Pseudomonas protegens MP12: A plant growth-promoting endophytic bacterium with broad-spectrum antifungal activity against grapevine phytopathogens

Physiological and genomic insights into a psychrotrophic drought-tolerant bacterial consortium for crop improvement in cold, semiarid regions

The agricultural land in the Indian Himalayan region (IHR) is susceptible to various spells of snowfall, which can cause nutrient leaching, low temperatures, and drought conditions. The current study, therefore, sought an indigenous psychrotrophic plant growth-promoting (PGP) bacterial inoculant with the potential to alleviate crop productivity under cold and drought stress. Psychrotrophic bacteria preisolated from the night-soil compost of the Lahaul Valley of northwestern Himalaya were screened for phosphate (P) and potash (K) solubilization, nitrogen fixation, indole acetic acid (IAA) production, siderophore and HCN production) in addition to their tolerance to drought conditions for consortia development. Furthermore, the effects of the selected consortium on the growth and development of wheat (Triticum aestivum L.) and maize (Zea mays L.) were assessed in pot experiments under cold semiarid conditions (50 % field capacity). Among 57 bacteria with P and K solubilization, nitrogen fixation, IAA production, siderophore and HCN production, Pseudomonas protegens LPH60, Pseudomonas atacamensis LSH24, Psychrobacter faecalis LUR13, Serratia proteamaculans LUR44, Pseudomonas mucidolens LUR70, and Glutamicibacter bergerei LUR77 exhibited tolerance to drought stress (-0.73 MPa). The colonization of wheat and maize seeds with these drought-tolerant PGP strains resulted in a germination index >150, indicating no phytotoxicity under drought stress. Remarkably, a particular strain, Pseudomonas sp. LPH60 demonstrated antagonistic activity against three phytopathogens Ustilago maydis, Fusarium oxysporum, and Fusarium graminearum. Treatment with the consortium significantly increased the foliage (100 % and 160 %) and root (200 % and 133 %) biomasses of the wheat and maize plants, respectively. Furthermore, whole-genome sequence comparisons of LPH60 and LUR13 with closely related strains revealed genes associated with plant nutrient uptake, phytohormone synthesis, siderophore production, hydrogen cyanide (HCN) synthesis, volatile organic compound production, trehalose and glycine betaine transport, cold shock response, superoxide dismutase activity, and gene clusters for nonribosomal peptide synthases and polyketide synthetases. With their PGP qualities, biocontrol activity, and ability to withstand environmental challenges, the developed consortium represents a promising cold- and drought-active PGP bioinoculant for cereal crops grown in cold semiarid regions.

Genomic Insights into Pseudomonas protegens E1BL2 from Giant Jala Maize: A Novel Bioresource for Sustainable Agriculture and Efficient Management of Fungal Phytopathogens

The relationships between plants and bacteria are essential in agroecosystems and bioinoculant development. The leaf endophytic Pseudomonas protegens E1BL2 was previously isolated from giant Jala maize, which is a native Zea mays landrace of Nayarit, Mexico. Using different Mexican maize landraces, this work evaluated the strain's plant growth promotion and biocontrol against eight phytopathogenic fungi in vitro and greenhouse conditions. Also, a plant field trial was conducted on irrigated fields using the hybrid maize Supremo. The grain productivity in this assay increased compared with the control treatment. The genome analysis of P. protegens E1BL2 showed putative genes involved in metabolite synthesis that facilitated its beneficial roles in plant health and environmental adaptation (bdhA, acoR, trpE, speE, potA); siderophores (ptaA, pchC); and extracellular enzymes relevant for PGPB mechanisms (cel3, chi14), protection against oxidative stress (hscA, htpG), nitrogen metabolism (nirD, nit1, hmpA), inductors of plant-induced systemic resistance (ISR) (flaA, flaG, rffA, rfaP), fungal biocontrol (phlD, prtD, prnD, hcnA-1), pest control (vgrG-1, higB-2, aprE, pslA, ppkA), and the establishment of plant-bacteria symbiosis (pgaA, pgaB, pgaC, exbD). Our findings suggest that P. protegens E1BL2 significantly promotes maize growth and offers biocontrol benefits, which highlights its potential as a bioinoculant.

The Roles of Plant-Growth-Promoting Rhizobacteria (PGPR)-Based Biostimulants for Agricultural Production Systems

The application of biostimulants has been proven to be an advantageous tool and an appropriate form of management towards the effective use of natural resources, food security, and the beneficial effects on plant growth and yield. Plant-growth-promoting rhizobacteria (PGPR) are microbes connected with plant roots that can increase plant growth by different methods such as producing plant hormones and molecules to improve plant growth or providing increased mineral nutrition. They can colonize all ecological niches of roots to all stages of crop development, and they can affect plant growth and development directly by modulating plant hormone levels and enhancing nutrient acquisition such as of potassium, phosphorus, nitrogen, and essential minerals, or indirectly via reducing the inhibitory impacts of different pathogens in the forms of biocontrol parameters. Many plant-associated species such as Pseudomonas, Acinetobacter, Streptomyces, Serratia, Arthrobacter, and Rhodococcus can increase plant growth by improving plant disease resistance, synthesizing growth-stimulating plant hormones, and suppressing pathogenic microorganisms. The application of biostimulants is both an environmentally friendly practice and a promising method that can enhance the sustainability of horticultural and agricultural production systems as well as promote the quantity and quality of foods. They can also reduce the global dependence on hazardous agricultural chemicals. Science Direct, Google Scholar, Springer Link, CAB Direct, Scopus, Springer Link, Taylor and Francis, Web of Science, and Wiley Online Library were checked, and the search was conducted on all manuscript sections in accordance with the terms Acinetobacter, Arthrobacter, Enterobacter, Ochrobactrum, Pseudomonas, Rhodococcus, Serratia, Streptomyces, Biostimulants, Plant growth promoting rhizobactera, and Stenotrophomonas. The aim of this manuscript is to survey the effects of plant-growth-promoting rhizobacteria by presenting case studies and successful paradigms in various agricultural and horticultural crops.

Combined omics approaches expose metabolite-microbiota correlations in grape berries of three cultivars of Douro wine region

This study hypothesized the existence of cultivar-associated correlations between grape berry metabolites and its microbial residents, in Douro wine region. Integrated metabolomics with metabarcoding showed that the microbial biodiversity is not associated to berry sugar concentration, but closely connected to the profile of amino acids, flavonoids and wax compounds, which drove cultivar differentiation together with the prevalence of pathogenic fungi, yeasts and bacteria, mainly Dothideomycetes and Gammaproteobacteria. Over 7000 metabolite-microbiota correlations with ρ >|0.99| exposed a core of 15 metabolites linked to 11 microbial taxa. Serine, oxalate, cyanidin-3-O-glucoside, petunidin-3-O-glucoside, gallic acid, germanicol, sitosterol and erythrodiol correlated negatively to the abundance of most taxa, including Alternaria, Aureobasidium, Pseudopithomyces, Pseudomonas and Sphingomonas. In contrast, phenylalanine, asparagine, alanine, (epi)gallocatechin and procyanidin gallate mediated positive metabolite-OTU correlations. E. necator and A. carbonarius correlated negatively with stigmasterol and amyrin. Complex fungi-bacteria relationships ruled by Dothideomycetes and Alphaproteobacteria further suggest tight host-microbe interactions at the carposphere.

Biocontrol potential of Pseudomonas protegens ML15 against Botrytis cinerea causing gray mold on postharvest tomato (Solanum lycopersicum var. cerasiforme)

Gray mold, caused by Botrytis cinerea is a major cause of post-harvest rot of fresh fruits and vegetables. The utilization of selected microorganisms as biocontrol agents is a promising alternative to effectively control gray mold on tomatoes. The current study was conducted to explore potential biocontrol mechanisms of the Pseudomonas strain to control infections on post-harvest tomatoes. Among the 8 tested bacterial isolates, Pseudomonas protegens ML15 demonstrated antagonistic activity to Botrytis cinerea. Moreover, P. protegens ML15 exhibited the production of siderophores, hydrogen cyanide, ammonia, exopolysaccharides, lipase, biosurfactant, 2,4-diacetylphloroglucinol, and several other antifungal compounds, such as 1-tetradecanol, cyclododecane, 2,4-di-tert-butylphenol, and 2-methyl-1-hexadecanol. A comprehensive genomic analysis of P. protegens ML15 unravels 18 distinct genetic regions with the potential for biosynthesizing secondary metabolites, known for their pivotal role in biocontrol responses against plant pathogens. In vivo, experiments showed that both culture suspension and cell-free supernatant of P. protegens ML15 significantly reduced fungal growth (53.0 ± 0.63%) and mitigated disease development (52.8 ± 1.5%) in cherry tomatoes at four days post-B. cinerea inoculation. During the infection, the application of P. protegens ML15 resulted in the augmentation of total antioxidant, phenolic content, and ascorbic acids content. Thus, our results suggested that P. protegens ML15's role as a biocontrol agent against B. cinerea-induced postharvest tomato decay achieved through the secretion of antifungal substances, induction of tomato defense responses, and inhibition of mycelial growth of B. cinerea. These findings provide a significant contribution to the ongoing search for alternative, eco-friendly methods of controlling gray mold in fresh products. The utilization of P. protegens ML15 as a biocontrol agent could help to reduce the reliance on chemical fungicides and promote sustainable agriculture practices.

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.

New Potential Biological Limiters of the Main Esca-Associated Fungi in Grapevine

The strains Trichoderma harzianum TH07.1-NC (TH), Aphanocladium album MX95 (AA), Pleurotus eryngii AL142PE (PE) and Pleurotus ostreatus ALPO (PO) were tested as biological limiters against Fomitiporia mediterranea Fme22.12 (FM), Phaeoacremonium minimum Pm22.53 (PM) and Phaeomoniella chlamydospora Pc22.65 (PC). Pathogens were obtained from naturally Esca-affected 'Nero di Troia' vines cropped in Grumo Appula (Puglia region, Southern Italy). The antagonistic activity of each challenge organism was verified in a dual culture. TH and PO completely overgrew the three pathogens. Partial replacement characterized PE-FM, PE-PM, PE-PC and AA-PC interactions. Deadlock at mycelial contact was observed in AA-FM and AA-PM cultures. The calculated antagonism index (AI) indicated TH and PE as moderately active antagonists (10 < AI < 15), while AA and PO were weakly active (AI < 10). The maximum value of the re-isolation index (s) was associated with deadlock among AA-PM, AA-PC and PE-FM dual cultures. The tested biological limiters were always re-isolated when PO and TH completely replaced the three tested pathogens. TH and AA confirmed their efficiencies as biological limiters when inoculated on detached canes of 'Nero di Troia' in dual combination with FM, PC and PM. Nevertheless, additional experiments should be performed for a solid conclusion, along with validation experiments in the field.

Characterization of trehalolipid biosurfactant produced by the novel marine strain Rhodococcus sp. SP1d and its potential for environmental applications

BACKGROUND

Biosurfactants are surface-active compounds with environmental and industrial applications. These molecules show higher biocompatibility, stability and efficiency compared to synthetic surfactants. On the other hand, biosurfactants are not cost-competitive to their chemical counterparts. Cost effective technology such as the use of low-cost substrates is a promising approach aimed at reducing the production cost. This study aimed to evaluate the biosurfactant production and activity by the novel strain Rhodococcus sp. SP1d by using different growth substrates. Therefore, to exploit the biosurfactant synthesized by SP1d for environmental applications, the effect of this compound on the bacteria biofilm formation was evaluated. Eventually, for a possible bioremediation application, the biosurfactant properties and its chemical characteristics were investigated using diesel as source of carbon.

RESULTS

Rhodococcus sp. SP1d evidence the highest similarity to Rhodococcus globerulus DSM 43954^T and the ability to biosynthesize surfactants using a wide range of substrates such as exhausted vegetable oil, mineral oil, butter, n-hexadecane, and diesel. The maximum production of crude biosurfactant after 10 days of incubation was reached on n-hexadecane and diesel with a final yield of 2.38 ± 0.51 and 1.86 ± 0.31 g L^- 1 respectively. Biosurfactants produced by SP1d enhanced the biofilm production of P. protegens MP12. Moreover, the results showed the ability of SP1d to produce biosurfactants on diesel even when grown at 10 and 18 °C. The biosurfactant activity was maintained over a wide range of NaCl concentration, pH, and temperature. A concentration of 1000 mg L^- 1 of the crude biosurfactant showed an emulsification activity of 55% towards both xylene and olive oil and a reduction of 25.0 mN m^- 1 of surface tension of water. Eventually, nuclear magnetic resonance spectroscopy indicated that the biosurfactant is formed by trehalolipids.

CONCLUSIONS

The use of low-cost substrates such as exhausted oils and waste butter reduce both the costs of biosurfactant synthesis and the environmental pollution due to the inappropriate disposal of these residues. High production yields, stability and emulsification properties using diesel and n-hexadecane as substrates, make the biosurfactant produced by SP1d a sustainable biocompound for bioremediation purpose. Eventually, the purified biosurfactant improved the biofilm formation of the fungal antagonistic strain P. protegens MP12, and thus seem to be exploitable to increase the adherence and colonization of plant surfaces by this antagonistic strain and possibly enhance antifungal activity.

From salty to thriving: plant growth promoting bacteria as nature's allies in overcoming salinity stress in plants

Soil salinity is one of the main problems that affects global crop yield. Researchers have attempted to alleviate the effects of salt stress on plant growth using a variety of approaches, including genetic modification of salt-tolerant plants, screening the higher salt-tolerant genotypes, and the inoculation of beneficial plant microbiome, such as plant growth-promoting bacteria (PGPB). PGPB mainly exists in the rhizosphere soil, plant tissues and on the surfaces of leaves or stems, and can promote plant growth and increase plant tolerance to abiotic stress. Many halophytes recruit salt-resistant microorganisms, and therefore endophytic bacteria isolated from halophytes can help enhance plant stress responses. Beneficial plant-microbe interactions are widespread in nature, and microbial communities provide an opportunity to understand these beneficial interactions. In this study, we provide a brief overview of the current state of plant microbiomes and give particular emphasis on its influence factors and discuss various mechanisms used by PGPB in alleviating salt stress for plants. Then, we also describe the relationship between bacterial Type VI secretion system and plant growth promotion.

Microbial Biological Control of Fungi Associated with Grapevine Trunk Diseases: A Review of Strain Diversity, Modes of Action, and Advantages and Limits of Current Strategies

Grapevine trunk diseases (GTDs) are currently among the most important health challenges for viticulture in the world. Esca, Botryosphaeria dieback, and Eutypa dieback are the most current GTDs caused by fungi in mature vineyards. Their incidence has increased over the last two decades, mainly after the ban of sodium arsenate, carbendazim, and benomyl in the early 2000s. Since then, considerable efforts have been made to find alternative approaches to manage these diseases and limit their propagation. Biocontrol is a sustainable approach to fight against GTD-associated fungi and several microbiological control agents have been tested against at least one of the pathogens involved in these diseases. In this review, we provide an overview of the pathogens responsible, the various potential biocontrol microorganisms selected and used, and their origins, mechanisms of action, and efficiency in various experiments carried out in vitro, in greenhouses, and/or in vineyards. Lastly, we discuss the advantages and limitations of these approaches to protect grapevines against GTDs, as well as the future perspectives for their improvement.

Evaluation of Bacillus subtilis PTA-271 and Trichoderma atroviride SC1 to control Botryosphaeria dieback and black-foot pathogens in grapevine propagation material

BACKGROUND

Grapevine trunk diseases (GTDs) are a complex group of diseases that lead to major economic losses in all wine-producing countries. The investigation of biocontrol agents (BCAs) capable of forestalling or at least minimizing the development of GTDs has, recently, become a priority. Nursery experiments were set up to (i) assess the biocontrol effect of Trichoderma atroviride (Ta) SC1 and Bacillus subtilis (Bs) PTA-271, alone and in simultaneous application, against Botryosphaeria dieback (BOT)- and black-foot (BF)- associated pathogens during the grapevine propagation process and (ii) evaluate the success of the BCA inoculation during the grapevine propagation process, using quantitative reverse-transcription polymerase chain reaction techniques.

RESULTS

The results demonstrated a significant reduction in the percentage of potentially infected plants and the percentage of fungal isolation from wood fragments of BOT and BF pathogens in nursery material treated with Ta SC1 and Bs PTA-271, respectively. In one of the experiments, simultaneous treatments with Bs PTA-271 and Ta SC1 caused a reduction in percentages of potentially infected plants and fungal isolation, from wood fragments containing BOT and BF pathogens.

CONCLUSION

These biological treatments may be relevant components of an integrated approach, using complementary management strategies to limit infection by GTD pathogens, but further research is still needed to elucidate the effectiveness of Bs PTA-271 and the benefits of simultaneous application with Ta SC1 for the control of GTD pathogens in nurseries. © 2022 Society of Chemical Industry.

Evaluation of the biocontrol activity of Frateuria defendens-derived metabolites against mollicutes

Frateuria defendens is a candidate biocontrol agent that has been shown to reduce phytoplasma-related disease symptoms in grapevines and periwinkle plants. While a crude filtrate prepared from F. defendens can inhibit mollicute growth, the specific growth parameters for this bacterium, necessary to enhance this protective inhibitory response, remain unknown. Moreover, the separation of filtrate preparations from bacterial cells via centrifugation and filtration is laborious and time-consuming. As such, the present study was conducted to define the optimal growth conditions associated with maximal inhibitory activity of F. defendens and to establish a better approach to separating these bacterial cells from their secreted metabolites. To conduct these analyses, F. defendens was cultured in a range of media types, while associated inhibitory effects were tested in vitro using Spiroplasma melliferum as a model mollicute bacterium, and in planta using phytoplasma-infected periwinkle plantlets. These analyses revealed F. defendens growth patterns change based upon media composition, with filtrates prepared from a specific rich medium (S-medium) exhibiting beneficial activities, including the inhibition of S. melliferum and enhanced plant growth. When F. defendens cells were grown within semi-permeable, membrane-coated Small Bioreactor Platform (SBP) capsules, they could be more readily separated from the secreted metabolite fraction, obviating the need for filtration and/or centrifugation. This study is the first to have reported the use of SBP capsules to separate bacterial cells from their secreted metabolites under sterile conditions while retaining the ability of these metabolites to inhibit S. melliferum growth and to benefit the host plant. The results highlight promising new approaches to the effective biocontrol of phytoplasma-driven diseases in grapevines and other economically important plant species.

Endophytic bacterium Pseudomonas protegens suppresses mycelial growth of Botryosphaeria dothidea and decreases its pathogenicity to postharvest fruits

Apple (Malus domestica Borkh.), one of the most economically important fruits widely consumed worldwide, has been suffering from apple ring rot caused by Botryosphaeria dothidea, which dramatically affects its quality and yield. In the present study, we demonstrated that Pseudomonas protegens, isolated from Chinese leek (Allium tuberosum), significantly suppressed the mycelial growth and propagation of B. dothidea, respectively, further displayed a considerably inhibitory effect on the apple ring rot of postharvest fruits. In addition, P. protegens significantly improved the total soluble solid/titrable acidity (TSS/TA) ratio and soluble sugar/titrable acidity (SS/TA) ratio and drastically maintained the fruit firmness. Further analysis manifested that P. protegens substantially induced the defense-related genes such as MdGLU, MdPAL, MdPOD, MdCAL, and transcription factors related to the resistance to B. dothidea, including MdWRKY15, MdPUB29, MdMyb73, and MdERF11 in apple fruits. Meanwhile, P. protegens considerably restrained the expressions of the pathogenicity-related genes in B. dothidea, including the BdCYP450, BdADH, BdGHY, BdATS, Bdα/β-HY, and BdSTR. By inference, P. protegens inhibited the apple ring rot on postharvest fruits by activating the defense system of apple fruit and repressing the pathogenic factor of B. dothidea. The study provided a theoretical basis and a potential alternative to manage the apple ring rot on postharvest fruits.

Evaluation of the Antifungal Activity of Endophytic and Rhizospheric Bacteria against Grapevine Trunk Pathogens

Grapevine trunk diseases (GTDs) are caused by multiple unrelated fungal pathogens, and their management remains difficult worldwide. Biocontrol is an attractive and sustainable strategy given the current need for a cleaner viticulture. In this study, twenty commercial vineyards were sampled across California to isolate endophytic and rhizospheric bacteria from different grapevine cultivars with the presence and absence of GTD symptoms. A collection of 1344 bacterial isolates were challenged in vitro against Neofusicoccum parvum and Diplodia seriata, from which a subset of 172 isolates exerted inhibition levels of mycelial growth over 40%. Bacterial isolates were identified as Bacillus velezensis (n = 154), Pseudomonas spp. (n = 12), Serratia plymuthica (n = 2) and others that were later excluded (n = 4). Representative isolates of B. velezensis, P. chlororaphis, and S. plymuthica were challenged against six other fungal pathogens responsible for GTDs. Mycelial inhibition levels were consistent across bacterial species, being slightly higher against slow-growing fungi than against Botryosphaeriaceae. Moreover, agar-diffusible metabolites of B. velezensis strongly inhibited the growth of N. parvum and Eutypa lata, at 1, 15, and 30% v/v. The agar-diffusible metabolites of P. chlororaphis and S. plymuthica, however, caused lower inhibition levels against both pathogens, but their volatile organic compounds showed antifungal activity against both pathogens. These results suggest that B. velezensis, P. chlororaphis and S. plymuthica constitute potential biocontrol agents (BCAs) against GTDs and their application in field conditions should be further evaluated.

Prolific contribution of Pseudomonas protegens in Zn biofortification of wheat by modulating multifaceted physiological response under saline and non-saline conditions

The current study aimed to characterize the contribution of bacterium CP17 in zinc (Zn) biofortification in wheat under saline and non-saline conditions. This bacterial strain effectively solubilized Zn and tolerated up to 20% NaCl concentration. The Zn-solubilization potential was also quantified using AAS in a liquid broth supplemented with zinc oxide and zinc carbonate at various NaCl concentrations. Lowering the pH of liquid broth and analyzing a wide range of organic acids (thioacetic acid, glutamic acid, carboxylic acid, propionic acid, and so on) using UPLC-MS provided mechanistic insight for zinc solubilization. This strain was also shown to possess plant probiotic characteristics like phosphate solubilization, production of siderophore, indole acetic acid (IAA), exopolysaccharide (EPS), ACC deaminase, and ammonia. CP17 was identified as a Pseudomonas protegens based on the 16S rRNA gene analysis. In addition, the amplified product of the ACC deaminase producing gene (acdS) provided a molecular indication of the strain's endurance towards stress. The towel paper assay confirmed that the inoculation of Pseudomonas protegens CP17 significantly increased wheat seedlings' germination, growth, and biomass under different NaCl concentrations (0 mM, 100 mM, and 150 mM). Afterward, In situ pot experiment study was designed with the inoculation of Pseudomonas protegens in wheat under saline and non-saline conditions. The harvested wheat plants showed an elevated pattern of zinc content in the grain (i.e. 24.33 and 29.33mg/kg), straw (i.e. 45.73 and 50.23mg/kg) and soil (i.e. 0.978 and 1.32mg/kg) under saline and non-saline conditions, respectively and shown significant improvement over control. The results of the pot study revealed the amelioration in plant health, yield and uptake of available zinc from rhizospheric soil to straw and grain, along with enhanced dehydrogenase and phosphatase activities of rhizospheric soil under saline and non-saline conditions. This study supports the integrative role of Pseudomonas protegens CP17 as a bioinoculant for the efficacious strategy of zinc biofortification and growth promotion in wheat and ensures sustainable nutrient quality production under salinity stress.

Fusarium oxysporum Disrupts Microbiome-Metabolome Networks in Arabidopsis thaliana Roots

While the plant host metabolome drives distinct enrichment of detrimental and beneficial members of the microbiome, the mechanistic interomics relationships remain poorly understood. Here, we studied microbiome and metabolome profiles of two Arabidopsis thaliana accessions after Fusarium oxysporum f.sp. mathioli (FOM) inoculation, Landsberg erecta (Ler-0) being susceptible and Col-0 being resistant against FOM. By using bacterial and fungal amplicon sequencing and targeted metabolite analysis, we observed highly dynamic microbiome and metabolome profiles across FOM host progression, while being markedly different between FOM-inoculated and noninoculated Col-0 and Ler-0. Co-occurrence network analysis revealed more robust microbial networks in the resistant Col-0 compared to Ler-0 during FOM infection. Correlation analysis revealed distinct metabolite-OTU correlations in Ler-0 compared with Col-0 which could possibly be explained by missense variants of the Rfo3 and Rlp2 genes in Ler-0. Remarkably, we observed positive correlations in Ler-0 between most of the analyzed metabolites and the bacterial phyla Proteobacteria, Bacteroidetes, Planctomycetes, Acidobacteria, and Verrucomicrobia, and negative correlations with Actinobacteria, Firmicutes, and Chloroflexi. The glucosinolates 4-methyoxyglucobrassicin, glucoerucin and indole-3 carbinol, but also phenolic compounds were strongly correlating with the relative abundances of indicator and hub OTUs and thus could be active in structuring the A. thaliana root-associated microbiome. Our results highlight interactive effects of host plant defense and root-associated microbiota on Fusarium infection and progression. Our findings provide significant insights into plant interomic dynamics during pathogen invasion and could possibly facilitate future exploitation of microbiomes for plant disease control. IMPORTANCE Plant health and fitness are determined by plant-microbe interactions which are guided by host-synthesized metabolites. To understand the orchestration of this interaction, we analyzed the distinct interomic dynamics in resistant and susceptible Arabidopsis ecotypes across different time points after infection with Fusarium oxysporum (FOM). Our results revealed distinct microbial profiles and network resilience during FOM infection in the resistant Col-0 compared with the susceptible Ler-0 and further pinpointed specific microbe-metabolite associations in the Arabidopsis microbiome. These findings provide significant insights into plant interomics dynamics that are likely affecting fungal pathogen invasion and could possibly facilitate future exploitation of microbiomes for plant disease control.

Evaluation of existing guidelines for their adequacy for the food and feed risk assessment of microorganisms obtained through synthetic biology

EFSA was asked by the European Commission to evaluate synthetic biology (SynBio) developments for agri-food use in the near future and to determine whether or not they are expected to constitute potential new hazards/risks. Moreover, EFSA was requested to evaluate the adequacy of existing guidelines for risk assessment of SynBio and if updated guidance is needed. The scope of this Opinion covers food and feed risk assessment, the variety of microorganisms that can be used in the food/feed chain and the whole spectrum of techniques used in SynBio. This Opinion complements a previously adopted Opinion with the evaluation of existing guidelines for the microbial characterisation and environmental risk assessment of microorganisms obtained through SynBio. The present Opinion confirms that microbial SynBio applications for food and feed use, with the exception of xenobionts, could be ready in the European Union in the next decade. New hazards were identified related to the use or production of unusual and/or new-to-nature components. Fifteen cases were selected for evaluating the adequacy of existing guidelines. These were generally adequate for assessing the product, the production process, nutritional and toxicological safety, allergenicity, exposure and post-market monitoring. The comparative approach and a safety assessment per se could be applied depending on the degree of familiarity of the SynBio organism/product with the non-genetically modified counterparts. Updated guidance is recommended for: (i) bacteriophages, protists/microalgae, (ii) exposure to plant protection products and biostimulants, (iii) xenobionts and (iv) feed additives for insects as target species. Development of risk assessment tools is recommended for assessing nutritional value of biomasses, influence of microorganisms on the gut microbiome and the gut function, allergenic potential of new-to-nature proteins, impact of horizontal gene transfer and potential risks of living cell intake. A further development towards a strain-driven risk assessment approach is recommended.

Microbial Metabolites Beneficial to Plant Hosts Across Ecosystems

Plants are intimately connected with their associated microorganisms. Chemical interactions via natural products between plants and their microbial symbionts form an important aspect in host health and development, both in aquatic and terrestrial ecosystems. These interactions range from negative to beneficial for microbial symbionts as well as their hosts. Symbiotic microbes synchronize their metabolism with their hosts, thus suggesting a possible coevolution among them. Metabolites, synthesized from plants and microbes due to their association and coaction, supplement the already present metabolites, thus promoting plant growth, maintaining physiological status, and countering various biotic and abiotic stress factors. However, environmental changes, such as pollution and temperature variations, as well as anthropogenic-induced monoculture settings, have a significant influence on plant-associated microbial community and its interaction with the host. In this review, we put the prominent microbial metabolites participating in plant-microbe interactions in the natural terrestrial and aquatic ecosystems in a single perspective and have discussed commonalities and differences in these interactions for adaptation to surrounding environment and how environmental changes can alter the same. We also present the status and further possibilities of employing chemical interactions for environment remediation. Our review thus underlines the importance of ecosystem-driven functional adaptations of plant-microbe interactions in natural and anthropogenically influenced ecosystems and their possible applications.

Pseudomonas aeruginosa Ld-08 isolated from Lilium davidii exhibits antifungal and growth-promoting properties

A plant growth-promoting and antifungal endophytic bacteria designated as Ld-08 isolated from the bulbs of Lilium davidii was identified as Pseudomonas aeruginosa based on phenotypic, microscopic, and 16S rRNA gene sequence analysis. Ld-08 exhibited antifungal effects against Fusarium oxysporum, Botrytis cinerea, Botryosphaeria dothidea, and Fusarium fujikuroi. Ld-08 showed the highest growth inhibition, i.e., 83.82±4.76% against B. dothidea followed by 74.12±3.87%, 67.56±3.35%, and 63.67±3.39% against F. fujikuroi, B. cinerea, and F. oxysporum, respectively. The ethyl acetate fraction of Ld-08 revealed the presence of several bioactive secondary metabolites. Prominent compounds were quinolones; 3,9-dimethoxypterocarpan; cascaroside B; dehydroabietylamine; epiandrosterone; nocodazole; oxolinic acid; pyochelin; rhodotulic acid; 9,12-octadecadienoic acid; di-peptides; tri-peptides; ursodiol, and venlafaxine. The strain Ld-08 showed organic acids, ACC deaminase, phosphate solubilization, IAA, and siderophore. The sterilized bulbs of a Lilium variety, inoculated with Ld-08, were further studied for plant growth-promoting traits. The inoculated plants showed improved growth than the control plants. Importantly, some growth parameters such as plant height, leaf length, bulb weight, and root length were significantly (P ≤0.05) increased in the inoculated plants than in the control un-inoculated plants. Further investigations are required to explore the potential of this strain to be used as a plant growth-promoting and biocontrol agent in sustainable agriculture.

2,4-Diacetylphloroglucinol producing Pseudomonas fluorescens JM-1 for management of ear rot disease caused by Fusarium moniliforme in Zea mays L

Maize (Zea mays L.) is a major cereal crop grown in a large number of countries. Loss in maize yield due to biotic stresses including fungal phytopathogens is a matter of immense concern. Control measures applied for eradication of fungal phytopathogens in maize are not up to the mark and more often involve harsh chemical(s)/pesticide(s) that cause deleterious effects both in humans and soil biota. Greener alternatives, such as the use of rhizosphere microbes in the form of bioinoculants, have proven to be very successful in terms of enhancing crop yield and suppressing fungal phytopathogens. In the present study, fluorescent pseudomonads were isolated from the maize rhizosphere and monitored for their plant growth-promoting (PGP) and biocontrol activities against Fusarium moniliforme. Based on various PGP traits and biocontrol potential, isolate JM-1 was found to be most effective and as per 16S rRNA gene sequencing analysis was identified as Pseudomonas fluorescens. Further experiments showed that the biocontrol potential of JM-1 against ear rot fungus involved the production of antifungal compound 2,4-diacetylphloroglucinol (DAPG). When examined for antagonistic interaction under scanning electron microscopy (SEM), structural abnormality, hyphal lysis, and deformity in fungal mycelium were observed. In the pot experiment, application of talc-based JM-1 containing bioformulation (in pot trials) showed significant enhancement in maize growth parameters (including the seed number and weight) in comparison to control even in presence of the phytopathogen. Ear fresh weight, dry weight, number of seeds per plant, and 100-grain weight were found to increase significantly by 34, 34, 52, and 18% respectively, in comparison to control. P. fluorescens JM-1 can therefore be used as a bioinoculant for ear rot disease control and sustainably enhancing maize yield.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-022-03201-7.

Non-Rhizobial Endophytes Associated with Nodules of Vigna radiata L. and Their Combined Activity with Rhizobium sp

Root nodules of legume plants are devoted for hosting endophytic symbiotic bacteria that fix atmospheric nitrogen but recently proved as a niche for various non-rhizobial endophytes (NRE) also. In the present investigation, one rhizobial and two NRE were isolated and characterized as Rhizobium sp. AAU B3, Bacillus sp. AAU B6 and Bacillus sp. AAU B12. These isolates were studied for in vitro biocontrol activity against two pathogenic fungi. NRE isolates exhibited antifungal activity against root rot causing Macrophomina phaseolina (ITCC-6749) isolated from Vigna radiata and wilt causing pathogen Fusarium udum Butler isolated from Cajanus cajan in liquid as well as on solid medium. Furthermore, their antagonism was increased markedly when combined with Rhizobium sp. Moreover, Bacillus sp. AAU B6 showed amplification of the zwittermicin A gene (~ 950 bp) which is evident for the production of antibiotics. All three isolates showed HCN production in vitro also, Bacillus sp. AAU B12 exhibited amplification of its gene hcnC. Pathogenic fungal hyphae became thin, transparent, and bent as well as fungi lost their normal growth and branching patterns when exposed to volatile compounds produced by NRE. All the 3 isolates produced siderophores, however siderophore production was increased considerably when all three strains are mixed together. Furthermore, all the three isolates produced cell wall degrading enzymes (chitinase, protease, and cellulase) but lipolytic activity was exhibited only by Rhizobium sp. AAU B3. When NRE inoculated in combination of Rhizobium; overcomes the disease severity against M. phaseolina under pot study. Thus, from present study it is concluded that co-inoculation of NRE and Rhizobium sp. can be exploited as biocontrol bio-agents against M. phaseolina in green gram at field levels.

Phyto-Beneficial Traits of Rhizosphere Bacteria: In Vitro Exploration of Plant Growth Promoting and Phytopathogen Biocontrol Ability of Selected Strains Isolated from Harsh Environments

Beneficial interactions between plants and some bacterial species have been long recognized, as they proved to exert various growth-promoting and health-protective activities on economically relevant crops. In this study, the growth promoting and antifungal activity of six bacterial strains, Paenarthrobacter ureafaciens, Beijerinckia fluminensis, Pseudomonas protegens, Arthrobacter sp., Arthrobacter defluii, and Arthrobacter nicotinovorans, were investigated. The tested strains resulted positive for some plant growth promoting (PGP) traits, such as indole-3-acetic acid (IAA), 1-aminocyclopropane-1-carboxylate-deaminase (ACC-deaminase), siderophore production, and solubilization of phosphates. The effect of the selected bacteria on Arabidopsis thaliana seedlings growth was assessed using different morphological parameters. Bacterial activity against the phytopathogenic fungal species Aspergillus flavus, Fusarium proliferatum, and Fusarium verticillioides was also assessed, since these cause major yield losses in cereal crops and are well-known mycotoxin producers. Strains Pvr_9 (B. fluminensis) and PHA_1 (P. protegens) showed an important growth-promoting effect on A. thaliana coupled with a high antifungal activity on all the three fungal species. The analysis of bacterial broths through ultra performance liquid chromatography-mass spectrometry (UPLC-MS) and liquid chromatography-electrospray ionization-mass spectrometry (LC-ESI-MS/MS) confirmed the presence of potential PGP-compounds, among these are desferrioxamine B, aminochelin, asperchrome B, quinolobactin siderophores, and salicylic acid.

Cadophora sabaouae sp. nov. and Phaeoacremonium Species Associated with Petri Disease on Grapevine Propagation Material and Young Grapevines in Algeria

A field survey conducted on asymptomatic grapevine propagation material from nurseries and symptomatic young grapevines throughout different regions of Algeria yielded a collection of 70 Phaeoacremonium-like isolates and three Cadophora-like isolates. Based on morphology and DNA sequence data of β-tubulin (tub2) and actin, five Phaeoacremonium species were identified including Phaeoacremonium minimum (22 isolates), Phaeoacremonium venezuelense (19 isolates), Phaeoacremonium parasiticum (17 isolates), Phaeoacremonium australiense (8 isolates), and Phaeoacremonium iranianum (4 isolates). The latter two species (P. australiense and P. iranianum) were reported for the first time in Algeria. Multilocus phylogenetic analyses (internal transcribed spacer, tub2, and translation elongation factor 1-α) and morphological features, allowed the description of the three isolates belonging to the genus Cadophora (WAMC34, WAMC117, and WAMC118) as a novel species, named Cadophora sabaouae sp. nov. Pathogenicity tests were conducted on grapevine cuttings cultivar Cardinal. All the identified species were pathogenic on grapevine cuttings.

Endophytic bacteria from strawberry plants control gray mold in fruits via production of antifungal compounds against Botrytis cinerea L

Botrytis cinerea causes the gray mold disease in a wide range of plant hosts, especially in post-harvest periods. The control of this phytopathogen has been accomplished through the application of fungicides. However, this practice can cause environmental problems and increase fruit production costs. In addition, this fungus species has developed resistance to conventional synthetic fungicides. In this context, plant growth-promoting bacteria have shown potential for application in agricultural production because they are able to stimulate plant growth through different mechanisms, including the biological control of phytopathogens (indirect growth promotion mechanism). The aim of this work was to evaluate in vitro and in fruits the potential for indirect plant growth-promotion of bacteria isolated from strawberry leaves and roots. Dual plate method and inverted plate method were used to verify the ability of controlling in vitro the growth of Botrytis cinerea via the production of diffusible and volatile antifungal compounds, respectively. The effect of six bacterial isolates that showed greater potential for biological control in vitro was evaluated by scanning electron microscopy. Antifungal compounds produced by these bacterial isolates were identified by liquid chromatography coupled with mass spectrometry. Six bacterial strains were tested on strawberry pseudofruits. Five selected strains belong to the genus Bacillus and one to the genus Pantoea sp. Selected strains were able to inhibit more than 80 % of the mycelial growth of B. cinerea by the production of diffusible compounds and 90 % by volatile antifungal compounds production. Scanning electron microscopy showed the intense degradation of fungal hyphae caused by the presence of all bacterial strains. Bioactive compounds (salycilamide, maculosin, herniarin, lauroyl diethanolamide, baptifoline, undecanedioic acid, botrydial, 8 3-butylidene-7-hydroxyphthalide and N-(3-oxo-henoyl)-homoserine lactone) were obtained from liquid culture of these strains and extraction with ethyl acetate. All six isolates tested in vivo reduced the incidence of gray mold in strawberry pseudofruits in postharvest. It is concluded that isolates 26, 29, 65, 69, 132 (Bacillus sp.) and MQT16M1 (Pantoea sp.) have potential application for the biological control of Botrytis cinerea in strawberry via the production of diffusible and volatile antifungal compounds.

Comparative genomics of the Pseudomonas corrugata subgroup reveals high species diversity and allows the description of Pseudomonas ogarae sp. nov

Pseudomonas corrugata constitute one of the phylogenomic subgroups within the Pseudomonas fluorescens species complex and include both plant growth-promoting rhizobacteria (PGPR) and plant pathogenic bacteria. Previous studies suggest that the species diversity of this group remains largely unexplored together with frequent misclassification of strains. Using more than 1800 sequenced Pseudomonas genomes we identified 121 genomes belonging to the P. corrugata subgroup. Intergenomic distances obtained using the genome-to-genome blast distance (GBDP) algorithm and the determination of digital DNA-DNA hybridization values were further used for phylogenomic and clustering analyses, which revealed 29 putative species clusters, of which only five correspond to currently named species within the subgroup. Comparative and functional genome-scale analyses also support the species status of these clusters. The search for PGPR and plant pathogenic determinants showed that approximately half of the genomes analysed could have a pathogenic behaviour based on the presence of a pathogenicity genetic island, while all analysed genomes possess PGPR traits. Finally, this information together with the characterization of phenotypic traits, allows the reclassification proposal of Pseudomonas fluorescens F113 as Pseudomonas ogarae sp. nov., nom rev., type strain F113T (=DSM 112162T=CECT 30235T), which is substantiated by genomic, functional genomics and phenotypic differences with their closest type strains.

Bacterial endophytes: Molecular interactions with their hosts

Plant growth promotion has been found associated with plants on the surface (epiphytic), inside (endophytic), or close to the plant roots (rhizospheric). Endophytic bacteria mainly have been researched for their beneficial activities in terms of nutrient availability, plant growth hormones, and control of soil-borne and systemic pathogens. Molecular communications leading to these interactions between plants and endophytic bacteria are now being unrevealed using multidisciplinary approaches with advanced techniques such as metagenomics, metaproteomics, metatranscriptomics, metaproteogenomic, microRNAs, microarray, chips as well as the comparison of complete genome sequences. More than 400 genes in both the genomes of host plant and bacterial endophyte are up- or downregulated for the establishment of endophytism and plant growth-promoting activity. The involvement of more than 20 genes for endophytism, about 50 genes for direct plant growth promotion, about 25 genes for biocontrol activity, and about 10 genes for mitigation of different stresses has been identified in various bacterial endophytes. This review summarizes the progress that has been made in recent years by these modern techniques and approaches.

Field evaluation of biocontrol agents against black-foot and Petri diseases of grapevine

BACKGROUND

Black-foot and Petri diseases are the main fungal diseases associated with young grapevine decline. Two field experiments were established to evaluate the preventive effect of two potential biocontrol agents (BCAs), that is Streptomyces sp. E1 + R4 and Pythium oligandrum Po37, and three BCA-commercial products containing Trichoderma atroviride SC1, Trichoderma koningii TK7 and Pseudomonas fluorescens + Bacillus atrophaeus on fungal infection in grafted plants and plant growth parameters.

RESULTS

The effectiveness of some BCA in reducing the incidence and severity of both diseases was dependent on the plant part analyzed and the plant age. No single BCA application was able to control both diseases. Streptomyces sp. E1 + R4 were able to reduce significantly the infection of the most prevalent black-foot disease fungi while P. oligandrum Po37 and Trichoderma spp. were able to reduce significantly Phaeomoniella chlamydospora and Phaeoacremonium minimum (Petri disease) infection. BCA treatments had no effect on the shoot weight, and root weight was significantly lower in all BCA treatments with respect to the control.

CONCLUSIONS

The combination of the disease-suppressive activity of two or more beneficial microbes in a biocontrol preparation is required to prevent infection by black-foot and Petri disease fungi in vineyards.

In Vivo Endophytic, Rhizospheric and Epiphytic Colonization of Vitis vinifera by the Plant-Growth Promoting and Antifungal Strain Pseudomonas protegens MP12

An evaluation was conducted of the colonization of Pseudomonas protegens MP12, a plant-growth promoting and antagonistic strain, inoculated in vine plants during a standard process of grapevine nursery propagation. Three in vivo inoculation protocols (endophytic, rhizospheric, and epiphytic) were implemented and monitored by means of both culture-dependent and independent techniques. Endophytic treatment resulted in the colonization of the bacterium inside the vine cuttings, which spread to young leaves during the forcing period. Microscopy analysis performed on transformed dsRed-tagged P. protegens MP12 cells confirmed the bacterium’s ability to penetrate the inner part of the roots. However, endophytic MP12 strain was no longer detected once the plant materials had been placed in the vine nursery field. The bacterium also displayed an ability to colonize the rhizosphere and, when the plants were uprooted at the end of the vegetative season, its persistence was confirmed. Epiphytic inoculation, performed by foliar spraying of cell suspension, was effective in controlling artificially-induced Botrytis cinerea infection in detached leaves. The success of rhizospheric and leaf colonization in vine plants suggests potential for the future exploitation of P. protegens MP12 as biofertilizer and biopesticide. Further investigation is required into the stability of the bacterium’s colonization of vine plants under real-world conditions in vineyards.

Paenibacillus alvei K165 and Fusarium oxysporum F2: Potential Biocontrol Agents against Phaeomoniella chlamydospora in Grapevines

In the last two decades grapevine trunk diseases (GTDs) have emerged as the most significant threat for grapevine sustainability worldwide. The tracheomycotic fungus Phaeomoniella chlamydospora (Pch) is the predominant GTD-associated species and cannot be controlled with available chemicals. In the present study, we evaluated the effectiveness of two microbial strains (Paenibacillus alvei K165 and Fusarium oxysporum F2) against Pch in grapevine. In vitro bioassays, performed in a growth culture medium simulating the xylem environment, indicated that F2 decreased Pch growth and sporulation, whereas K165 did not have any effect on Pch growth. In planta experiments revealed that root-drench and stem-puncture application of K165 and F2 reduced the endophytic relative DNA amount of Pch by 90% and 82%, respectively, compared to controls. However, wood discoloration, the typical symptom of Pch infection, was not reduced in the F2 treated grapevines. Nevertheless, the F2 treated grapevines harbored higher lignin levels compared to mocks, as it was also done by K165. Therefore, F2 and K165 have the potential to be used as biocontrol agents against Pch in grapevines.

Evaluation of Pseudomonas sp. for its multifarious plant growth promoting potential and its ability to alleviate biotic and abiotic stress in tomato (Solanum lycopersicum) plants

1-Aminocyclopropane-1-carboxylate (ACC) deaminase activity is one of the most beneficial traits of plant growth promoting (PGP) rhizobacteria responsible for protecting the plants from detrimental effects of abiotic and biotic stress. The strain S3 with ACC deaminase activity (724.56 nmol α-ketobutyrate mg-1 protein hr-1) was isolated from rhizospheric soil of turmeric (Curcuma longa), a medicinal plant, growing in Motihari district of Indian state, Bihar. The halotolerant strain S3, exhibited optimum growth at 8% (w/v) NaCl. It also exhibited multiple PGP traits such as indole acetic acid production (37.71 μg mL-1), phosphate solubilization (69.68 mg L-1), siderophore, hydrocyanic acid (HCN) and ammonia production as well as revealed antagonism against Rhizoctonia solani. The potential of isolated strain to alleviate salinity stress in tomato plants was investigated through pots trials by inoculating strain S3 through-seed bacterization, soil drenching, root dipping as well as seed treatment + soil drenching. The strain S3 inoculated through seed treatment and soil drenching method led to improved morphological attributes (root/shoot length, root/shoot fresh weight and root/shoot dry weight), photosynthetic pigment content, increased accumulation of osmolytes (proline and total soluble sugar), enhanced activities of antioxidants (Catalase and Peroxidase) and phenolic content in salt stressed tomato plants. The biochemical characterisation, FAMEs analysis and 16S rRNA gene sequencing revealed that strain S3 belongs to the genus Pseudomonas. The overall findings of the study revealed that Pseudomonas sp. strain S3 can be explored as an effective plant growth promoter which stimulate growth and improve resilience in tomato plants under saline condition.

Unlocking the potential of plant growth-promoting rhizobacteria on soil health and the sustainability of agricultural systems

The concept of soil health refers to specific soil properties and the ability to support and sustain crop growth and productivity, while maintaining long-term environmental quality. The key components of healthy soil are high populations of organisms that promote plant growth, such as the plant growth promoting rhizobacteria (PGPR). PGPR plays multiple beneficial and ecological roles in the rhizosphere soil. Among the roles of PGPR in agroecosystems are the nutrient cycling and uptake, inhibition of potential phytopathogens growth, stimulation of plant innate immunity, and direct enhancement of plant growth by producing phytohormones or other metabolites. Other important roles of PGPR are their environmental cleanup capacities (soil bioremediation). In this work, we review recent literature concerning the diverse mechanisms of PGPR in maintaining healthy conditions of agricultural soils, thus reducing (or eliminating) the toxic agrochemicals dependence. In conclusion, this review provides comprehensive knowledge on the current PGPR basic mechanisms and applications as biocontrol agents, plant growth stimulators and soil rhizoremediators, with the final goal of having more agroecological practices for sustainable agriculture.

Growth inhibition of pathogenic microorganisms by Pseudomonas protegens EMM-1 and partial characterization of inhibitory substances

The bacterial strain, EMM-1, was isolated from the rhizosphere of red maize ("Rojo Criollo") and identified as Pseudomonas protegens EMM-1 based on phylogenetic analysis of 16S rDNA, rpoB, rpoD, and gyrB gene sequences. We uncovered genes involved in the production of antimicrobial compounds like 2,4-diacetylphloroglucinol (2,4-DAPG), pyoluteorin, and lectin-like bacteriocins. These antimicrobial compounds are also produced by other fluorescent pseudomonads alike P. protegens. Double-layer agar assay showed that P. protegens EMM-1 inhibited the growth of several multidrug-resistant (MDR) bacteria, especially clinical isolates of the genera Klebsiella and β-hemolytic Streptococcus. This strain also displayed inhibitory effects against diverse fungi, such as Aspergillus, Botrytis, and Fusarium. Besides, a crude extract of inhibitory substances secreted into agar was obtained after the cold-leaching process, and physicochemical characterization was performed. The partially purified inhibitory substances produced by P. protegens EMM-1 inhibited the growth of Streptococcus sp. and Microbacterium sp., but no inhibitory effect was noted for other bacterial or fungal strains. The molecular weight determined after ultrafiltration was between 3 and 10 kDa. The inhibitory activity was thermally stable up to 60°C (but completely lost at 100°C), and the inhibitory activity remained active in a wide pH range (from 3 to 9). After treatment with a protease from Bacillus licheniformis, the inhibitory activity was decreased by 90%, suggesting the presence of proteic natural compounds. All these findings suggested that P. protegens EMM-1 is a potential source of antimicrobials to be used against pathogens for humans and plants.

Statement on the translocation potential by Pseudomonas chlororaphis MA342 in plants after seed treatment of cereals and peas and assessment of the risk to humans

The European Commission requested EFSA to provide scientific advice on the translocation potential by Pseudomonas chlororaphis MA342 in plants after seed treatment of cereals and peas and, if applicable, for a revision of the assessment of the risk to humans by its metabolite 2,3-deepoxy-2,3-didehydro-rhizoxin (DDR) and this based on the evidence available in the dossier for renewal of the approval. The information from other P. chlororaphis strains than MA342 was taken into account with care, because the studies available in the dossier did not confirm the identity of the strain MA342 as belonging to the species P. chlororaphis. It has been concluded that there is a potential for translocation of P. chlororaphis MA342 to edible plant parts following seed treatment till an estimated concentration up to about 105 cfu/g and some exposure can be assumed by consumption of fresh commodities. Also, production of the metabolite DDR in the plant cannot be excluded. Regarding levels of DDR in the raw agricultural commodities, exposure estimates based on the limit of quantification (LOQ) for DDR in cereals cannot be further refined while there is no information on the levels of DDR in peas in the dossier. As regards genotoxicity, DDR induced chromosomal damage; however, it was not possible to conclude whether it is through an aneugenic or clastogenic mechanism. Hence, it is not possible to draw a reliable conclusion that DDR is producing an aneugenic effect nor to determine a threshold dose for aneugenicity. Thus, it is not possible to revise the human risk assessment as regards exposure to DDR. The concerns identified in the EFSA conclusion of 2017 remain.

In vitro antibacterial activities and molecular characterization of bacterial species isolated from farmlands against selected pathogens

This study aims to screen bacterial isolates from Olabisi Onabanjo University Farmland for antibacterial activity against pathogenic microorganisms. Agar well diffusion method was used. Isolates were identified molecularly. Chi-square test revealed significant association between isolates, antibacterial activity with likelihood p-value = 0.000 and 5% significant level. Six among thirty-five isolates exhibited antibacterial activity against the test pathogenic species. A greater antibacterial activity (50 % inhibition) was observed in Lysinibacillus sphearicus strain PRE16. It inhibited the growth of Bacillus subtilis, Staphylococcus aureus and Escherichia coli by 23.00 ± 2.00, 18.00 ± 2.00 and 20.00 ± 4.00 respectively. DNA sequencing revealed antagonist isolates as Bacillus sp. BCN2, Brochothrix thermosphacta strain P30C4, Bacillus aryabhattai strain KNUC205, Alcaligenes faecalis strain KEM24, Bacillus arsenicus strain CSD05 and Lysinibacillus sphaericus strain PRE16. Phylogenetic analysis revealed close relatedness of most isolates with Bacillus species strains. These strains are suggested to be effective for the discovery of new antibacterial agents.

The Role of the Endophytic Microbiome in the Grapevine Response to Environmental Triggers

Endophytism within Vitis represents a topic of critical relevance due to the multiple standpoints from which it can be approached and considered. From the biological and botanical perspectives, the interaction between microorganisms and perennial woody plants falls within the category of stable relationships from which the plants can benefit in multiple ways. The life cycle of the host ensures persistence in all seasons, repeated chances of contact, and consequent microbiota accumulation over time, leading to potentially high diversity compared with that of herbaceous short-lived plants. Furthermore, grapevines are agriculturally exploited, highly selected germplasms where a profound man-driven footprint has indirectly and unconsciously shaped the inner microbiota through centuries of cultivation and breeding. Moreover, since endophyte metabolism can contribute to that of the plant host and its fruits' biochemical composition, the nature of grapevine endophytic taxa identities, ecological attitudes, potential toxicity, and clinical relevance are aspects worthy of a thorough investigation. Can endophytic taxa efficiently defend grapevines by acting against pests or confer enough fitness to the plants to endure attacks? What are the underlying mechanisms that translate into this or other advantages in the hosting plant? Can endophytes partially redirect plant metabolism, and to what extent do they act by releasing active products? Is the inner microbial colonization necessary priming for a cascade of actions? Are there defined environmental conditions that can trigger the unleashing of key microbial phenotypes? What is the environmental role in providing the ground biodiversity by which the plant can recruit microsymbionts? How much and by what practices and strategies can these symbioses be managed, applied, and directed to achieve the goal of a better sustainable viticulture? By thoroughly reviewing the available literature in the field and critically examining the data and perspectives, the above issues are discussed.

Antifungal Agents Based on Chitosan Oligomers, ε-polylysine and Streptomyces spp. Secondary Metabolites against Three Botryosphaeriaceae Species

Grapevine trunk diseases (GTDs) are a major threat to the wine and grape industry. The aim of the study was to investigate the antifungal activity against Neofusicoccum parvum, Diplodia seriata, and Botryosphaeria dothidea of ε-polylysine, chitosan oligomers, their conjugates, Streptomyces rochei and S. lavendofoliae culture filtrates, and their binary mixtures with chitosan oligomers. In vitro mycelial growth inhibition tests suggest that the efficacy of these treatments, in particular those based on ε-polylysine and ε-polylysine:chitosan oligomers 1:1 w/w conjugate, against the three Botryosphaeriaceae species would be comparable to or higher than that of conventional synthetic fungicides. In the case of ε-polylysine, EC₉₀ values as low as 227, 26.9, and 22.5 µg·mL^-1 were obtained for N. parvum, D. seriata, and B. dothidea, respectively. Although the efficacy of the conjugate was slightly lower, with EC₉₀ values of 507.5, 580.2, and 497.4 µg·mL^-1, respectively, it may represent a more cost-effective option to the utilization of pure ε-polylysine. The proposed treatments may offer a viable and sustainable alternative for controlling GTDs.

Biocontrol of Postharvest Fruit Fungal Diseases by Bacterial Antagonists: A Review

This review deals with the main mechanisms of action exerted by antagonistic bacteria, such as competition for space and nutrients, suppression via siderophores, hydrolytic enzymes, antibiosis, biofilm formation, and induction of plant resistance. These mechanisms inhibit phytopathogen growth that affects postharvest fruit since quality and safety parameters are influenced by the action of these microorganisms, which cause production losses in more than 50% of fruit tree species. The use of synthetic fungicide products has been the dominant control strategy for diseases caused by fungi. However, their excessive and inappropriate use in intensive agriculture has brought about problems that have led to environmental contamination, considerable residues in agricultural products, and phytopathogen resistance. Thus, there is a need to generate alternatives that are safe, ecological, and economically viable to face this problem. Phytopathogen inhibition in fruit utilizing antagonist microorganisms has been recognized as a type of biological control (BC), which could represent a viable and environmentally safe alternative to synthetic fungicides. Despite the ecological benefit that derives from the use of controllers and biological control agents (BCA) at a commercial level, their application and efficient use has been minimal at a global level.