321 bp). Structural analysis of the  repB  promoters and the RepB proteins showed that eleven of the plasmids replicate via the theta-type mechanism, while only plasmid pLd3 replicates via a rolling-circle replication mechanism. Plasmids pLd2, pLd7 and pLd10 contain a highly similar operon involved in mobilisation of the plasmids. Examination of the twelve plasmids of  L. lactis  FM03P showed that 10 of the plasmids carry putative genes known to be important for growth and survival in the dairy environment. These genes encode technological functions such as lactose utilisation ( lacR-lacABCDFEGX ) ,  citrate uptake ( citQRP ), peptide degradation ( pepO  and  pepE ) and oligopeptide uptake ( oppDFBCA ), uptake of magnesium and manganese (2  mntH ,  corA ), exopolysaccharides production ( eps  operon), bacteriophage resistance (1  hsdM , 1  hsdR  and 7 different  hsdS  genes of a type I restriction-modification system, an operon of three genes encoding a putative type II restriction-modification system and an abortive infection gene) and stress resistance (2  uspA ,  cspC  and  cadCA ). Acquisition of these plasmids most likely facilitated the adaptation of the recipient strain to the dairy environment. Some plasmids were already lost during a single propagation step signifying their instability in the absence of a selective pressure.    Conclusions   Lactococcus lactis  FM03P carries 12 plasmids important for its adaptation to the dairy environment. Some of the plasmids were easily lost demonstrating that propagation outside the dairy environment should be minimised when studying dairy isolates of  L. lactis .    Electronic supplementary material  The online version of this article (10.1186/s12864-018-5005-2) contains supplementary material, which is available to authorized users.

Large plasmidome of dairy Lactococcus lactis subsp. lactis biovar diacetylactis FM03P encodes technological functions and appears highly unstable