André C. Velásquez , José C. Huguet-Tapia, and Sheng Yang He

PNAS March 28, 2022 | 119 (14) e2114460119

Significance

Plants evolved in an environment colonized by a vast number of microbes, which collectively constitute the plant microbiota. The majority of microbiota taxa are nonpathogenic and may be beneficial to plants under certain ecological or environmental conditions. We conducted experiments to understand the features of long-term interactions of nonpathogenic microbiota members with plants. We found that a multiplication–death equilibrium explained the shared long-term static populations of nonpathogenic bacteria and that in planta bacterial transcriptomic signatures were characteristic of the stationary phase, a physiological state in which stress protection responses are induced. These results may have significant implications in understanding the bulk of “nonpathogenic” plant–microbiota interactions that occur in agricultural and natural ecosystems.

Abstract

Plants and animals are in constant association with a variety of microbes. Although much is known about how pathogenic and symbiotic microbes interact with plants, less is known about the population dynamics, adaptive traits, and transcriptional features of the vast number of microbes that make up the bulk of the plant microbiota. The majority of microbiota taxa are either commensal, natural mutants of pathogens, or pathogens that encounter strong immune responses due to plant recognition of pathogen effectors. How these “nonpathogenic” microbes interact with plants is poorly understood, especially during long-term, steady-state interactions, which are more reflective of plant–microbiota interactions in nature. In this study, we embarked upon long-term population and in planta transcriptomic studies of commensal endophytic bacteria and compared them to nonpathogenic or effector-triggered immunity-inducing strains of the bacterial pathogen Pseudomonas syringae. Our results led to the discovery of multiplication–death equilibrium as a common basis for the shared long-term static population densities of these bacteria. A comprehensive in planta transcriptomic analysis using multiple time points after inoculation revealed a striking similarity between the transcriptomic features of nonpathogenic P. syringae to that of bacteria in stationary phase in vitro, a metabolically active physiological state in which the production of adaptive secondary metabolites and stress responses are induced. We propose that the long-term population and transcriptomic features of nonpathogenic bacteria captured in this study likely reflect the physiological steady state encountered by the bulk of endophytic microbiota—excluding virulent pathogens—in their life-long interactions with plants in nature.

See: https://www.pnas.org/doi/10.1073/pnas.2114460119

Figure 2; Bacterial population stasis is caused by an equilibrium between bacterial cell death and multiplication. (A) In vitro growth of P. syringae pv. tomato (Pst) ΔhrcCΔCFA cultures in logarithmic or stationary phase after the addition of 400 µg mL⁻¹ of carbenicillin or H₂O control. The arrow indicates the time at which H₂O or the antibiotic was added to the culture. The y axis is in logarithmic scale. (B) In planta bacterial population density of Pst ΔhrcCΔCFA or Pandoraea sp. Col-0-28 in Col-0 plants after the addition of 400 µg mL⁻¹ of carbenicillin or cefotaxime, antibiotics that kill dividing bacteria. Circles show individual biological repetitions; error bars indicate the SEM. Different letters indicate different means (Tukey’s honestly significant difference test; P < 0.05). In t_x, x = number of days postinoculation.