Genome Sequencing of Pantoea agglomerans C1 Provides Insights into Molecular and Genetic Mechanisms of Plant Growth-Promotion and Tolerance to Heavy Metals

Preference and regulation mechanism mediated via mobile genetic elements for antibiotic and metal resistomes during composting amended with nano ZVI loaded on biochar

This study assessed the effectiveness of nano zero-valent iron loaded on biochar (BC-nZVI) during swine manure composting. BC-nZVI significantly reduced the abundance of antibiotic resistance genes (ARGs), metal resistance genes (MRGs), and mobile genetic elements (MGEs). BC-nZVI modified the preference of MGEs to carry ARGs and MRGs, and the corrosion products of BC-nZVI could destroy cell structure, hinder electron transfer between cells, and weaken the association between ARGs, MRGs, and host bacteria. Functional genes analysis revealed that BC-nZVI down-regulated the abundance of genes affecting the transmission and metabolism of ARGs and MRGs, including type IV secretion systems, transporter systems, two-component systems, and multidrug efflux pumps. Furthermore, the BC-nZVI decreased genes related to flagella and pili production and cell membrane permeability, thereby hindering the transfer of ARGs, MRGs, and MGEs in the environment. Redundancy analysis demonstrated that changes in the microbial community induced by BC-nZVI were pivotal factors impacting the abundance of ARGs, MRGs, and MGEs. Overall, this study confirmed the efficacy of BC-nZVI in reducing resistance genes during swine manure composting, offering a promising environmental strategy to mitigate the dissemination of these contaminants.

Pathway to industrial application of heterotrophic organisms in critical metals recycling from e-waste

The transition to renewable energies and electric vehicles has triggered an unprecedented demand for metals. Sustainable development of these technologies relies on effectively managing the lifecycle of critical raw materials, including their responsible sourcing, efficient use, and recycling. Metal recycling from electronic waste (e-waste) is of paramount importance owing to ore-exceeding amounts of critical elements and high toxicity of heavy metals and organic pollutants in e-waste to the natural ecosystem and human body. Heterotrophic microbes secrete numerous metal-binding biomolecules such as organic acids, amino acids, cyanide, siderophores, peptides, and biosurfactants which can be utilized for eco-friendly and profitable metal recycling. In this review paper, we presented a critical review of heterotrophic organisms in biomining, and current barriers hampering the industrial application of organic acid bioleaching and biocyanide leaching. We also discussed how these challenges can be surmounted with simple methods (e.g., culture media optimization, separation of microbial growth and metal extraction process) and state-of-the-art biological approaches (e.g., artificial microbial community, synthetic biology, metabolic engineering, advanced fermentation strategies, and biofilm engineering). Lastly, we showcased emerging technologies (e.g., artificially synthesized peptides, siderophores, and biosurfactants) derived from heterotrophs with the potential for inexpensive, low-impact, selective and advanced metal recovery from bioleaching solutions.

Exploring the Organic Acid Secretion Pathway and Potassium Solubilization Ability of Pantoea vagans ZHS-1 for Enhanced Rice Growth

Soil potassium deficiency is a common issue limiting agricultural productivity. Potassium-solubilizing bacteria (KSB) show significant potential in mitigating soil potassium deficiency, improving soil quality, and enhancing plant growth. However, different KSB strains exhibit diverse solubilization mechanisms, environmental adaptability, and growth-promoting abilities. In this study, we isolated a multifunctional KSB strain ZHS-1, which also has phosphate-solubilizing and IAA-producing capabilities. 16S rDNA sequencing identified it as Pantoea vagans. Scanning electron microscopy (SEM) showed that strain ZHS-1 severely corroded the smooth, compact surface of potassium feldspar into a rough and loose state. The potassium solubilization reached 20.3 mg/L under conditions where maltose was the carbon source, sodium nitrate was the nitrogen source, and the pH was 7. Organic acid metabolism profiling revealed that strain ZHS-1 primarily utilized the EMP-TCA cycle, supplemented by pathways involving pantothenic acid, glyoxylic acid, and dicarboxylic acids, to produce large amounts of organic acids and energy. This solubilization was achieved through direct solubilization mechanisms. The strain also secreted IAA through a tryptophan-dependent metabolic pathway. When strain ZHS-1 was inoculated into the rhizosphere of rice, it demonstrated significant growth-promoting effects. The rice plants exhibited improved growth and root development, with increased accumulation of potassium and phosphorus. The levels of available phosphorus and potassium in the rhizosphere soil also increased significantly. Additionally, we observed a decrease in the relative abundance of Actinobacteria and Proteobacteria in the rice rhizosphere soil, while the relative abundance of genera associated with acid production and potassium solubilization, such as Gemmatimonadota, Acidobacteria, and Chloroflexi, as well as Cyanobacteria, which are beneficial to plant growth, increased. These findings contribute to a deeper understanding of the potassium solubilization mechanisms of strain ZHS-1 and highlight its potential as a plant growth-promoting rhizobacteria.

Comparative Genomic and Functional Analyses for Insights into Pantoea agglomerans Strains Adaptability in Diverse Ecological Niches

Pantoea agglomerans inhabit diverse ecological niches, ranging from epiphytes and endophytes in plants, body of animals, and occasionally in the human system. This multifaceted bacterium contributes substantially to plant growth promotion, stress resilience, and biocontrol but can also act as a pathogen to its host. The genetic determinants underlying these diverse functions remain largely unfathomed and to uncover this phenomenon, nineteen strains of Pantoea agglomerans were selected and analyzed. Genome-to-Genome Distance Calculator (GGDC) which uses the Genome Blast Distance Phylogeny (GBDP) technique to calculate digital DDH values. Phylogenetic analysis via Genome-to-Genome distance, Average Nucleotide Identity, and Amino Acid Identity calculation revealed that all strains belonged to the genus Pantoea. However, strain 33.1 had a lower value than the threshold for the same species delineation. Bacterial Pan Genome Analysis (BPGA) Pipeline and MinPath analysis revealed genetic traits associated with environmental resilience, such as oxidative stress, UV radiation, temperature extremes, and metabolism of distinct host-specific carbohydrates. Protein-protein interactome analysis illustrated osmotic stress proteins closely linked with core proteins, while heavy metal tolerance, nitrogen metabolism, and Type III and VI secretion systems proteins generally associated with pathogenicity formed a separate network, indicating strain-specific characteristics. These findings shed new light on the intricate genetic architecture of Pantoea agglomerans, revealing its adaptability to inhabit diverse niches and thrive in varied environments.

Omics technology draws a comprehensive heavy metal resistance strategy in bacteria

The rapid industrial revolution significantly increased heavy metal pollution, becoming a major global environmental concern. This pollution is considered as one of the most harmful and toxic threats to all environmental components (air, soil, water, animals, and plants until reaching to human). Therefore, scientists try to find a promising and eco-friendly technique to solve this problem i.e., bacterial bioremediation. Various heavy metal resistance mechanisms were reported. Omics technologies can significantly improve our understanding of heavy metal resistant bacteria and their communities. They are a potent tool for investigating the adaptation processes of microbes in severe conditions. These omics methods provide unique benefits for investigating metabolic alterations, microbial diversity, and mechanisms of resistance of individual strains or communities to harsh conditions. Starting with genome sequencing which provides us with complete and comprehensive insight into the resistance mechanism of heavy metal resistant bacteria. Moreover, genome sequencing facilitates the opportunities to identify specific metal resistance genes, operons, and regulatory elements in the genomes of individual bacteria, understand the genetic mechanisms and variations responsible for heavy metal resistance within and between bacterial species in addition to the transcriptome, proteome that obtain the real expressed genes. Moreover, at the community level, metagenome, meta transcriptome and meta proteome participate in understanding the microbial interactive network potentially novel metabolic pathways, enzymes and gene species can all be found using these methods. This review presents the state of the art and anticipated developments in the use of omics technologies in the investigation of microbes used for heavy metal bioremediation.

Whole genome sequencing and characterization of Pantoea agglomerans DBM 3797, endophyte, isolated from fresh hop (Humulus lupulus L.)

Background

This paper brings new information about the genome and phenotypic characteristics of Pantoea agglomerans strain DBM 3797, isolated from fresh Czech hop (Humulus lupulus) in the Saaz hop-growing region. Although P. agglomerans strains are frequently isolated from different materials, there are not usually thoroughly characterized even if they have versatile metabolism and those isolated from plants may have a considerable potential for application in agriculture as a support culture for plant growth.

Methods

P. agglomerans DBM 3797 was cultured under aerobic and anaerobic conditions, its metabolites were analyzed by HPLC and it was tested for plant growth promotion abilities, such as phosphate solubilization, siderophore and indol-3-acetic acid productions. In addition, genomic DNA was extracted, sequenced and de novo assembly was performed. Further, genome annotation, pan-genome analysis and selected genome analyses, such as CRISPR arrays detection, antibiotic resistance and secondary metabolite genes identification were carried out.

Results and discussion

The typical appearance characteristics of the strain include the formation of symplasmata in submerged liquid culture and the formation of pale yellow colonies on agar. The genetic information of the strain (in total 4.8 Mb) is divided between a chromosome and two plasmids. The strain lacks any CRISPR-Cas system but is equipped with four restriction-modification systems. The phenotypic analysis focused on growth under both aerobic and anaerobic conditions, as well as traits associated with plant growth promotion. At both levels (genomic and phenotypic), the production of siderophores, indoleacetic acid-derived growth promoters, gluconic acid, and enzyme activities related to the degradation of complex organic compounds were found. Extracellular gluconic acid production under aerobic conditions (up to 8 g/l) is probably the result of glucose oxidation by the membrane-bound pyrroloquinoline quinone-dependent enzyme glucose dehydrogenase. The strain has a number of properties potentially beneficial to the hop plant and its closest relatives include the strains also isolated from the aerial parts of plants, yet its safety profile needs to be addressed in follow-up research.

Pantoea trifolii sp. nov., a novel bacterium isolated from Trifolium rubens root nodules

A novel bacterium, designated strain MMK2T, was isolated from a surface-sterilised root nodule of a Trifolium rubens plant growing in south-eastern Poland. Cells were Gram negative, non-spore forming and rod shaped. The strain had the highest 16S rRNA gene sequence similarity with P. endophytica (99.4%), P. leporis (99.4%) P. rwandensis (98.8%) and P. rodasii (98.45%). Phylogenomic analysis clearly showed that strain MMK2T and an additional strain, MMK3, should reside in the genus Pantoea and that they were most closely related to P. endophytica and P. leporis. Genome comparisons showed that the novel strain shared 82.96-93.50% average nucleotide identity and 26.2-53. 2% digital DNA:DNA hybridization with closely related species. Both strains produced siderophores and were able to solubilise phosphates. The MMK2T strain was also able to produce indole-3-acetic acid. The tested strains differed in their antimicrobial activity, but both were able to inhibit the growth of Sclerotinia sclerotiorum 10Ss01. Based on the results of the phenotypic, phylogenomic, genomic and chemotaxonomic analyses, strains MMK2T and MMK3 belong to a novel species in the genus Pantoea for which the name Pantoea trifolii sp. nov. is proposed with the type strain MMK2T (= DSM 115063T = LMG 33049T).

Effect of microbial plant biostimulants on fruit and vegetable quality: current research lines and future perspectives

Fruit and vegetables hold a prominent place in dietary guidance worldwide and, following the increasing awareness of the importance of their consumption for health, their demand has been on the rise. Fruit and vegetable production needs to be reconsidered so that it can be productive and, meantime, sustainable, resilient, and can deliver healthy and nutritious diets. Microbial plant biostimulants (PBs) are a possible approach to pursuing global food security and agricultural sustainability, and their application emerged as a promising alternative or substitute to the use of agrochemicals (e.g., more efficient use of mineral and organic fertilizers or less demand and more efficient use of pesticides in integrated production systems) and as a new frontier of investigation. To the best of our knowledge, no comprehensive reviews are currently available on the effects that microbial plant biostimulants' application can have specifically on each horticultural crop. This study thus aimed to provide a state-of-the-art overview of the effects that PBs can have on the morpho-anatomical, biochemical, physiological, and functional traits of the most studied crops. It emerged that most experiments occurred under greenhouse conditions; only a few field trials were carried out. Tomato, lettuce, and basil crops have been primarily treated with Arbuscular Mycorrhizal Fungi (AMF), while plant grow-promoting rhizobacteria (PGPR) metabolites were used for crops, such as strawberries and cucumbers. The literature review also pointed out that crop response to PBs is never univocal. Complex mechanisms related to the PB type, the strain, and the crop botanical family, occur.

Use of Pantoea agglomerans ASB05 as a biocontrol agent to inhibit the growth of Salmonella enterica on intact cantaloupe melons

AIMS

To identify biocontrol agents to prevent the growth of Salmonella serotype Enterica on cantaloupe melons during the pre- and postharvest periods.

METHODS AND RESULTS

We created a produce-associated bacterial library containing 8736 isolates and screened it using an in-vitro fluorescence inhibition assay to identify bacteria that inhibit the growth of S. Enterica. One isolate, Pantoea agglomerans ASB05, was able to grow, persist, and inhibit the growth of S. Enterica on intact cantaloupe melons under simulated pre- and postharvest conditions. We also demonstrated that the growth inhibition of S. Enterica by P. agglomerans ASB05 was due to the production of a phenazine type antibiotic.

CONCLUSIONS

Pantoea agglomerans ASB05 is an effective biocontrol agent for the prevention of S. Enterica growth on intact cantaloupe melons in both the pre- and postharvest environments.

Identification and Characterization of Beneficial Soil Microbial Strains for the Formulation of Biofertilizers Based on Native Plant Growth-Promoting Microorganisms Isolated from Northern Mexico

Plant growth-promoting microorganisms (PGPM) benefit plant health by enhancing plant nutrient-use efficiency and protecting plants against biotic and abiotic stresses. This study aimed to isolate and characterize autochthonous PGPM from important agri-food crops and nonagricultural plants to formulate biofertilizers. Native microorganisms were isolated and evaluated for PGP traits (K, P, and Zn solubilization, N2-fixation, NH3-, IAA and siderophore production, and antifungal activity against Fusarium oxysporum). Isolates were tested on radish and broccoli seedlings, evaluating 19 individual isolates and 12 microbial consortia. Potential bacteria were identified through DNA sequencing. In total, 798 bacteria and 209 fungi were isolated. Isolates showed higher mineral solubilization activity than other mechanisms; 399 bacteria and 156 fungi presented mineral solubilization. Bacteria were relevant for nitrogen fixation, siderophore, IAA (29-176 mg/L), and ammonia production, while fungi for Fusarium growth inhibition (40-69%). Twenty-four bacteria and eighteen fungi were selected for their PGP traits. Bacteria had significantly (ANOVA, p < 0.05) better effects on plants than fungi; treatments improved plant height (23.06-51.32%), leaf diameter (25.43-82.91%), and fresh weight (54.18-85.45%) in both crops. Most potential species belonged to Pseudomonas, Pantoea, Serratia, and Rahnella genera. This work validated a high-throughput approach to screening hundreds of rhizospheric microorganisms with PGP potential isolated from rhizospheric samples.

Methylglyoxal improves zirconium stress tolerance in Raphanus sativus seedling shoots by restricting zirconium uptake, reducing oxidative damage, and upregulating glyoxalase I

Raphanus sativus also known as radish is a member of the Brassicaceae family which is mainly cultivated for human and animal consumption. R. sativus growth and development is negatively affected by heavy metal stress. The metal zirconium (Zr) have toxic effects on plants and tolerance to the metal could be regulated by known signaling molecules such as methylglyoxal (MG). Therefore, in this study we investigated whether the application of the signaling molecule MG could improve the Zr tolerance of R. sativus at the seedling stage. We measured the following: seed germination, dry weight, cotyledon abscission (%), cell viability, chlorophyll content, malondialdehyde (MDA) content, conjugated diene (CD) content, hydrogen peroxide (H2O2) content, superoxide (O2•-) content, MG content, hydroxyl radical (·OH) concentration, ascorbate peroxidase (APX) activity, superoxide dismutase (SOD) activity, glyoxalase I (Gly I) activity, Zr content and translocation factor. Under Zr stress, exogenous MG increased the seed germination percentage, shoot dry weight, cotyledon abscission, cell viability and chlorophyll content. Exogenous MG also led to a decrease in MDA, CD, H2O2, O2•-, MG and ·OH, under Zr stress in the shoots. Furthermore, MG application led to an increase in the enzymatic activities of APX, SOD and Gly I as well as in the complete blocking of cotyledon abscission under Zr stress. MG treatment decreased the uptake of Zr in the roots and shoots. Zr treatment decreased the translocation factor of the Zr from roots to shoots and MG treatment decreased the translocation factor of Zr even more significantly compared to the Zr only treatment. Our results indicate that MG treatment can improve R. sativus seedling growth under Zr stress through the activation of antioxidant enzymes and Gly I through reactive oxygen species and MG signaling, inhibiting cotyledon abscission through H2O2 signaling and immobilizing Zr translocation.

Isolation and characterization of phosphate-solubilizing bacterium Pantoea rhizosphaerae sp. nov. from Acer truncatum rhizosphere soil and its effect on Acer truncatum growth

The Acer truncatum Bunge, widely distributed in North China, shows excellent tolerance to low-P soils. However, little information is available on potential phosphate-solubilizing bacterial (PSB) strains from the A. truncatum rhizosphere. The objectives of this work were to isolate and characterize PSB from A. truncatum rhizosphere soil and to evaluate the effect of inoculation with the selected strain on A. truncatum seedlings. The strains were characterized on the basis of phenotypic characteristics, carbon source utilization pattern, fatty acid methyl esters analysis, 16S rRNA gene and the whole-genome sequence. A Gram-negative and rod-shaped bacterium, designated MQR6^T, showed a high capacity to solubilize phosphate and produce indole-3-acetic acid (IAA) and siderophores. The strain can solubilize tricalcium phosphate (TCP) and rock phosphate (RP), and the solubilization of TCP was about 60% more effective than RP. Phylogenetic analyses based on the 16S rRNA gene and whole-genome sequences revealed that strain MQR6^T formed a distinct phyletic lineage as a new species within the genus Pantoea. The digital DNA-DNA hybridization value between strain MQR6^T and the closely related strains was 19.5-23.3%. The major cellular fatty acids were summed feature 3 (C_16:1ω7c and/or C_16:1ω6c), summed feature 8 (C_18:1ω6c and/or C_18:1ω7c), C_14:0, C_16:0, and C_17:0 cyclo. Several genes related to IAA production, phosphonate transport, phosphate solubilization and siderophore biogenesis were found in the MQR6^T genome. Furthermore, inoculation with the strain MQR6^T significantly improved plant height, trunk diameter, dry weight and P accumulation in roots and shoot of A. truncatum seedlings compared to non-inoculated control. These plant parameters were improved even further in the treatment with both inoculation and P fertilization. Our results suggested that MQR6^T represented a new species we named Pantoea rhizosphaerae, as a plant growth-promoting rhizobacterium that can solubilize inorganic P and improve growth of A. truncatum seedlings, emerging as a potential strategy to improve A. truncatum cultivation.

Complete Genome Sequence of Pantoea stewartii RON18713 from Brazil Nut Tree Phyllosphere Reveals Genes Involved in Plant Growth Promotion

The Amazonian rainforest is a hyper-diverse ecosystem in the number of species and the myriad of intertaxon relationships that are mostly understudied. In order to characterize a dominant and economically important Amazonian species, the Brazil nut tree (Bertholletia excelsa Bonpl.), at the genome level, wegenerated high-coverage long-read sequencing data from the leaves of a single individual. The genome assembly revealed an unexpected discovery: two circular contigs that could be assigned to the chromosome and a plasmid of a Pantoea stewartii strain. Comparative genomics revealed that this strain belongs to the indologenes subspecies and displays high synteny with other strains isolated from diseased leaves of the neotropical palm Bactris gasipaes Kunth. Investigation of pathogenicity-related genes revealed the absence of the entire type III secretion system gene cluster in the plasmid, which was otherwise highly similar to a plasmid from an isolate known to cause disease in Dracaena sanderiana Mast. In contrast, several genes associated with plant-growth promoting traits were detected, including genes involved in indole-3-acetic acid (IAA) production, phosphate solubilization, and biosynthesis of siderophores. In summary, we report the genome of an uncultivated P. stewartii subsp. indologenes strain associated with the Brazil nut tree and potentially a plant growth-promoting bacteria.

Comparative genomics reveals the acquisition of mobile genetic elements by the plant growth-promoting Pantoea eucrina OB49 in polluted environments

Heavy metal-tolerant plant growth-promoting bacteria (PGPB) have gained popularity in bioremediation in recent years. A genome-assisted study of a heavy metal-tolerant PGPB Pantoea eucrina OB49 isolated from the rhizosphere of wheat grown on a heavy metal-contaminated site is presented. Comparative pan-genome analysis indicated that OB49 acquired heavy metal resistance genes through horizontal gene transfer. On contigs S10 and S12, OB49 has two arsRBCH operons that give arsenic resistance. On the S12 contig, an arsRBCH operon was discovered in conjunction with the merRTPCADE operon, which provides mercury resistance. P. eucrina OB49 may be involved in an ecological alternative for heavy metal remediation and growth promotion of wheat grown in metal-polluted soils. Our results suggested the detection of mobile genetic elements that harbour the ars operon and the fluoride resistance genes adjacent to the mer operon.

Reconnoitering the capabilities of nodule endophytic Pantoea dispersa for improved nodulation and grain yield of chickpea (Cicer arietinum L.)

Microorganisms belonging to root and soil provide a wide range of services and benefits to the plant by promoting plant growth and controlling phytopathogens. This study aimed to isolate endophytic bacteria from the root nodules of chickpea (Cicer arietinum L.) and determine their potential in improving plant growth. A total of nineteen different bacterial morphotypes were isolated from root nodules of chickpea and characterized in vitro for plant growth promotion abilities. All bacterial isolates were able to produce indole acetic acid at varying levels, out of which MCA19 was screened as the most efficient indole acetic acid producer (10.25 µg mL^-1). MCA8, MCA9, MCA10, MCA11, MCA16, MCA17 and MCA19 were positive for phosphate solubilization, out of which MCA9 was best phosphate solubilizer (18.8 µg mL^-1). All bacterial strains showed varying ability to grow on nitrogen-free media. Hydrogen cyanide, pectinase, and cellulase production ability were also observed in isolates, in which MCA9, MCA12, MCA17 and MCA19 were found best. Based on in vitro testing, five isolates MCA2, MCA9, MCA11, MCA17 and MCA19 were selected for further studies. Bacterial isolates MCA9, MCA11, MCA17 and MCA19 were identified by 16S rRNA gene sequence analysis as Pantoea dispersa while MCA2 as Rhizobium pusense. This is the first report on the existence of Pantoea dispersa in the root nodules of chickpea. In pot experiment, a maximum increase of 30% was recorded in plant dry weight upon the application of MCA19. Under field conditions, bacterial isolates, MCA2, MCA11 and MCA19 significantly enhanced nodulation and yield parameters of chickpea, compared to control. Pantoea dispersa MCA19 displayed the highest plant growth-promoting potential by increasing 38% grain yield. Our results indicate that Pantoea dispersa MCA19 is a promising biofertilizer for future applications.

Optimization of the growth conditions through response surface methodology and metabolomics for maximizing the auxin production by Pantoea agglomerans C1

Introduction

The fermentative production of auxin/indole 3-acetate (IAA) using selected Pantoea agglomerans strains can be a promising approach to developing novel plant biostimulants for agriculture use.

Methods

By integrating metabolomics and fermentation technologies, this study aimed to define the optimal culture conditions to obtain auxin/IAA-enriched plant postbiotics using P. agglomerans strain C1. Metabolomics analysis allowed us to demonstrate that the production of a selected.

Results and discussion

Array of compounds with plant growth-promoting- (IAA and hypoxanthine) and biocontrol activity (NS-5, cyclohexanone, homo-L-arginine, methyl hexadecenoic acid, and indole-3-carbinol) can be stimulated by cultivating this strain on minimal saline medium amended with sucrose as a carbon source. We applied a three-level-two-factor central composite design (CCD) based response surface methodology (RSM) to explore the impact of the independent variables (rotation speed and medium liquid-to-flask volume ratio) on the production of IAA and IAA precursors. The ANOVA component of the CCD indicated that all the process-independent variables investigated significantly impacted the auxin/IAA production by P. agglomerans strain C1. The optimum values of variables were a rotation speed of 180 rpm and a medium liquid-to-flask volume ratio of 1:10. Using the CCD-RSM method, we obtained a maximum indole auxin production of 208.3 ± 0.4  mg IAA_equ/L, which was a 40% increase compared to the growth conditions used in previous studies. Targeted metabolomics allowed us to demonstrate that the IAA product selectivity and the accumulation of the IAA precursor indole-3-pyruvic acid were significantly affected by the increase in the rotation speed and the aeration efficiency.

Complete genome analysis of sugarcane root associated endophytic diazotroph Pseudomonas aeruginosa DJ06 revealing versatile molecular mechanism involved in sugarcane development

Sugarcane is an important sugar and bioenergy source and a significant component of the economy in various countries in arid and semiarid. It requires more synthetic fertilizers and fungicides during growth and development. However, the excess use of synthetic fertilizers and fungicides causes environmental pollution and affects cane quality and productivity. Plant growth-promoting bacteria (PGPB) indirectly or directly promote plant growth in various ways. In this study, 22 PGPB strains were isolated from the roots of the sugarcane variety GT42. After screening of plant growth-promoting (PGP) traits, it was found that the DJ06 strain had the most potent PGP activity, which was identified as Pseudomonas aeruginosa by 16S rRNA gene sequencing. Scanning electron microscopy (SEM) and green fluorescent protein (GFP) labeling technology confirmed that the DJ06 strain successfully colonized sugarcane tissues. The complete genome sequencing of the DJ06 strain was performed using Nanopore and Illumina sequencing platforms. The results showed that the DJ06 strain genome size was 64,90,034 bp with a G+C content of 66.34%, including 5,912 protein-coding genes (CDSs) and 12 rRNA genes. A series of genes related to plant growth promotion was observed, such as nitrogen fixation, ammonia assimilation, siderophore, 1-aminocyclopropane-1-carboxylic acid (ACC), deaminase, indole-3-acetic acid (IAA) production, auxin biosynthesis, phosphate metabolism, hydrolase, biocontrol, and tolerance to abiotic stresses. In addition, the effect of the DJ06 strain was also evaluated by inoculation in two sugarcane varieties GT11 and B8. The length of the plant was increased significantly by 32.43 and 12.66% and fresh weight by 89.87 and 135.71% in sugarcane GT11 and B8 at 60 days after inoculation. The photosynthetic leaf gas exchange also increased significantly compared with the control plants. The content of indole-3-acetic acid (IAA) was enhanced and gibberellins (GA) and abscisic acid (ABA) were reduced in response to inoculation of the DJ06 strain as compared with control in two sugarcane varieties. The enzymatic activities of oxidative, nitrogen metabolism, and hydrolases were also changed dramatically in both sugarcane varieties with inoculation of the DJ06 strain. These findings provide better insights into the interactive action mechanisms of the P. aeruginosa DJ06 strain and sugarcane plant development.

Opposite Sides of Pantoea agglomerans and Its Associated Commercial Outlook

Multifaceted microorganisms such as the bacterium Pantoea colonize a wide range of habitats and can exhibit both beneficial and harmful behaviors, which provide new insights into microbial ecology. In the agricultural context, several strains of Pantoea spp. can promote plant growth through direct or indirect mechanisms. Members of this genus contribute to plant growth mainly by increasing the supply of nitrogen, solubilizing ammonia and inorganic phosphate, and producing phytohormones (e.g., auxins). Several other studies have shown the potential of strains of Pantoea spp. to induce systemic resistance and protection against pests and pathogenic microorganisms in cultivated plants. Strains of the species Pantoea agglomerans deserve attention as a pest and phytopathogen control agent. Several of them also possess a biotechnological potential for therapeutic purposes (e.g., immunomodulators) and are implicated in human infections. Thus, the differentiation between the harmful and beneficial strains of P. agglomerans is mandatory to apply this bacterium safely as a biofertilizer or biocontroller. This review specifically evaluates the potential of the strain-associated features of P. agglomerans for bioprospecting and agricultural applications through its biological versatility as well as clarifying its potential animal and human health risks from a genomic point of view.

Microbial and metabolic characterization of organic artisanal sauerkraut fermentation and study of gut health-promoting properties of sauerkraut brine

Sauerkraut is a traditionally fermented cabbage, and recent evidence suggests that it has beneficial properties for human health. In this work, a multi-disciplinary approach was employed to characterize the fermentation process and gut health-promoting properties of locally produced, organic sauerkraut from two distinct producers, SK1 and SK2. 16S rRNA metataxonomics showed that bacterial diversity gradually decreased as fermentation progressed. Differences in sauerkraut microbiota composition were observed between the two producers, especially at the start of fermentation. Lactic acid bacteria (LAB) dominated the microbiota after 35 days, with Lactiplantibacillus being the dominant genus in both sauerkraut products, together with Leuconostoc and Paucilactobacillus in SK1, and with Pediococcus, Levilactibacillus, and Leuconostoc in SK2. LAB reached between 7 and 8 Log CFU/mL brine at the end of fermentation (35 days), while pH lowering happened within the first week of fermentation. A total of 220 LAB strains, corresponding to 133 RAPD-PCR biotypes, were successfully isolated. Lactiplantibacillus plantarum and Lactiplantibacillus pentosus accounted for 67% of all SK1 isolates, and Lactiplantibacillus plantarum/paraplantarum and Leuconostoc mesenteroides represented 72% of all the isolates from SK2. ¹H-NMR analysis revealed significant changes in microbial metabolite profiles during the fermentation process, with lactic and acetic acids, as well as amino acids, amines, and uracil, being the dominant metabolites quantified. Sauerkraut brine did not affect trans-epithelial electrical resistance through a Caco-2 cell monolayer as a measure of gut barrier function. However, significant modulation of inflammatory response after LPS stimulation was observed in PBMCs-Caco-2 co-culture. Sauerkraut brine supported a robust inflammatory response to endotoxin, by increasing TNF-α and IL-6 production while also stimulating the anti-inflammatory IL-10, therefore suggesting positive resolution of inflammation after 24 h and supporting the potential of sauerkraut brine to regulate intestinal immune function.

Genome Sequencing of Rahnella victoriana JZ-GX1 Provides New Insights Into Molecular and Genetic Mechanisms of Plant Growth Promotion

Genomic information for bacteria within the genus Rahnella remains limited. Rahnella sp. JZ-GX1 was previously isolated from the Pinus massoniana rhizosphere in China and shows potential as a plant growth-promoting (PGP) bacterium. In the present work, we combined the GridION Nanopore ONT and Illumina sequencing platforms to obtain the complete genome sequence of strain JZ-GX1, and the application effects of the strain in natural field environment was assessed. The whole genome of Rahnella sp. JZ-GX1 comprised a single circular chromosome (5,472,828 bp, G + C content of 53.53%) with 4,483 protein-coding sequences, 22 rRNAs, and 77 tRNAs. Based on whole genome phylogenetic and average nucleotide identity (ANI) analysis, the JZ-GX1 strain was reidentified as R. victoriana. Genes related to indole-3-acetic acid (IAA), phosphorus solubilization, nitrogen fixation, siderophores, acetoin, 1-aminocyclopropane-1-carboxylate (ACC) deaminase, gamma-aminobutyric acid (GABA) production, spermidine and volatile organic compounds (VOCs) biosynthesis were present in the genome of strain JZ-GX1. In addition, these functions were also confirmed by in vitro experiments. Importantly, compared to uninoculated control plants, Pyrus serotina, Malus spectabilis, Populus euramericana (Dode) Guinier cv. “San Martino” (I-72 poplar) and Pinus elliottii plants inoculated with strain JZ-GX1 showed increased heights and ground diameters. These findings improve our understanding of R. victoriana JZ-GX1 as a potential biofertilizer in agriculture.

Production of Indole Auxins by Enterobacter sp. Strain P-36 under Submerged Conditions

Bioactive compounds produced by plant growth-promoting bacteria through a fermentation process can be valuable for developing innovative second-generation plant biostimulants. The purpose of this study is to investigate the biotechnological potential of Enterobacter on the production of auxin—a hormone with multiple roles in plant growth and development. The experiments were carried in Erlenmeyer flasks and a 2-L fermenter under batch operating mode. The auxin production by Enterobacter sp. strain P-36 can be doubled by replacing casein with vegetable peptone in the culture medium. Cultivation of strain P36 in the benchtop fermenter indicates that by increasing the inoculum size 2-fold, it is possible to reduce the fermentation time from 72 (shake flask cultivation) to 24 h (bioreactor cultivation) and increase the auxin volumetric productivity from 6.4 to 17.2 mg [IAAequ]/L/h. Finally, an efficient storage procedure to preserve the bacterial auxin was developed. It is noteworthy that by sterilizing the clarified fermentation broth by filtration and storing the filtrated samples at +4 °C, the level of auxin remains unchanged for at least three months.

Ecological Role of Volatile Organic Compounds Emitted by Pantoea agglomerans as Interspecies and Interkingdom Signals

Volatile organic compounds (VOCs) play an essential role in microbe–microbe and plant–microbe interactions. We investigated the interaction between two plant growth-promoting rhizobacteria, and their interaction with tomato plants. VOCs produced by Pantoea agglomerans MVC 21 modulates the release of siderophores, the solubilisation of phosphate and potassium by Pseudomonas (Ps.) putida MVC 17. Moreover, VOCs produced by P. agglomerans MVC 21 increased lateral root density (LRD), root and shoot dry weight of tomato seedlings. Among the VOCs released by P. agglomerans MVC 21, only dimethyl disulfide (DMDS) showed effects similar to P. agglomerans MVC 21 VOCs. Because of the effects on plants and bacterial cells, we investigated how P. agglomerans MVC 21 VOCs might influence bacteria–plant interaction. Noteworthy, VOCs produced by P. agglomerans MVC 21 boosted the ability of Ps. putida MVC 17 to increase LRD and root dry weight of tomato seedlings. These results could be explained by the positive effect of DMDS and P. agglomerans MVC 21 VOCs on acid 3-indoleacetic production in Ps. putida MVC 17. Overall, our results clearly indicated that P. agglomerans MVC 21 is able to establish a beneficial interaction with Ps. putida MVC 17 and tomato plants through the emission of DMDS.

Complete genome sequence of plant growth-promoting and heavy metal-tolerant Enterobacter tabaci 4M9 (CCB-MBL 5004)

Enterobacter tabaci 4M9 (CCB-MBL 5004) was reported to have plant growth-promoting and heavy metal tolerance traits. It was able to tolerate more than 300 mg/L Cd, 600 mg/L As, and 500 mg/L Pb and still maintained the ability to produce plant growth-promoting substances under metal stress conditions. To explore the genetic basis of these beneficial traits, the complete genome sequencing of 4M9 was carried out using Pacific Bioscience (PacBio) sequencing technology. The complete genome consisted of one chromosome of 4,654,430 bp with a GC content of 54.6% and one plasmid of 51,135 bp with a GC content of 49.4%. Genome annotation revealed several genes involved in plant growth-promoting traits, including the production of siderophore, indole acetic acid, and 1-aminocyclopropane-1-carboxylate deaminase; solubilization of phosphate and potassium; and nitrogen metabolism. Similarly, genes involved in heavy metals (As, Co, Zn, Cu, Mn, Se, Cd, and Fe) tolerance were detected. These support its potential as a heavy metal-tolerant plant growth-promoting bacterium and a good genetic resource that can be employed to improve phytoremediation efficiency of heavy metal-contaminated soil via biotechnological techniques. This, to the best of our knowledge, is the first report on the complete genome sequence of heavy metal-tolerant plant growth-promoting E. tabaci.

Harnessing the plant microbiome to promote the growth of agricultural crops

The rhizosphere microbiome is composed of diverse microbial organisms, including archaea, viruses, fungi, bacteria as well as eukaryotic microorganisms, which occupy a narrow region of soil directly associated with plant roots. The interactions between these microorganisms and the plant can be commensal, beneficial or pathogenic. These microorganisms can also interact with each other, either competitively or synergistically. Promoting plant growth by harnessing the soil microbiome holds tremendous potential for providing an environmentally friendly solution to the increasing food demands of the world's rapidly growing population, while also helping to alleviate the associated environmental and societal issues of large-scale food production. There recently have been many studies on the disease suppression and plant growth promoting abilities of the rhizosphere microbiome; however, these findings largely have not been translated into the field. Therefore, additional research into the dynamic interactions between crop plants, the rhizosphere microbiome and the environment are necessary to better guide the harnessing of the microbiome to increase crop yield and quality. This review explores the biotic and abiotic interactions that occur within the plant's rhizosphere as well as current agricultural practices, and how these biotic and abiotic factors, as well as human practices, impact the plant microbiome. Additionally, some limitations, safety considerations, and future directions to the study of the plant microbiome are discussed.

Metabolites Secreted by a Plant-Growth-Promoting Pantoea agglomerans Strain Improved Rooting of Pyrus communis L. cv Dar Gazi Cuttings

Strains belonging to Pantoea agglomerans species are known for their ability to produce metabolites that can act in synergy with auxins to induce the adventitious root (AR) formation. The latter is critically important in the agamic propagation of several woody species, including pear (Pyrus communis L.), playing a considerable role in the commercial nursery farms including those using micropropagation techniques. When grown on a medium amended with tryptophan, the plant-growth-promoting (PGP) strain P. agglomerans C1 produces a cocktail of auxin and auxin-like molecules that can be utilized as biostimulants to improve the rooting of vegetable (Solanum lycopersicum L.) and woody crop species (Prunus rootstock GF/677 and hazelnut). In this study, we evaluated the morphological and molecular responses induced by strain C1 exometabolites in microcuttings of P. communis L. cv Dar Gazi and the potential benefits arising from their application. Results showed that exometabolites by P. agglomerans C1 induced a direct and earlier emergence of roots from stem tissues and determined modifications of root morphological parameters and root architecture compared to plants treated with the synthetic hormone indole-3-butyric acid (IBA). Transcription analysis revealed differences in the temporal expression pattern of ARF17 gene when IBA and C1 exometabolites were used alone, while together they also determined changes in the expression pattern of other key auxin-regulated plant genes. These results suggest that the phenotypic and molecular changes triggered by P. agglomerans C1 are dependent on different stimulatory and inhibitory effects that auxin-like molecules and other metabolites secreted by this strain have on the gene regulatory network of the plant. This evidence supports the hypothesis that the strategies used to harness the metabolic potential of PGP bacteria are key factors in obtaining novel biostimulants for sustainable agriculture. Our results demonstrate that metabolites secreted by strain C1 can be successfully used to increase the efficiency of micropropagation of pear through tissue culture techniques.

High-throughput sequencing-based analysis of the composition and diversity of endophytic bacterial community in seeds of upland rice

Upland rice is an ecotype crop resulting from the long-term domestication and evolution of rice in dry land without a water layer. Generally, the stems and leaves are thick and luxuriant, while the leaves also typically broad and light. The root system is developed with abundant root hair, and the osmotic pressure of the root and cell juice concentration in the leaves is high, while this plant is drought-resistant, heat-resistant, and water absorbent. This study aims to reveal the "core flora" of the endophytes in upland rice seeds by examining their diversity and community structures. It further intends to reveal the impact of the soil environment on the formation of endophyte community structures in upland rice seeds by comparing the environmental soil microorganisms in upland rice habitats. In this study, high-throughput sequencing technology based on the Illumina Hiseq 2500 platform was used to investigate the structure and diversity of endophytic bacterial communities using upland rice varieties collected from different locations and soil samples from unified planting sites as materials. Here, 42 endophytic OTUs were found to coexist in the 14 samples. At the phylum level, the first dominant phyla in all the samples were Proteobacteria (93.81-99.99%). At the genus level, Pantoea (8.77-87.77%), Pseudomonas (1.15-61.58%), Methylobacterium (0.40-4.64%), Sphingomonas (0.26-3.85%), Microbacterium (0.01-4.67%) and Aurantimonas (0.04-4.34%), which represent the core microflora in upland rice seeds, served as the dominant genera that coexisted in all the upland rice seeds tested. This study significant for the isolation, screening, functional evaluation, and re-action of various functional microorganisms in upland rice to improve its agronomic traits. It also provides a specific reference for the interaction between microorganisms and plants.

A Genetic and Metabolomic Perspective on the Production of Indole-3-Acetic Acid by Pantoea agglomerans and Use of Their Metabolites as Biostimulants in Plant Nurseries

The species Pantoea agglomerans includes strains that are agronomically relevant for their growth-promoting or biocontrol traits. Molecular analysis demonstrated that the IPDC pathway involved in the conversion of tryptophan (Trp) to indole-3-acetic acid (IAA) is highly conserved among P. agglomerans strains at both gene and protein levels. Results also indicated that the promoter region controlling the inducible expression of ipdC gene differs from the model system Enterobacter cloacae, which is in accordance with the observation that P. agglomerans accumulates higher levels of IAA when cells are collected in the exponential phase of growth. To assess the potential applications of these microorganisms for IAA production, P. agglomerans C1, an efficient auxin-producer strain, was cultivated in 5 L fermenter so as to evaluate the effect of the medium formulation, the physiological state of the cells, and the induction timing on the volumetric productivity. Results demonstrated that higher IAA levels were obtained by using a saline medium amended with yeast extract and saccharose and by providing Trp, which acts both as a precursor and an inducer, to a culture in the exponential phase of growth. Untargeted metabolomic analysis revealed a significant effect of the carbon source on the exometabolome profile relative to IAA-related compounds and other plant bioactive signaling molecules. The IAA-enriched metabolites secreted in the culture medium by P. agglomerans C1 were used as plant biostimulants to run a series of trials at a large-scale nursery farm. Tests were carried out with in vitro and ex vitro systems following the regular protocols used for large-scale plant tree agamic propagation. Results obtained with 4,540 microcuttings of Prunus rootstock GF/677 and 1,080 plantlets of Corylus avellana L. showed that metabolites from strain C1 improved percentage of rooted-explant, number of adventitious root formation, plant survival, and quality of plant as vigor, with an increase in the leaf area between 17.5 and 42.7% compared to IBA-K (indole-3-butyric acid potassium salt)-treated plants.