Unravelling the bacterial community composition of Valerianella locusta, a cold tolerant plant

Abstract

Low temperatures greatly affect plant growth. Besides the development of own protection mechanisms, plants may rely on microorganisms to help them cope with cold. As Valerianella locusta (lamb’s lettuce) is a cold-adapted plant, it represents an interesting plant to understand how cold affects the root bacteriome. By means of amplicon sequencing of 16S rRNA genes, we identified the taxa forming the main cold root bacteriome of lamb’s lettuce. The analysis of the root microbiome of a naturally growing V. locusta population and the study of the changes in the root microbiome of cultivated V. locusta grown under cold and ambient conditions allowed us to detect four cold-responsive families, of which Oxalobacteraceae presented the strongest shift under chilling temperatures. Moreover, the plant genotype had a small, but significant, effect on the response of the root bacteriome to cold. Finally, several bacterial candidates were discovered that may possibly alleviate the effect of low temperatures on plant fitness, namely Massilia ASV2, Flavobacterium ASV5 and ASV11, or Acidovorax ASV20. However, currently, only ten cold-enriched isolates could be obtained in cultivation, of which Flavobacterium R-83141, Polaromonas R-83176, R-83177, R-83175 and Acidovorax R-83129, were able to increase either the root, shoot and/or total fresh weight of a cold sensitive ecotype of A. thaliana (Cvi-0). Our results provide an overview of the taxa forming the root microbiome of this species and of the compositional shift that occurs under cold temperature treatment, demonstrating the impact of low temperatures on the composition of the root microbiome.