Root mediated uptake of Salmonella is different from phyto-pathogen and associated with the colonization of edible organs

Bacterial inoculation prevents cold-induced electrolyte leakage from tomato seeds and reduces thermal fluctuations in the rhizosphere

BACKGROUND

Low soil temperature and its fluctuation can negatively impact the growth of seedlings. The district of Cooch Behar (India), belonging to the Cwa zone (according to Koppen's classification), receives several cold waves during winter. Our previous study demonstrated that a constant temperature of 20 °C (chilling but not freezing) can cause a loss in the vigor of tomatoes. Since the temperature of the soil is not uniform throughout the day, we hypothesized that the duration of cold exposure can have variable effects on seed vigor.

RESULTS

It was observed that increasing the duration of cold stress can slow down the germination process and reduce vigor. This was due to the cold-mediated damage to cell membranes (due to dehydration) which caused electrolyte leakage and reduced levels of glutathione reductase. In this regard, biopriming seeds with microbes that produce exopolysaccharide (EPS) can be useful as it can form a protective layer on the seeds. Indigenous EPS-producing bacteria, Bacillus, Phytobacter and Priestia sp., were used for biopriming. Priestia and Phytobacter sp. not only reduced the electrolyte leakage but also increased the levels of antioxidant genes. This improved the germination speed and vigor. In a field trial, the rhizosphere of the seedlings pretreated with bioinoculants displayed a reduced thermal fluctuation compared with the untreated seeds.

CONCLUSION

The seedlings treated with bioinoculants grew faster in soil in spite of low soil temperature. This can reduce the nursery time of seedlings. © 2025 Society of Chemical Industry.

Sewage Sludge Promotes the Accumulation of Antibiotic Resistance Genes in Tomato Xylem

Xylem serves as a conduit linking soil to the aboveground plant parts and facilitating the upward movement of microbes into leaves and fruits. Despite this potential, the composition of the xylem microbiome and its associated risks, including antibiotic resistance, are understudied. Here, we cultivated tomatoes and analyzed their xylem sap to assess the microbiome and antibiotic resistance profiles following treatment with sewage sludge. Our findings show that xylem microbes primarily originate from soil, albeit with reduced diversity in comparison to those of their soil microbiomes. Using single-cell Raman spectroscopy coupled with D2O labeling, we detected significantly higher metabolic activity in xylem microbes than in rhizosphere soil, with 87% of xylem microbes active compared to just 36% in the soil. Additionally, xylem was pinpointed as a reservoir for antibiotic resistance genes (ARGs), with their abundance being 2.4-6.9 times higher than in rhizosphere soil. Sludge addition dramatically increased the abundance of ARGs in xylem and also increased their mobility and host pathogenicity. Xylem represents a distinct ecological niche for microbes and is a significant reservoir for ARGs. These results could be used to manage the resistome in crops and improve food safety.

Microgravity and evasion of plant innate immunity by human bacterial pathogens

Spaceflight microgravity and modeled-microgravity analogs (MMA) broadly alter gene expression and physiology in both pathogens and plants. Research elucidating plant and bacterial responses to normal gravity or microgravity has shown the involvement of both physiological and molecular mechanisms. Under true and simulated microgravity, plants display differential expression of pathogen-defense genes while human bacterial pathogens exhibit increased virulence, antibiotic resistance, stress tolerance, and reduced LD50 in animal hosts. Human bacterial pathogens including Salmonella enterica and E. coli act as cross-kingdom foodborne pathogens by evading and suppressing the innate immunity of plants for colonization of intracellular spaces. It is unknown if evasion and colonization of plants by human pathogens occurs under microgravity and if there is increased infection capability as demonstrated using animal hosts. Understanding the relationship between microgravity, plant immunity, and human pathogens could prevent potentially deadly outbreaks of foodborne disease during spaceflight. This review will summarize (1) alterations to the virulency of human pathogens under microgravity and MMA, (2) alterations to plant physiology and gene expression under microgravity and MMA, (3) suppression and evasion of plant immunity by human pathogens under normal gravity, (4) studies of plant-microbe interactions under microgravity and MMA. A conclusion suggests future study of interactions between plants and human pathogens under microgravity is beneficial to human safety, and an investment in humanity's long and short-term space travel goals.

Role of lactoyl-glutathione lyase of Salmonella in the colonization of plants under salinity stress

Salmonella, a foodborne human pathogen, can colonize the members of the kingdom Plantae. However, the basis of the persistence of Salmonella in plants is largely unknown. Plants encounter various biotic and abiotic stress agents in soil. We conjectured that methylglyoxal (MG), one of the common metabolites that accumulate in plants during both biotic and abiotic stress, plays a role in regulating the plant-Salmonella interaction. The interaction of Salmonella Typhimurium with plants under salinity stress was investigated. It was observed that wild-type Salmonella Typhimurium can efficiently colonize the root, but mutant bacteria lacking MG detoxifying enzyme, lactoyl-glutathione lyase (Lgl), showed lower colonization in roots exclusively under salinity stress. This colonization defect is due to the poor viability of the mutated bacterial strains under these conditions. This is the first report to prove the role of MG-detoxification genes in the colonization of stressed plants and highlights the possible involvement of metabolic genes in the evolution of the plant-associated life of Salmonella.

New insights into engineered plant-microbe interactions for pesticide removal

Over the past decades, rapid industrialization along with the overutilization of organic pollutants/pesticides has altered the environmental circumstances. Moreover, various anthropogenic, xenobiotics and natural activities also affected plants, soil, and human health, in both direct and indirect ways. To counter this, several conventional methods are currently practiced, but are uneconomical, noxious, and is yet inefficient for large-scale application. Plant-microbe interactions are mediated naturally in an ecosystem and are practiced in several areas. Plant growth promoting rhizobacteria (PGPR) possess certain attributes affecting plant and soil consequently performing decontamination activity via a direct and indirect mechanism. PGPR also harbors indispensable genes stimulating the mineralization of several organic and inorganic compounds. This makes microbes potential candidates for contributing to sustainably remediating the harmful pesticide contaminants. There is a limited piece of information about the plant-microbe interaction pertaining predict and understand the overall interaction concerning a sustainable environment. Therefore, this review focuses on the plant-microbe interaction in the rhizosphere and inside the plant's tissues, along with the utilization augmenting the crop productivity, reduction in plant stress along with decontamination of pesticides/organic pollutants in soil for sustainable environmental management.

RpoS contributes in a host-dependent manner to Salmonella colonization of the leaf apoplast during plant disease

Contaminated fresh produce has been routinely linked to outbreaks of Salmonellosis. Multiple studies have identified Salmonella enterica factors associated with successful colonization of diverse plant niches and tissues. It has also been well documented that S. enterica can benefit from the conditions generated during plant disease by host-compatible plant pathogens. In this study, we compared the capacity of two common S. enterica research strains, 14028s and LT2 (strain DM10000) to opportunistically colonize the leaf apoplast of two model plant hosts Arabidopsis thaliana and Nicotiana benthamiana during disease. While S. enterica 14028s benefited from co-colonization with plant-pathogenic Pseudomonas syringae in both plant hosts, S. enterica LT2 was unable to benefit from Pto co-colonization in N. benthamiana. Counterintuitively, LT2 grew more rapidly in ex planta N. benthamiana apoplastic wash fluid with a distinctly pronounced biphasic growth curve in comparison with 14028s. Using allelic exchange, we demonstrated that both the N. benthamiana infection-depedent colonization and apoplastic wash fluid growth phenotypes of LT2 were associated with mutations in the S. enterica rpoS stress-response sigma factor gene. Mutations of S. enterica rpoS have been previously shown to decrease tolerance to oxidative stress and alter metabolic regulation. We identified rpoS-dependent alterations in the utilization of L-malic acid, an abundant carbon source in N. benthamiana apoplastic wash fluid. We also present data consistent with higher relative basal reactive oxygen species (ROS) in N. benthamiana leaves than in A. thaliana leaves. The differences in basal ROS may explain the host-dependent disease co-colonization defect of the rpoS-mutated LT2 strain. Our results indicate that the conducive environment generated by pathogen modulation of the apoplast niche can vary from hosts to host even with a common disease-compatible pathogen.

Lysinibacillus macroides-mediated control of cellulose-producing morphotype of Salmonella

BACKGROUND

Soil-dwelling human pathogens like Salmonella are transmitted by fresh produce such as tomato, spinach, onion and cabbage. With >2600 serovars, it is difficult to classify the good plant colonizers from the non-colonizers. Generally, soil microbiota are classified as autochthonous or zymogenous organisms, based on their ability to survive in soil. However, such information for soil-dwelling human pathogens is not available Thus there is a need to classify these organisms for designing a strategy to prevent their outbreak. Moreover, soil harbours a plethora of microbes, which can be screened for competitive organisms to control such human pathogens.

RESULTS

In this study, we examined whether the morphotype based on the attachment factors (e.g., cellulose and curli fimbri) of Salmonella was important for its colonization of roots. Secondly, we tracked the location of the bacteria in the plant cell. Interestingly, most of the epidermal cells occupied by Salmonella showed propidium iodide-positive nuclei. As an extension of the study, a screening of competitive rhizospheric bacteria was performed. One isolate, identified as Lysinibacillus macroides, was able to inhibit the biofilm of Salmonella and subsequently reduced its colonization on roots.

CONCLUSION

Based on this study, we classified the Rdar (red, dry and rough) morphotypes as good plant colonists. The ability to colonize and subsequent kill the live plant cell throws light on the zymogenous life cycle of soil-dwelling Salmonella. Additionally, Lysinibacillus macroides served as a biocontrol agent by reducing the burden of Salmonella in various vegetables. Such organisms can further be explored to prevent contamination of the food chain. © 2022 Society of Chemical Industry.

Internalisation of Salmonella spp. by Typha latifolia and Cyperus papyrus in vitro and implications for pathogen removal in Constructed Wetlands

ABSTRACTFreshwater contamination by enteric pathogens is implicated in the high frequency of diarrhoeal diseases in low to middle income countries, typically due to poor wastewater management. Constructed Wetlands are a cost-effective and sustainable alternative to conventional/mechanical treatment technologies, but the pathogen removal mechanisms in Constructed Wetlands are not fully understood. This study investigated for the first time the internalisation of Salmonella spp. by Typha latifolia and Cyperus papyrus in hydroponic microcosms. Presence of Salmonella spp. within roots, rhizomes and shoots was assayed using agar-based methods over a period of 12 days. Concentration of Salmonella spp. in growth media showed 2.7 and 4.8 log unit reduction with T. latifolia and C. papyrus, respectively, and 1.8 and 6.0 log unit in unplanted units. Salmonella spp. was recovered from root and rhizome tissues of T. latifolia (up to 4.4 logCFU/g) and C. papyrus (up to 3.4 logCFU/g), and the bacteria were highly concentrated in the epidermis and cortex. However, Salmonella spp. was not detected in the stems and leaves of the two plant species. The present study demonstrates for the first time that these macrophytes internalise cells of Salmonella spp., which could be one pathogen removal mechanism employed by wetland plants.

Antagonistic Interaction between Auxin and SA Signaling Pathways Regulates Bacterial Infection through Lateral Root in Arabidopsis

Pathogen entry into host tissues is a critical and first step in infections. In plants, the lateral roots (LRs) are a potential entry and colonization site for pathogens. Here, using a GFP-labeled pathogenic bacterium Pseudomonas syringae pv. tomato strain DC3000 (Pto DC3000), we observe that virulent Pto DC3000 invades plants through emerged LRs in Arabidopsis. Pto DC3000 strongly induced LR formation, a process that was dependent on the AUXIN RESPONSE FACTOR7 (ARF7)/ARF19-LATERAL ORGAN BOUNDARIES-DOMAIN (LBD) regulatory module. We show that salicylic acid (SA) represses LR formation, and several mutants defective in SA signaling are also involved in Pto DC3000-induced LR development. Significantly, ARF7, a well-documented positive regulator of LR development, directly represses the transcription of PR1 and PR2 to promote LR development. This study indicates that ARF7-mediated auxin signaling antagonizes with SA signaling to control bacterial infection through the regulation of LR development.

Impact of Plant Pathogen Infection on Salmonella enterica subsp. enterica Serotype Typhimurium Persistence in Tomato Plants

ABSTRACT

We investigated whether the co-occurrence of phytopathogens (Clavibacter michiganensis subsp. michiganensis [Cmm] and Xanthomonas gardneri [Xg]) frequently encountered in tomato production and Salmonella enterica subsp. enterica serotype Typhimurium (strain JSG626) affects the persistence of these pathogens in tomato plant tissues during the early stages of plant growth. Cmm increased the recovery of Salmonella Typhimurium (up to 1.8 log CFU per plant at 21 days postinoculation [DPI]) from coinoculated tomato plants compared with plants inoculated with Salmonella Typhimurium alone (P < 0.05). Xg had no effect on Salmonella Typhimurium persistence in the plants. Increased persistence of Salmonella Typhimurium was also observed when it was inoculated 7 days after Cmm inoculation of the same plant (P < 0.05). In contrast, Salmonella Typhimurium reduced the population of both Cmm and Xg (up to 1.5 log CFU per plant at 21 DPI; P < 0.05) in coinoculated plants compared with plants inoculated with Cmm or Xg alone. The Xg population increased (1.16 log CFU per plant at 21 DPI; P < 0.05) when Salmonella Typhimurium was inoculated 7 days after Xg inoculation compared with plants inoculated with Xg alone. Our findings indicate that the type of phytopathogen present in the phyllosphere and inoculation time influence the persistence of Salmonella Typhimurium JSG626 and its interactions with phytopathogens cocolonized in tomato plants. Salmonella reduced the phytopathogen load in plant tissues, and Cmm enhanced the recovery of Salmonella from the coinoculated plant tissues. However, further investigations are needed to understand the mechanisms behind these interactions.

HIGHLIGHTS

Factors influencing the persistence of enteropathogenic bacteria in wetland habitats and implications for water quality

AIMS

To better understand the persistence dynamics of enteropathogenic bacteria in freshwater wetland habitats, we constructed lab-scale mesocosms planted with two different wetland plant species using a subsurface flow wetland design. Mesocosms were treated with either a high-quality or a poor-quality water source to examine the effects of water quality exposure and plant species on Escherichia coli, Salmonella spp. and Enterococcus spp. in the rhizoplane, rhizosphere and water of wetland habitats.

METHODS AND RESULTS

Quantities of study micro-organisms were detected using real-time PCR in wetland mesocosms. A combination of molecular and culture-based methods was also used to enumerate these organisms from surface water and plant material at high, medium and poor water quality sites in the field. We found that all three enteropathogenic micro-organisms were influenced by microhabitat type and plant species. Organisms differed with respect to their predominant microhabitat and the extent of persistence associated with wetland plant species in the mesocosm study. Of the monitored pathogens, only E. coli was influenced by both water quality treatment and plant species. Salmonella spp. quantities in the rhizoplane consistently increased in all treatments over the course of the mesocosm experiment.

CONCLUSIONS

Plant species selection appears to be an overlooked aspect of constructed wetland design with respect to the removal of enteropathogenic micro-organisms. Escherichia coli and Enterococcus concentrations in wetland outflow were significantly different between the two plant species tested, with Enterococcus concentrations being significantly higher in mesocosms planted with Phalaris arundinaceae and E. coli concentrations being higher in mesocosms planted with Veronica anagallis-aquatica. Furthermore, there is evidence that the rhizoplane is a significant reservoir for Salmonella spp. within wetland habitats.

SIGNIFICANCE AND IMPACT OF THE STUDY

This is the first time that Salmonella spp. has been shown to proliferate under natural conditions within the rhizoplane. This will contribute to our understanding of wetland removal mechanisms for enteropathogenic bacteria. This study identifies the rhizoplane as a potentially important reservoir for human pathogenic micro-organisms and warrants additional study to establish whether this finding is applicable in non-wetland habitats.

Co-cultivation of Beta vulgaris limits the pre-harvest colonization of foodborne pathogen (Salmonella spp.) on tomato

Soil-borne Salmonella is associated with a large number of food-related disease outbreaks linked to pre-harvest contamination of plants (like tomato) in agricultural fields. Controlling the spread of Salmonella at field is very important in order to prevent various food-borne illnesses. One such approach involves the utilization of antimicrobial secondary metabolite of plant origin. We screened common salad vegetables for anti-Salmonella activity. Beta vulgaris root (beetroot) had very low colonization of Salmonella under in vitro conditions. We hypothesized that beetroot can be used to reclaim the soil contaminated with Salmonella. Cultivation of B. vulgaris in Salmonella treated soil brings down its CFU significantly. Since these antimicrobial effects are non-specific, a co-cultivation system of beet and tomato (a Salmonella susceptible plant) was used to analyze the effect on soil and its microbiota. The soil physicochemical properties and bacterial diversity were unaffected when tomato and beet co-cultivation was used. However, Salmonella burden on the tomato was reduced and its yield was restored. Thus, the inclusion of these crops in the crop-rotation or as a mixed/intercrop or as a bio-control crop can be a fruitful tool to reclaim the Salmonella contaminated soil.

Salmonella adapts to plants and their environment during colonization of tomatoes

Humans and animals are considered typical hosts for Salmonella, however, also plants can be colonized. Tomatoes were linked to salmonellosis outbreaks already on several occasions. The aim of this study was, therefore, to establish a comprehensive view on the interaction between Salmonella enterica and tomatoes, and to test the hypothesis that colonization of plants is an interactive process. We assessed the persistence of Salmonella in agricultural soil, the colonization pattern in and on tomatoes, as well as the reciprocal responses of tomatoes to different Salmonella strains and Salmonella to root exudates and tomato-related media. This study revealed that Salmonella can persist in the soil and inside the tomato plant. Additionally, we show that Salmonella strains have particular colonization pattern, although the persistence inside the plant differs between the tested strains. Furthermore, the transcriptome response of tomato showed an up-regulation of several defense-related genes. Salmonella transcriptome analysis in response to the plant-based media showed differentially regulated genes related to amino acid and fatty acid synthesis and stress response, while the response to root exudates revealed regulation of the glyoxylate cycle. Our results indicate that both organisms actively engage in the interaction and that Salmonella adapts to the plant environment.

Rhizospheric life of Salmonella requires flagella-driven motility and EPS-mediated attachment to organic matter and enables cross-kingdom invasion

Salmonella is an established pathogen of the members of the kingdom Animalia. Reports indicate that the association of Salmonella with fresh, edible plant products occurs at the pre-harvest state, i.e. in the field. In this study, we follow the interaction of Salmonella Typhimurium with the model plant Arabidopsis thaliana to understand the process of migration in soil. Plant factors like root exudates serve as chemo-attractants. Our ex situ experiments allowed us to track Salmonella from its free-living state to the endophytic state. We found that genes encoding two-component systems and proteins producing extracellular polymeric substances are essential for Salmonella to adhere to the soil and roots. To understand the trans-kingdom flow of Salmonella, we fed the contaminated plants to mice and observed that it invades and colonizes liver and spleen. To complete the disease cycle, we re-established the infection in plant by mixing the potting mixture with the fecal matter collected from the diseased animals. Our experiments revealed a cross-kingdom invasion by the pathogen via passage through a murine intermediate, a mechanism for its persistence in the soil and invasion in a non-canonical host. These results form a basis to break the life-cycle of Salmonella before it reaches its animal host and thus reduce Salmonella contamination of food products.