Phenazine-Producing Rhizobacteria Promote Plant Growth and Reduce Redox and Osmotic Stress in Wheat Seedlings Under Saline Conditions

Global insights into endophytic bacterial communities of terrestrial plants: Exploring the potential applications of endophytic microbiota in sustainable agriculture

Endophytic microorganisms are indispensable symbionts during plant growth and development and often serve functions such as growth promotion and stress resistance in plants. Therefore, an increasing number of researchers have applied endophytes for multifaceted phytoremediation (e.g., organic pollutants and heavy metals) in recent years. With the availability of next-generation sequencing technologies, an increasing number of studies have shifted the focus from culturable bacteria to total communities. However, information on the composition, structure, and function of bacterial endophytic communities is still not widely synthesized. To explore the general patterns of variation in bacterial communities between plant niches, we reanalyzed data from 1499 samples in 30 individual studies from different continents and provided comprehensive insights. A group of bacterial genera were commonly found in most plant roots and shoots. Our analysis revealed distinct variations in the diversity, composition, structure, and function of endophytic bacterial communities between plant roots and shoots. These variations underscore the sophisticated mechanisms by which plants engage with their endophytic microbiota, optimizing these interactions to bolster growth, health, and resilience against stress. Highlighting the strategic role of endophytic bacteria in promoting sustainable agricultural practices and environmental stewardship, our study not only offers global insights into the endophytic bacterial communities of terrestrial plants but also underscores the untapped potential of these communities as invaluable resources for future research.

Trichoderma virens and Pseudomonas chlororaphis Differentially Regulate Maize Resistance to Anthracnose Leaf Blight and Insect Herbivores When Grown in Sterile versus Non-Sterile Soils

Soil-borne Trichoderma spp. have been extensively studied for their biocontrol activities against pathogens and growth promotion ability in plants. However, the beneficial effect of Trichoderma on inducing resistance against insect herbivores has been underexplored. Among diverse Trichoderma species, consistent with previous reports, we showed that root colonization by T. virens triggered induced systemic resistance (ISR) to the leaf-infecting hemibiotrophic fungal pathogens Colletotrichum graminicola. Whether T. virens induces ISR to insect pests has not been tested before. In this study, we investigated whether T. virens affects jasmonic acid (JA) biosynthesis and defense against fall armyworm (FAW) and western corn rootworm (WCR). Unexpectedly, the results showed that T. virens colonization of maize seedlings grown in autoclaved soil suppressed wound-induced production of JA, resulting in reduced resistance to FAW. Similarly, the bacterial endophyte Pseudomonas chlororaphis 30-84 was found to suppress systemic resistance to FAW due to reduced JA. Further comparative analyses of the systemic effects of these endophytes when applied in sterile or non-sterile field soil showed that both T. virens and P. chlororaphis 30-84 triggered ISR against C. graminicola in both soil conditions, but only suppressed JA production and resistance to FAW in sterile soil, while no significant impact was observed when applied in non-sterile soil. In contrast to the effect on FAW defense, T. virens colonization of maize roots suppressed WCR larvae survival and weight gain. This is the first report suggesting the potential role of T. virens as a biocontrol agent against WCR.

Draft genome analysis for Enterobacter kobei, a promising lead bioremediation bacterium

Lead pollution of the environment poses a major global threat to the ecosystem. Bacterial bioremediation offers a promising alternative to traditional methods for removing these pollutants, that are often hindered by various limitations. Our research focused on isolating lead-resistant bacteria from industrial wastewater generated by heavily lead-containing industries. Eight lead-resistant strains were successfully isolated, and subsequently identified through molecular analysis. Among these, Enterobacter kobei FACU6 emerged as a particularly promising candidate, demonstrating an efficient lead removal rate of 83.4% and a remarkable lead absorption capacity of 571.9 mg/g dry weight. Furthermore, E. kobei FACU6 displayed a remarkable a maximum tolerance concentration (MTC) for lead reaching 3,000 mg/L. To further investigate the morphological changes in E. kobei FACU6 in response to lead exposure, scanning electron microscopy (SEM) and transmission electron microscopy (TEM) were employed. These analyses revealed significant lead adsorption and intracellular accumulation in treated bacteria in contrast to the control bacterium. Whole-genome sequencing was performed to gain deeper insights into E. kobei's lead resistance mechanisms. Structural annotation revealed a genome size of 4,856,454 bp, with a G + C content of 55.06%. The genome encodes 4,655 coding sequences (CDS), 75 tRNA genes, and 4 rRNA genes. Notably, genes associated with heavy metal resistance and their corresponding regulatory elements were identified within the genome. Furthermore, the expression levels of four specific heavy metal resistance genes were evaluated. Our findings revealed a statistically significant upregulation in gene expression under specific environmental conditions, including pH 7, temperature of 30°C, and high concentrations of heavy metals. The outstanding potential of E. kobei FACU6 as a source of diverse genes related to heavy metal resistance and plant growth promotion makes it a valuable candidate for developing safe and effective strategies for heavy metal disposal.

Salt tolerant Pseudomonas taiwanensis PWR-1 in combination with a reduced dose of mineral fertilizers improves the nutritional and antioxidant properties of wheatgrass grown in saline soil

Salt-tolerant plant growth promoting rhizobacteria (ST-PGPR) are known to ameliorate salt stress in plants by various mechanisms. The current study aims to investigate the role of an ST-PGPR strain Pseudomonas taiwanensis PWR-1 applied along with a reduced dose of mineral fertilizers (N, P, and K) in the improvement of the antioxidant and nutritional properties of wheatgrass (Triticum aestivum L.) grown in saline soil. Application of P. taiwanensis PWR-1 along with 50% of the recommended dose of mineral fertilizers resulted in a significant improvement of growth parameters including shoot length (22.79%), root length (20.38%), fresh weight (13.15%), dry weight (92.34%), vigor index (13.36%), and relative water content (48.24%). The combined application of PWR-1 and mineral fertilizers increased the production of osmoprotectants (proline, total soluble sugars, glycine betaine), antioxidants (SOD, POD, APX, CAT, PPO, and reduced glutathione), and free radical scavengers (DPPH and H2O2) in wheatgrass. Furthermore, the concentration of micronutrients (Zn and Fe), macronutrients (N, and P), and vitamins (B1 and E) also increased in the above treatment. Oxidative stress markers (malondialdehyde and electrolyte leakage) and Na+ accumulation were significantly reduced whilst K+ content increased in the shoot, which helped in maintaining the K+/Na+ ratio in wheatgrass under saline conditions. The results indicated that the application of ST-PGPR could not only reduce the dosage of mineral fertilizers but might be useful for improving the nutritional and antioxidant properties of medicinal crops such as wheatgrass under salt-stress conditions. Implementing this approach could result in the reduction of chemical usage, while also facilitating enhanced uptake of micronutrients in crops, particularly in regions affected by salinity.

Exogenous Ethylene Alleviates the Inhibition of Sorbus pohuashanensis Embryo Germination in a Saline-Alkali Environment (NaHCO3)

Saline-alkali stress is a major environmental stress affecting the growth and development of plants such as Sorbus pohuashanensis. Although ethylene plays a crucial role in plant response to saline-alkaline stress, its mechanism remains elusive. The mechanism of action of ethylene (ETH) may be related to the accumulation of hormones, reactive oxygen species (ROS), and reactive nitrogen species (RNS). Ethephon is the exogenous ethylene donor. Therefore, for the present study we initially used different concentrations of ethephon (ETH) to treat S. pohuashanensis embryos and identified the best treatment concentration and method to promote the release of dormancy and the germination of S. pohuashanensis embryos. We then analyzed the physiological indexes, including endogenous hormones, ROS, antioxidant components, and reactive nitrogen, in embryos and seedlings to elucidate the mechanism via which ETH manages stress. The analysis showed that 45 mg/L was the best concentration of ETH to relieve the embryo dormancy. ETH at this concentration improved the germination of S. pohuashanensis by 183.21% under saline-alkaline stress; it also improved the germination index and germination potential of the embryos. Further analysis revealed that ETH treatment increased the levels of 1-aminocyclopropane-1-carboxylic acid (ACC), gibberellin (GA), soluble protein, nitric oxide (NO), and glutathione (GSH); increased the activities of superoxide dismutase (SOD), peroxidase (POD), catalase (CAT), nitrate reductase (NR), and nitric oxide synthase (NOS); and decreased the levels of abscisic acid (ABA), hydrogen peroxide (H₂O₂), superoxide anion, and malondialdehyde (MDA) of S. pohuashanensis under saline-alkali stress. These results indicate that ETH mitigates the inhibitory effects of saline-alkali stress and provides a theoretical basis by which to establish precise control techniques for the release of seed dormancy of tree species.

Genetic Circuit Design in Rhizobacteria

Genetically engineered plants hold enormous promise for tackling global food security and agricultural sustainability challenges. However, construction of plant-based genetic circuitry is constrained by a lack of well-characterized genetic parts and circuit design rules. In contrast, advances in bacterial synthetic biology have yielded a wealth of sensors, actuators, and other tools that can be used to build bacterial circuitry. As root-colonizing bacteria (rhizobacteria) exert substantial influence over plant health and growth, genetic circuit design in these microorganisms can be used to indirectly engineer plants and accelerate the design-build-test-learn cycle. Here, we outline genetic parts and best practices for designing rhizobacterial circuits, with an emphasis on sensors, actuators, and chassis species that can be used to monitor/control rhizosphere and plant processes.

Dissection of Paenibacillus polymyxa NSY50-Induced Defense in Cucumber Roots against Fusarium oxysporum f. sp. cucumerinum by Target Metabolite Profiling

Simple Summary

Plant growth-promoting rhizobacteria (PGPR) have significant potential to enhance the tolerance of biotic and abiotic stresses and the productivity of crops. However, the mechanism of PGPR in improving plant resistance to pathogens is unclear. Recently, the newly isolated Paenibacillus polymyxa strain NSY50 was shown to considerably suppress the Fusarium wilt of cucumber plants. This study was carried out to explore the underlying mechanism of NSY50 in improving plant resistance to pathogen invasion via target metabolite profiling, and the results indicated that strain NSY50 was able to alleviate Fusarium wilt stress by activating GSH metabolism and improving redox balance. Our research findings enable a deeper understanding of P. polymyxa NSY50-induced enhanced defense against F. oxysporum in cucumber.

Abstract

To gain insights into the roles of beneficial PGPR in controlling soil-borne disease, we adopted a metabolomics approach to investigate the beneficial impacts of P. polymyxa NSY50 on cucumber seedling roots under the pathogen of Fusarium oxysporum f. sp. cucumerinum (FOC). We found that NSY50 pretreatment (NSY50 + FOC) obviously reduced the production of reactive oxygen species (ROS). Untargeted metabolomic analysis revealed that 106 metabolites responded to NSY50 and/or FOC inoculation. Under FOC stress, the contents of root osmotic adjustment substances, such as proline and betaine were significantly increased, and dehydroascorbic acid and oxidized glutathione (GSH) considerably accumulated. Furthermore, the contents of free amino acids such as tryptophan, phenylalanine, and glutamic acid were also significantly accumulated under FOC stress. Similarly, FOC stress adversely affected glycolysis and the tricarboxylic acid cycles and transferred to the pentose phosphate pathway. Conversely, NSY50 + FOC better promoted the accumulation of α-ketoglutaric acid, ribulose-5-phosphate, and 7-phosphosodiheptanone compared to FOC alone. Furthermore, NSY50 + FOC activated GSH metabolism and increased GSH synthesis and metabolism-related enzyme activity and their encoding gene expressions, which may have improved redox homoeostasis, energy flow, and defense ability. Our results provide a novel perspective to understanding the function of P. polymyxa NSY50, accelerating the application of this beneficial PGPR in sustainable agricultural practices.

The Type VI Secretion Systems in Plant-Beneficial Bacteria Modulate Prokaryotic and Eukaryotic Interactions in the Rhizosphere

Rhizosphere colonizing plant growth promoting bacteria (PGPB) increase their competitiveness by producing diffusible toxic secondary metabolites, which inhibit competitors and deter predators. Many PGPB also have one or more Type VI Secretion System (T6SS), for the delivery of weapons directly into prokaryotic and eukaryotic cells. Studied predominantly in human and plant pathogens as a virulence mechanism for the delivery of effector proteins, the function of T6SS for PGPB in the rhizosphere niche is poorly understood. We utilized a collection of Pseudomonas chlororaphis 30-84 mutants deficient in one or both of its two T6SS and/or secondary metabolite production to examine the relative importance of each T6SS in rhizosphere competence, bacterial competition, and protection from bacterivores. A mutant deficient in both T6SS was less persistent than wild type in the rhizosphere. Both T6SS contributed to competitiveness against other PGPB or plant pathogenic strains not affected by secondary metabolite production, but only T6SS-2 was effective against strains lacking their own T6SS. Having at least one T6SS was also essential for protection from predation by several eukaryotic bacterivores. In contrast to diffusible weapons that may not be produced at low cell density, T6SS afford rhizobacteria an additional, more immediate line of defense against competitors and predators.

Interplay between Ca2+/Calmodulin-Mediated Signaling and AtSR1/CAMTA3 during Increased Temperature Resulting in Compromised Immune Response in Plants

Changing temperatures are known to affect plant–microbe interactions; however, the molecular mechanism involved in plant disease resistance is not well understood. Here, we report the effects of a moderate change in temperature on plant immune response through Ca²⁺/calmodulin-mediated signaling. At 30 °C, Pst DC3000 triggered significantly weak and relatively slow Ca²⁺ influx in plant cells, as compared to that at 18 °C. Increased temperature contributed to an enhanced disease susceptibility in plants; the enhanced disease susceptibility is the result of the compromised stomatal closure induced by pathogens at high temperature. A Ca²⁺ receptor, AtSR1, contributes to the decreased plant immunity at high temperatures and the calmodulin-binding domain (CaMBD) is required for its function. Furthermore, both salicylic acid biosynthesis (ICS) and salicylic acid receptor (NPR1) are involved in this process. In addition to stomatal control, AtSR1 is involved in high temperature-compromised apoplastic immune response through the salicylic acid signaling pathway. The qRT-PCR data revealed that AtSR1 contributed to increased temperatures-mediated susceptible immune response by regulating SA-related genes in atsr1, such as PR1, ICS1, NPR1, as well as EDS1. Our results indicate that Ca²⁺ signaling has broad effects on the molecular interplay between changing temperatures as well as plant defense during plant–pathogen interactions.

Absence of Nanoparticle-Induced Drought Tolerance in Nutrient Sufficient Wheat Seedlings

Strategies to reduce crop losses due to drought are needed as climate variability affects agricultural productivity. Wheat (Triticum aestivum var. Juniper) growth in a nutrient-sufficient, solid growth matrix containing varied doses of CuO, ZnO, and SiO₂ nanoparticles (NPs) was used to evaluate NP mitigation of drought stress. NP amendments were at fertilizer levels, with maxima of 30 Cu, 20 Zn, and 200 Si (mg metal/kg matrix). Seeds of this drought-tolerant cultivar were inoculated with Pseudomonas chlororaphis O6 (PcO6) to provide a protective root microbiome. An 8 day drought imposed on 14 day-old wheat seedlings decreased shoot and root mass, shoot water content, and the quantum yield of photosystem II when compared to watered plants. PcO6 root colonization was not impaired by drought or NPs. A dose-dependent increase in the Cu, Zn, and Si from the NPs was observed from analysis of the rhizosphere solution, and this process was not affected by drought. Consequently, fertilizer concentrations of the NPs did not further improve drought tolerance in wheat seedlings under the growth conditions of adequate mineral nutrition and the presence of a beneficial microbiome. These findings suggest that potential NP benefits in promoting plant drought tolerance occur only under certain environmental conditions.

Calmodulin-binding transcription activator AtSR1/CAMTA3 fine-tunes plant immune response by transcriptional regulation of the salicylate receptor NPR1

Calcium (Ca²⁺ ) signalling regulates salicylic acid (SA)-mediated immune response through calmodulin-meditated transcriptional activators, AtSRs/CAMTAs, but its mechanism is not fully understood. Here, we report an AtSR1/CAMTA3-mediated regulatory mechanism involving the expression of the SA receptor, NPR1. Results indicate that the transcriptional expression of NPR1 was regulated by AtSR1 binding to a CGCG box in the NPR1 promotor. The atsr1 mutant exhibited resistance to the virulent strain of Pseudomonas syringae pv. tomato (Pst), however, was susceptible to an avirulent Pst strain carrying avrRpt2, due to the failure of the induction of hypersensitive responses. These resistant/susceptible phenotypes in the atsr1 mutant were reversed in the npr1 mutant background, suggesting that AtSR1 regulates NPR1 as a downstream target during plant immune response. The virulent Pst strain triggered a transient elevation in intracellular Ca²⁺ concentration, whereas the avirulent Pst strain triggered a prolonged change. The distinct Ca²⁺ signatures were decoded into the regulation of NPR1 expression through AtSR1's IQ motif binding with Ca²⁺ -free-CaM2, while AtSR1's calmodulin-binding domain with Ca²⁺ -bound-CaM2. These observations reveal a role for AtSR1 as a Ca²⁺ -mediated transcription regulator in controlling the NPR1-mediated plant immune response.

Electrochemical enrichment of haloalkaliphilic nitrate-reducing microbial biofilm at the cathode of bioelectrochemical systems

Electrotrophic microorganisms have not been well studied in extreme environments. Here, we report on the nitrate-reducing cathodic microbial biofilm from a haloalkaline environment. The biofilm enriched via electrochemical approach under 9.5 pH and 20 g NaCl/L salinity conditions achieved −43.5±7.2μA/cm2 current density and 49.5±13.2%nitrate reduction efficiency via partial and complete denitrification. Voltammetric characterization of the biocathodes revealed a redox center with −0.294±0.003V (vs. Ag/AgCl) formal potential putatively involved in the electron uptake process. The lack of soluble redox mediators and hydrogen-driven nitrate reduction suggests direct-contact cathodic electron uptake by the nitrate-reducing microorganisms in the enriched biofilm. 16S-rRNA amplicon sequencing of the cathodic biofilm revealed the presence of unreported Pseudomonas, Natronococcus, and Pseudoalteromonas spp. at 31.45%,11.82%, and 9.69% relative sequence abundances, respectively. The enriched nitrate-reducing microorganisms also reduced nitrate efficiently using soluble electron donors found in the lake sediments, thereby suggesting their role in N-cycling in such environments.

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Enrichment of haloalkaliphilic nitrate-reducing microbial biofilm at the cathode

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Cathodic reduction current corresponded to the nitrate reduction process

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Pseudomonas, Natronococcus, and Pseudoalteromonas spp. enriched in the cathodic biofilm

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Enriched culture reduced nitrate efficiently with soluble electron donor sources

Pseudomonas chlororaphis metabolites as biocontrol promoters of plant health and improved crop yield

The Pseudomonas fluorescens complex contains at least eight phylogenetic groups and each of these includes several bacterial species sharing ecological and physiological traits. Pseudomonas chlororaphis classified in a separate group is represented by three different subspecies that show distinctive traits exploitable for phytostimulation and biocontrol of phytopathogens. The high level of microbial competitiveness in soil as well as the effectiveness in controlling several plant pathogens and pests can be related to the P. chlororaphis ability to implement different stimulating and toxic mechanisms in its interaction with plants and the other micro- and macroorganisms. Pseudomonas chlororaphis strains produce antibiotics, such as phenazines, pyrrolnitrine, 2-hexyl, 5-propyl resorcinol and hydrogen cyanide, siderophores such as pyoverdine and achromobactine and a complex blend of volatile organic compounds (VOCs) that effectively contribute to the control of several plant pathogens, nematodes and insects. Phenazines and some VOCs are also involved in the induction of systemic resistance in plants. This complex set of beneficial strategies explains the high increasing interest in P. chlororaphis for commercial and biotechnological applications. The aim of this review is to highlight the role of the different mechanisms involved in the biocontrol activity of P. chlororaphis strains.

Rhizosphere plant-microbe interactions under water stress

Climate change, with its extreme temperature, weather and precipitation patterns, is a major global concern of dryland farmers, who currently meet the challenges of climate change agronomically and with growth of drought-tolerant crops. Plants themselves compensate for water stress by modifying aerial surfaces to control transpiration and altering root hydraulic conductance to increase water uptake. These responses are complemented by metabolic changes involving phytohormone network-mediated activation of stress response pathways, resulting in decreased photosynthetic activity and the accumulation of metabolites to maintain osmotic and redox homeostasis. Phylogenetically diverse microbial communities sustained by plants contribute to host drought tolerance by modulating phytohormone levels in the rhizosphere and producing water-sequestering biofilms. Drylands of the Inland Pacific Northwest, USA, illustrate the interdependence of dryland crops and their associated microbiota. Indigenous Pseudomonas spp. selected there by long-term wheat monoculture suppress root diseases via the production of antibiotics, with soil moisture a critical determinant of the bacterial distribution, dynamics and activity. Those pseudomonads producing phenazine antibiotics on wheat had more abundant rhizosphere biofilms and provided improved tolerance to drought, suggesting a role of the antibiotic in alleviation of drought stress. The transcriptome and metabolome studies suggest the importance of wheat root exudate-derived osmoprotectants for the adaptation of these pseudomonads to the rhizosphere lifestyle and support the idea that the exchange of metabolites between plant roots and microorganisms profoundly affects and shapes the belowground plant microbiome under water stress.