Rhizosphere provides a new paradigm on the prevalence of lysogeny in the environment

Abstract Bacteria and phage enter into lysogeny to survive under nutrient-limiting environment. Plant-soil feedback improves nutrients and increases density and diversity of bacteria in the rhizosphere soil, however, its impact on lysogeny is not understood. The rhizosphere and bulk soil of plants colonizing nutrient-deficient abandoned mines may serve as ideal habitats to analyze the role of plants in governing lifestyle of bacteria and phage. Therefore, to unravel the importance of rhizosphere as a determinant of lysogeny, we analyzed bulk and rhizosphere soils of wild grass, Saccharum munja from an abandoned mine in Delhi (India) for nutrient concentration, bacterial density and diversity, and lysogens. We hypothesized that the rhizosphere, though nutrient-rich, remains nutrient-limiting and favours lysogeny because of an intense competition among bacteria for nutrients. Soil analyses confirmed that Bhatti mine soil was sandy loam with low concentration of nutrients but wild grass exerts a strong rhizosphere effect on the mine soil and improves its nutrient concentration and bacterial density and diversity. The rhizosphere soil, though nutrient-rich, supports 94–100% Mitomycin C-induced lysogens, whereas, the bulk soil, though nutrient-limiting, harbors 70–71% of Mitomycin C-induced lysogens only. The 16S rRNA sequencing showed a similar trend of bacterial diversity as bulk soil harbours bacteria of 2 genera and 3 species, whereas rhizosphere soil supports bacteria of 8 genera, 25 species. The rhizosphere soil showed 170 times higher colony-forming units than the bulk soil. Lysogeny in the rhizosphere is a characteristic of the highly competitive environment of the species-rich bacterial community. We emphasize that the gross concentration of nutrients alone provides a limited view of nutrient scarcity because high density and diversity rhizobacteria create a challenge of access to nutrients and thus present a nutrient-limiting environment. The rhizosphere, therefore, provides a new paradigm to explain lysogeny in soil. A factorial design experiment involving varying nutrients and bacterial competition would further help in unraveling the ecological significance of lysogeny in soils.