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Abstract
BackgroundImportant industrial traits have been linked to plasmids in Lactococcus lactis.ResultsThe 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.ConclusionsLactococcus 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.
Highlights
Important industrial traits have been linked to plasmids in Lactococcus lactis
Sequencing Lactococcus lactis subsp. lactis biovar diacetylactis FM03P has been isolated from 10-week-old Samsø cheese
Subsequent next-generation sequencing attempts of L. lactis FM03-V1, a single colony isolate of a culture of L. lactis FM03P, using only Illumina revealed the sequence of 5 other plasmids, designated pLd8 to pLd12
Summary
Lactococcus lactis is a lactic acid bacterium which is extensively used in food fermentation processes. It is one of the main species used in starter cultures for the production of fermented dairy products, such as cheese, quark, cottage cheese and sour cream [1, 2]. Self-replicating extrachromosomal DNA molecules which can be lost and acquired in van Mastrigt et al BMC Genomics (2018) 19:620 response to changing environmental conditions. This behaviour facilitates their distribution among bacteria occupying the same ecological niche. They could give the bacteria the ability to grow better on particular nutrients or survive better under harsh conditions, but at the same time they can be a metabolic burden by either replication of the plasmids or by expression of the plasmid-encoded genes [12]
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