Survival of Listeria monocytogenes in Soil Requires AgrA-Mediated Regulation

Abstract

In a recent paper, we demonstrated that inactivation of the Agr system affects the patterns of survival of Listeria monocytogenes (A.-L. Vivant, D. Garmyn, L. Gal, and P. Piveteau, Front Cell Infect Microbiol 4:160, http://dx.doi.org/10.3389/fcimb.2014.00160). In this study, we investigated whether the Agr-mediated response is triggered during adaptation in soil, and we compared survival patterns in a set of 10 soils. The fate of the parental strain L. monocytogenes L9 (a rifampin-resistant mutant of L. monocytogenes EGD-e) and that of a ΔagrA deletion mutant were compared in a collection of 10 soil microcosms. The ΔagrA mutant displayed significantly reduced survival in these biotic soil microcosms, and differential transcriptome analyses showed large alterations of the transcriptome when AgrA was not functional, while the variations in the transcriptomes between the wild type and the ΔagrA deletion mutant were modest under abiotic conditions. Indeed, in biotic soil environments, 578 protein-coding genes and an extensive repertoire of noncoding RNAs (ncRNAs) were differentially transcribed. The transcription of genes coding for proteins involved in cell envelope and cellular processes, including the phosphotransferase system and ABC transporters, and proteins involved in resistance to antimicrobial peptides was affected. Under sterilized soil conditions, the differences were limited to 86 genes and 29 ncRNAs. These results suggest that the response regulator AgrA of the Agr communication system plays important roles during the saprophytic life of L. monocytogenes in soil.

FIG 1

Principal component analysis (PCA) of soils. The length and direction of the lines represent the contribution of each parameter. The numbers indicate soil sample numbers, and the letters indicate whether soils were from an agricultural field (AF), a prairie (P), or a forest (F). CEC, cation-exchange capacity.

FIG 2

L. monocytogenes parental strain (blue lines) and ΔagrA mutant (red lines) dynamics in soil microcosms. Error bars represent standard deviations from three independent replicates. *, significant differences (P < 0.05) were observed after ANOVA.

FIG 3

L. monocytogenes parental strain and ΔagrA mutant abundance after 14 days of incubation in soil microcosms. Error bars represent standard deviations from three independent replicates. Letters indicate that significant differences were observed after ANOVA.

FIG 4

Heat map of the set of genes with significant differences in levels of expression between the ΔagrA mutant and the parental strain under biotic soil conditions. Expression levels were standardized so that those of the parental strain under sterilized conditions were set as the baseline. Genes are represented in rows. The expression levels of these genes under sterilized conditions are also presented.

FIG 5

Functional categories identified to be significant by gene ontology and the percentage of genes from the set of genes with lower transcript levels in the ΔagrA mutant than in parental strain L. monocytogenes L9 under biotic conditions. The values in parentheses represent the number of genes with significant variations in transcript levels/the total number of genes in the functional category. IS, insertion sequence.

FIG 6

Heat map of the set of genes with significant differences in levels of expression between the ΔagrA mutant and the parental strain under sterilized soil conditions. Expression levels were standardized so that those of the parental strain under sterilized conditions were set as the baseline. Genes are represented in rows. The expression levels of these genes under biotic conditions are also presented.