Genome-scale genotype-phenotype matching of two Lactococcus lactis plant isolates identifies adaptation mechanisms to the plant niche

NIZO food research, Kluyver Centre for Genomics of Industrial Fermentation, PO Box 20, 6710 BA Ede, The Netherlands; TI Food and Nutrition, P.O. Box 557, 6700 AN Wageningen, The Netherlands; Centre for Molecular and Biomolecular Informatics (CMBI 260), Nijmegen Center for Molecular Life Sciences, Radboud University Medical Centre, P.O. Box 9101, 6500HB, Nijmegen, The Netherlands

^* To whom correspondence should be addressed. Email: roland.siezen{at}nizo.nl.

	Abstract

Lactococcus lactis is a primary constituent of many starter cultures used for the manufacturing of fermented dairy products, but the species also occurs in various non-dairy niches such as (fermented) plant material. Three genome sequences of L. lactis dairy strains (IL1403, SK11, MG1363) are publicly available. An extensive molecular and phenotypic diversity analysis was now performed on two L. lactis plant isolates. Diagnostic sequencing of their genomes resulted in over 2.5 Mb sequence for each strain. A high synteny was found with the genome of L. lactis IL1403, which was used as a template for contig mapping and locating deletions and insertions in the plant L. lactis genomes. Numerous genes were identified that do not have homologs in the published genome sequences of dairy L. lactis strains. Adaptation to growth on substrates derived from plant cell walls is evident from the presence of gene sets for the degradation of complex plant polymers such as xylan, arabinan, glucans and fructans, but also for the uptake and conversion of typical plant cell-wall degradation products such as -galactosides, -glucosides, arabinose, xylose, galacturonate, glucuronate, and gluconate. Further niche-specific differences are found in genes for defense (nisin biosynthesis), stress response (non-ribosomal peptide synthesis, various transporters) and exopolysaccharide biosynthesis, as well as the expected differences in various mobile elements such as prophages, plasmids, R-M systems and IS elements. Many of these genes were identified for the first time in Lactococcus lactis. In most cases good correspondence was found with the phenotypic characteristics of these two strains.