Alginate genes are required for optimal soil colonization and persistence by Pseudomonas fluorescens Pf0-1

Molecular insights into PGPR fluorescent Pseudomonads complex mediated intercellular and interkingdom signal transduction mechanisms in promoting plant's immunity

The growth-promoting and immune modulatory properties of different strains of plant growth promoting rhizobacteria (PGPR) fluorescent Pseudomonads complex (PFPC) can be explored to combat food security challenges. These PFPC prime plants through induced systemic resistance, fortify plants to overcome future pathogen-mediated vulnerability by eliciting robust systemic acquired resistance through regulation by nonexpressor of pathogenesis-related genes 1. Moreover, outer membrane vesicles released from Pseudomonas fluorescens also elicit a broad spectrum of immune responses, presenting a rapid viable alternative to whole cells. Thus, PFPC can help the host to maintain an equilibrium between growth and immunity, ultimately leads to increased crop yield.

Role of extracellular matrix components in biofilm formation and adaptation of Pseudomonas ogarae F113 to the rhizosphere environment

Regulating the transition of bacteria from motile to sessile lifestyles is crucial for their ability to compete effectively in the rhizosphere environment. Pseudomonas are known to rely on extracellular matrix (ECM) components for microcolony and biofilm formation, allowing them to adapt to a sessile lifestyle. Pseudomonas ogarae F113 possesses eight gene clusters responsible for the production of ECM components. These gene clusters are tightly regulated by AmrZ, a major transcriptional regulator that influences the cellular levels of c-di-GMP. The AmrZ-mediated transcriptional regulation of ECM components is primarily mediated by the signaling molecule c-di-GMP and the flagella master regulator FleQ. To investigate the functional role of these ECM components in P. ogarae F113, we performed phenotypic analyses using mutants in genes encoding these ECM components. These analyses included assessments of colony morphology, dye-staining, static attachment to abiotic surfaces, dynamic biofilm formation on abiotic surfaces, swimming motility, and competitive colonization assays of the rhizosphere. Our results revealed that alginate and PNAG polysaccharides, along with PsmE and the fimbrial low molecular weight protein/tight adherence (Flp/Tad) pilus, are the major ECM components contributing to biofilm formation. Additionally, we found that the majority of these components and MapA are needed for a competitive colonization of the rhizosphere in P. ogarae F113.

Corner Flows Induced by Surfactant-Producing Bacteria Bacillus subtilis and Pseudomonas fluorescens

A mechanistic understanding of bacterial spreading in soil, which has both air and water in angular pore spaces, is critical to control pathogenic contamination of soil and to design bioremediation projects. A recent study (J. Q. Yang, J. E. Sanfilippo, N. Abbasi, Z. Gitai, et al., Proc Natl Acad Sci U S A 118:e2111060118, 2021, https://doi.org/10.1073/pnas.2111060118) shows that Pseudomonas aeruginosa can self-generate flows along sharp corners by producing rhamnolipids, a type of biosurfactants that change the hydrophobicity of solid surfaces. We hypothesize that other types of biosurfactants and biosurfactant-producing bacteria can also generate corner flows. Here, we first demonstrate that rhamnolipids and surfactin, biosurfactants with different chemical structures, can generate corner flows. We identify the critical concentrations of these two biosurfactants to generate corner flow. Second, we demonstrate that two common soil bacteria, Pseudomonas fluorescens and Bacillus subtilis (which produce rhamnolipids and surfactin, respectively), can generate corner flows along sharp corners at the speed of several millimeters per hour. We further show that a surfactin-deficient mutant of B. subtilis cannot generate corner flow. Third, we show that, similar to the finding for P. aeruginosa, the critical corner angle for P. fluorescens and B. subtilis to generate corner flows can be predicted from classic corner flow theories. Finally, we show that the height of corner flows is limited by the roundness of corners. Our results suggest that biosurfactant-induced corner flows are prevalent in soil and should be considered in the modeling and prediction of bacterial spreading in soil. The critical biosurfactant concentrations we identify and the mathematical models we propose will provide a theoretical foundation for future predictions of bacterial spreading in soil. IMPORTANCE The spread of bacteria in soil is critical in soil biogeochemical cycles, soil and groundwater contamination, and the efficiency of soil-based bioremediation projects. However, the mechanistic understanding of bacterial spreading in soil remains incomplete due to a lack of direct observations. Here, we simulate confined spaces of hydrocarbon-covered soil using a transparent material with similar hydrophobicity and visualize the spread of two common soil bacteria, Pseudomonas fluorescens and Bacillus subtilis. We show that both bacteria can generate corner flows at the velocity of several millimeters per hour by producing biosurfactants, soap-like chemicals. We provide quantitative equations to predict the critical corner angle for bacterial corner flow and the maximum distance of the corner spreading. We anticipate that bacterial corner flow is prevalent because biosurfactant-producing bacteria and angular pores are common in soil. Our results will help improve predictions of bacterial spreading in soil and facilitate the design of soil-related bioremediation projects.

Transcriptional Response and Plant Growth Promoting Activity of Pseudomonas fluorescens DR397 under Drought Stress Conditions

Drought is one of the most vulnerable factors that affect crop productivity. Little is known about plant-associated microbiomes and their functional roles in assisting plant growth under drought. We investigated the genetic and transcriptomic characteristics of opportunistic beneficial microorganisms that selectively alleviate stress through plant-bacteria interactions under drought. Pseudomonas fluorescens DR397 was isolated from the drought-prone rhizospheric soil of soybean and showed high metabolic activity at -1.25 Mpa. The genome of DR397 possesses several genes related to the synthesis of compatible solutes (choline and glycine-betaine), exopolysaccharides (alginate and cellulose), and secretion systems (type II, III, IV, and VI), as well as genes related to plant growth promotion (indole-3-acetic acid, transketolase, and thiamine phosphate synthesis). The expression of these genes was significantly upregulated (8- to 263-fold change) only under drought conditions with plant root exudate treatment, whereas subtle transcriptomic changes were observed under solely root exudate treatment. When DR397 was placed on both legume cultivars (Pisum sativum and Phaseolus vulgaris), growth was hardly affected under well-watered conditions, but the shoot and root growths were increased by up from 62.0% to 149.1% compared with the control group under drought conditions. These results provide fundamental insight on the plant-bacterial interactions that alleviate plant stress as an important ecological strategy for improving drought tolerance. IMPORTANCE Drought is a serious abiotic stress on plants as wells as the microbes that coexist with plants, which significantly lowers their fitness. The plant-bacterial interaction is an important strategy to enhance their fitness under drought. However, many knowledge gaps still exist in our understanding of transcriptomic features of bacteria interacting with plant under drought. Here, by investigating the transcriptomic profiles and pot cultivation with legume, we show that the interactions of Pseudomonas fluorescens DR397 with plants change with drought. We, therefore, provide a fundamental evidence of a hidden hero in the soil that promote plant fitness from external stress.

Drought-tolerant Pseudomonas sp. showed differential expression of stress-responsive genes and induced drought tolerance in Arabidopsis thaliana

The growth and persistence of rhizobacteria in soils are highly impacted by moisture stress. In this study, we report the first transcript analysis of four Pseudomonas strains (PS1, PS2, PS3, and PS4) isolated from the root-soil interface of rice and maize associated with different moisture levels during water deprivation. Filtered Pseudomonas sp. cells incubated at low (RH10%) and high (RH85%) relative humidity showed decreased survival of all Pseudomonas sp. at RH10% when compared with RH85%. RT-PCR showed differential expression of treS (trehalose synthase), rpoS (sigma factor), mucA (alginate regulatory gene), and fliM (flagellar motor switch protein gene) in response to exposure to RH10%. However, molecular fingerprinting and nutrient assimilation profile of Pseudomonas strains demonstrated genetic and physiological variation between the four strains irrespective of water regime and host. In vitro testing of these strains showed ACC deaminase activity and gibberellic acid, abscisic acid, indole acetic acid, and exopolysaccharide production. We determined that 50 μl of 1.2 × 10³  CFU ml^-1 of these Pseudomonas strains was enough to protect Arabidopsis plants against drought stress in a pot experiment. Inoculated plants increased their root colonization ability and biomass; however, PS2 showed higher survival (95%), relative water content (59%), chlorophyll (30%), glycine betaine (38%), proline (23%), and reduced MDA (43%) in shoots than irrigated control under induced water deprivation. It can be concluded that all Pseudomonas strains were effective in mitigating drought stress, however, PS2 appears to impart more resistance to drought than the other strains by upregulating key defense mechanisms.

Leveraging Pseudomonas Stress Response Mechanisms for Industrial Applications

Members of the genus Pseudomonas are metabolically versatile and capable of adapting to a wide variety of environments. Stress physiology of Pseudomonas strains has been extensively studied because of their biotechnological potential in agriculture as well as their medical importance with regards to pathogenicity and antibiotic resistance. This versatility and scientific relevance led to a substantial amount of information regarding the stress response of a diverse set of species such as Pseudomonas chlororaphis, P. fluorescens, P. putida, P. aeruginosa, and P. syringae. In this review, environmental and industrial stressors including desiccation, heat, and cold stress, are cataloged along with their corresponding mechanisms of survival in Pseudomonas. Mechanisms of survival are grouped by the type of inducing stress with a focus on adaptations such as synthesis of protective substances, biofilm formation, entering a non-culturable state, enlisting chaperones, transcription and translation regulation, and altering membrane composition. The strategies Pseudomonas strains utilize for survival can be leveraged during the development of beneficial strains to increase viability and product efficacy.

Role of extracellular matrix components in the formation of biofilms and their contribution to the biocontrol activity of Pseudomonas chlororaphis PCL1606

Pseudomonas chlororaphis PCL1606 (PcPCL1606) displays plant-colonizing features and exhibits antagonistic traits against soil-borne phytopathogenic fungi. Biofilm formation could be relevant for the PcPCL1606 lifestyle, and in this study the role of some putative extracellular matrix components (EMC; Fap-like fibre, alginate and Psl-like polysaccharides) in the biofilm architecture and biocontrol activity of this bacterium were determined. EMC such as the Fap-like fibre and alginate polysaccharide play secondary roles in biofilm formation in PcPCL1606, because they are not fundamental to its biofilm architecture in flow cell chamber, but synergistically they have shown to favour bacterial competition during biofilm formation. Conversely, studies on Psl-like polysaccharide have revealed that it may contain mannose, and that it is strongly involved in the PcPCL1606 biofilm architecture and niche competition. Furthermore, the Fap-like fibre and Psl-like exopolysaccharide play roles in early surface attachment and contribute to biocontrol activity against the white root rot disease caused by Rosellinia necatrix in avocado plants. These results constitute the first report regarding the study of the extracellular matrix of the PcPCL1606 strain and highlight the importance of a putative Fap-like fibre and Psl-like exopolysaccharide produced by PcPCL1606 in the biofilm formation process and interactions with the host plant root.

Genetic factors involved in rhizosphere colonization by phytobeneficial Pseudomonas spp

Plant growth-promoting rhizobacteria (PGPR) actively colonize the soil portion under the influence of plant roots, called the rhizosphere. Many plant-beneficial Pseudomonas spp. have been characterized as PGPR. They are ubiquitous rod-shaped motile Gram-negative bacteria displaying a high metabolic versatility. Their capacity to protect plants from pathogens and improve plant growth closely depends on their rhizosphere colonization abilities. Various molecular and cellular mechanisms are involved in this complex process, such as chemotaxis, biofilm formation, secondary metabolites biosynthesis, metabolic versatility, and evasion of plant immunity. The burst in Pseudomonas spp. genome sequencing in recent years has been crucial to better understand how they colonize the rhizosphere. In this review, we discuss the recent advances regarding these mechanisms and the underlying bacterial genetic factors required for successful rhizosphere colonization.