Antimicrobial activity screening of rhizosphere soil bacteria from tomato and genome-based analysis of their antimicrobial biosynthetic potential

Discovery, Biosynthesis, and Characterization of Rodencin, a Two-Component Lanthipeptide, Harboring d-Amino Acids Introduced by the Unusual Dehydrogenase RodJA

Lanthipeptides, a group of ribosomally synthesized and post-translationally modified peptides (RiPPs), exhibit diverse structures and bioactivities. Their biosynthetic enzymes serve as valuable tools for peptide bioengineering. Here, we report a class II lanthipeptide biosynthetic gene cluster in a Bacillus strain, driving the biosynthesis of a two-component lanthipeptide, termed rodencin, featured by the presence of two different d-amino acids, i.e., d-Ala and d-Abu. Rodencin displays synergistic antimicrobial activity against food-borne pathogens such as Bacillus cereus, Staphylococcus aureus, and Listeria monocytogenes. The α-peptide of rodencin contains one d-Ala and the β-peptide features both d-Ala and d-Abu. These are installed by dehydratases RodM1 and RodM2 and dehydrogenase RodJA, the activities of which were successfully reconstituted using a dedicated E. coli expression system. To illustrate the unusual d-Abu incorporation potential of the enzymes, analogous to the d-amino acid-containing β peptide of lacticin 3147, was successfully produced with the rodencin heterologous expression system, by employing RodM2 and the dehydrogenase RodJA.

Applicability of metabolomics to improve sustainable grapevine production

Metabolites represent the end product of gene expression, protein interaction and other regulatory mechanisms. The metabolome reflects a biological system's response to genetic and environmental changes, providing a more accurate description of plants' phenotype than the transcriptome or the proteome. Grapevine (Vitis vinifera L.), established for the production of wine grapes, table grapes, and raisins, holds immense agronomical and economic significance not only in the Mediterranean region but worldwide. As all plants, grapevines face the adverse impact of biotic and abiotic stresses that negatively affect multiple stages of grape and wine industry, including plant and berry development pre- and post-harvest, fresh grapes processing and consequently wine quality. In the present review we highlight the applicability of metabolome analysis in the understanding of the mechanisms involved in grapevine response and acclimatization upon the main biotic and abiotic constrains. The metabolome of induced morphogenic processes such as adventitious rooting and somatic embryogenesis is also explored, as it adds knowledge on the physiological and molecular phenomena occurring in the explants used, and on the successfully propagation of grapevines with desired traits. Finally, the microbiome-induced metabolites in grapevine are discussed in view of beneficial applications derived from the plant symbioses.

Advances in microbial based bio-inoculum for amelioration of soil health and sustainable crop production

The adoption of sustainable agricultural practices is increasingly imperative in addressing global food security and environmental concerns, with microbial based bio-inoculums emerging as a promising approach for nurturing soil health and fostering sustainable crop production.This review article explores the potential of microbial based bio-inoculumsor biofertilizers as a transformative approach toenhance plant disease resistance and growth. It explores the commercial prospects of biofertilizers, highlighting their role in addressing environmental concerns associated with conventional fertilizers while meeting the growing demand for eco-friendly agricultural practices. Additionally, this review discusses the future prospects of biofertilizers, emphasizing the ongoing advancements in biotechnology and formulation techniques that are expected to enhance their efficacy and applicability. Furthermore, this article provides insights into strategies for the successful acceptance of biofertilizers among farmers, including the importance of quality control, assurance, and education initiatives to raise awareness about their benefits and overcome barriers to adoption. By synthesizing the current research findings and industrial developments, this review offers valuable guidance for stakeholders seeking to exploit the potential of biofertilizers or beneficial microbes to promote soil health, ensure sustainable crop production, and addressing the challenges of modern agriculture.

Exploring the interplay between the core microbiota, physicochemical factors, agrobiochemical cycles in the soil of the historic tokaj mád wine region

A Hungarian survey of Tokaj-Mád vineyards was conducted. Shotgun metabarcoding was applied to decipher the microbial-terroir. The results of 60 soil samples showed that there were three dominant fungal phyla, Ascomycota 66.36% ± 15.26%, Basidiomycota 18.78% ± 14.90%, Mucoromycota 11.89% ± 8.99%, representing 97% of operational taxonomic units (OTUs). Mutual interactions between microbiota diversity and soil physicochemical parameters were revealed. Principal component analysis showed descriptive clustering patterns of microbial taxonomy and resistance gene profiles in the case of the four historic vineyards (Szent Tamás, Király, Betsek, Nyúlászó). Linear discriminant analysis effect size was performed, revealing pronounced shifts in community taxonomy based on soil physicochemical properties. Twelve clades exhibited the most significant shifts (LDA > 4.0), including the phyla Verrucomicrobia, Bacteroidetes, Chloroflexi, and Rokubacteria, the classes Acidobacteria, Deltaproteobacteria, Gemmatimonadetes, and Betaproteobacteria, the order Sphingomonadales, Hypomicrobiales, as well as the family Sphingomonadaceae and the genus Sphingomonas. Three out of the four historic vineyards exhibited the highest occurrences of the bacterial genus Bradyrhizobium, known for its positive influence on plant development and physiology through the secretion of steroid phytohormones. During ripening, the taxonomical composition of the soil fungal microbiota clustered into distinct groups depending on altitude, differences that were not reflected in bacteriomes. Network analyses were performed to unravel changes in fungal interactiomes when comparing postveraison and preharvest samples. In addition to the arbuscular mycorrhiza Glomeraceae, the families Mycosphaerellacae and Rhyzopodaceae and the class Agaricomycetes were found to have important roles in maintaining soil microbial community resilience. Functional metagenomics showed that the soil Na content stimulated several of the microbiota-related agrobiogeochemical cycles, such as nitrogen and sulphur metabolism; steroid, bisphenol, toluene, dioxin and atrazine degradation and the synthesis of folate.

Rhizosphere: Role of bacteria to manage plant diseases and sustainable agriculture-A review

General plant diseases as well as soil-borne pathogens severely reduce agricultural yield. The rhizosphere (the region of the soil that includes and surrounds the roots) is an important niche for microbial diversity in particular phytobeneficial bacteria including plant growth-promoting rhizobacteria (PGPR) which have been used for a very long time to combat plant diseases. Pathogen control and crop productivity can both be improved through the use of PGPR several mechanisms, including iron-based nutrition, antibiotics, volatile substances, enzymes, biofilm, allelochemicals, and so on. Their modes of action and molecular mechanisms have improved our comprehension of how they are used to control crop disease. Therefore, there is a lot of literal information available regarding PGPR, but this review stands out since it starts with the fundamentals: the concept of the rhizosphere and the colonization process of the latter, particularly because it covers the most mechanisms. A broad figure is used to present the study's findings. The advantages of using PGPR as bioinoculants in sustainable agriculture are also mentioned.

Antimicrobial Activity of Syzygium aromaticum Essential Oil in Human Health Treatment

The use of natural compounds to prevent and treat infective diseases is increasing its importance, especially in the case of multidrug-resistant (MDR) microorganisms-mediated infections. The drug resistance phenomenon is today a global problem, so it is important to have available substances able to counteract MDR infections. Syzygium aromaticum (L.) Merr. & L.M. Perry (commonly called clove) is a spice characterized by several biological properties. Clove essential oil (EO) consists of numerous active molecules, being eugenol as the principal component; however, other compounds that synergize with each other are responsible for the biological properties of the EO. S. aromaticum is traditionally used for bowel and stomach disorders, cold and flu, oral hygiene, tooth decay, and for its analgesic action. Its EO has shown antioxidant, antimicrobial, anti-inflammatory, neuro-protective, anti-stress, anticancer, and anti-nociceptive activities. This review aims to investigate the role of E. S. aromaticum EO in the counteraction of MDR microorganisms responsible for human disorders, diseases, or infections, such as Escherichia coli, Pseudomonas aeruginosa, Staphylococcus aureus, Salmonella typhi, Candida albicans, Giardia lamblia, Streptococcus mutans, Porphyromonas gingivalis, and Klebsiella pneumoniae. This study might orient clinical researchers on future therapeutic uses of S. aromaticum EO in the prevention and treatment of infectious diseases.

Searching for Antimicrobial-Producing Bacteria from Soils through an Educational Project and Their Evaluation as Potential Biocontrol Agents

Antimicrobial resistance (AMR) is a serious threat to public health due to the lack of effective drugs to combat infectious diseases, which generates the need to search for new antimicrobial substances. In this study, the potential of soil as a source of antimicrobial-producing bacteria (APB) was investigated and the importance of the connection between education and science was emphasized, using service-learning methodologies. Sixty-one soil samples were collected, and 1220 bacterial isolates were recovered. Eighteen of these isolates showed antimicrobial activity against at least 1 of the 12 indicator bacteria tested (including multidrug-resistant and relevant pathogens). The 18 APB were identified by MALDI-TOF and 6 different genera (Bacillus, Brevibacillus, Lysinobacillus, Peribacillus, Streptomyces, and Advenella) and 10 species were identified. The 18 APB were tested for antifungal activity against four phytopathogenic fungi (Botritis cynerea, Lecanicillium fungicola, Trichoderma harzianum, and Cladobotryum mycophilum). Moreover, the antibiotic susceptibility of APB was tested using the disk-diffusion method as well as their β-hemolytic activity (important safety criteria for potential future applications). A total of 10 of the 18 APB were able to inhibit at least 50% of indicator bacteria tested, including methicillin-resistant Staphylococcus aureus (MRSA), among others. A total of 4 of the 18 APB (3 Bacillus pumilus and 1 Bacillus altitudinis) showed inhibitory activity against two of the four fungal pathogens tested (B. cinerea and L. fungicola), as well as against 5-7 of the 12 bacterial pathogen indicators; these 4 isolates showed susceptibility to the antibiotics tested and lacked β-hemolytic activity and were considered promising APB for use as potential biocontrol agents. In addition, one Brevibacillus laterosporus strain had activity against 83% of indicator bacteria tested including Escherichia coli, MRSA and other methicillin-resistant staphylococci, as well as vancomycin-resistant enterococci (but not against fungi). These results show that soil is a source of APB with relevant antibacterial and antifungal activities, and also emphasize the importance of education and science to raise public awareness of the AMR problem and the strategies to control it.

A review of biocontrol agents in controlling late blight of potatoes and tomatoes caused by Phytophthora infestans and the underlying mechanisms

Phytophthora infestans causes late blight on potatoes and tomatoes, which has a significant economic impact on agriculture. The management of late blight has been largely dependent on the application of synthetic fungicides, which is not an ultimate solution for sustainable agriculture and environmental safety. Biocontrol strategies are expected to be alternative methods to the conventional chemicals in controlling plant diseases in the integrated pest management (IPM) programs. Well-studied biocontrol agents against Phytophthora infestans include fungi, oomycetes, bacteria, and compounds produced by these antagonists, in addition to certain bioactive metabolites produced by plants. Laboratory and glasshouse experiments suggest a potential for using biocontrol in practical late blight disease management. However, the transition of biocontrol to field applications is problematic for the moment, due to low and variable efficacies. In this review, we provide a comprehensive summary on these biocontrol strategies and the underlying corresponding mechanisms. To give a more intuitive understanding of the promising biocontrol agents against Phytophthora infestans in agricultural systems, we discuss the utilizations, modes of action and future potentials of these antagonists based on their taxonomic classifications. To achieve a goal of best possible results produced by biocontrol agents, it is suggested to work on field trials, strain modifications, formulations, regulations, and optimizations of application. Combined biocontrol agents having different modes of action or biological adaptation traits may be used to strengthen the biocontrol efficacy. More importantly, biological control agents should be applied in the coordination of other existing and forthcoming methods in the IPM programs. © 2023 Society of Chemical Industry.

Bacillus subtilis and Bacillus amyloliquefaciens Mix Suppresses Rhizoctonia Disease and Improves Rhizosphere Microbiome, Growth and Yield of Potato (Solanum tuberosum L.)

Black scurf and stem canker caused by Rhizoctonia solani is a significant disease problem of potatoes. Currently, chemical methods are the primary means of controlling this pathogen. This study sought to explore an alternative approach by harnessing the biocontrol potential of a bacterial mix of Bacillus subtilis and Bacillus amyloliquefaciens against black scurf, and to determine their effect on rhizosphere microorganisms of soil microbiota. This study showed that these bacteria demonstrate antagonistic activity against Rhizoctonia solani. Reduced damage to potato plants during the growing season in Siberia was observed. The index of disease development decreased from 40.9% to 12.0%. The treatment of tubers with this mix of bacteria also led to a change in the composition of the rhizosphere microbiota (according to CFU, 16S and ITS sequencing). This effect was accompanied by a positive change in plant physiological parameters (spectrophotometric analysis). The concentration of chlorophyll in potatoes with the bacterial mix treatment increased by 1.3 fold (p ≤ 0.001), and of carotenoids by 1.2 fold (p ≤ 0.01) compared with the control. After bacterial mix treatment, the length of the aerial parts of plants was 1.3 fold higher (p ≤ 0.001), and the number of stems 1.4 fold higher (p ≤ 0.05). The yield of potatoes was increased by 8.2 t/ha, while the large tuber fraction was increased by 16% (p ≤ 0.05). The bacteria mix of Bacillus subtilis and Bacillus amyloliquefaciens suppressed the plant pathogenic fungus Rhizoctonia solani, and simultaneously enhanced the physiological parameters of potato plants. This treatment can be used to enhance the yield/quality of potato tubers under field conditions.

Food safety and biological control; genomic insights and antimicrobial potential of Bacillus velezensis FB2 against agricultural fungal pathogens

Development of natural, broad-spectrum, and eco-friendly bio-fungicides is of high interest in the agriculture and food industries. In this context, Bacillus genus has shown great potential for producing a wide range of antimicrobial metabolites against various pathogens. A Bacillus velezensis strain FB2 was isolated from an agricultural field of National Institute for Biotechnology and Genetic Engineering (NIBGE) Faisalabad, Pakistan, exhibiting good antifungal properties. The complete genome of this strain was sequenced, and its antifungal potential was assayed by dual culture method. Moreover, structural characterization of its antifungal metabolites, produced in vitro, were studied. Genome analysis and mining revealed the secondary metabolite gene clusters, encoding non-ribosomal peptides (NRPs) production (e.g., surfactin, iturin and fengycin) and polyketide (PK) synthesis (e.g., difficidin, bacillaene and macrolactin). Furthermore, the Bacillus velezensis FB2 strain was observed to possess in vitro antifungal activity; 41.64, 40.38 and 26% growth inhibition against major fungal pathogens i.e. Alternaria alternata, Fusarium oxysporum and Fusarium solani respectively. Its lipopeptide extract obtained by acid precipitation method was also found effective against the above-mentioned fungal pathogens. The ESI-MS/MS analysis indicated various homologs of surfactin and iturin-A, responsible for their antifungal activities. Overall, this study provides a better understanding of Bacillus velezensis FB2, as a promising candidate for biocontrol purposes, acting in a safe and sustainable way, to control plant pathogens.

Bacillus cabrialesii: Five Years of Research on a Novel Species of Biological Control and Plant Growth-Promoting Bacteria

Bacillus cabrialesii is a novel bacterial species isolated from wheat (Triticum turgidum L. subsp. durum) plants in the Yaqui Valley, Mexico, by our research team. Over years of research studying this strain at the cutting-edge level, it has shown different mechanisms of action. B. cabrialesii is strongly reported as a plant-growth-promoting bacterium and a biological control agent on wheat crops. Knowing this, B. cabrialesii has been brought from lab to field as part of a bacterial consortium, not to mention that there are ongoing investigations into formulating a cost-effective bioinoculant to increase the yield and/or quality of wheat. Moreover, studies of this novel species as a biocontrol agent in other crops (pepper, tomato, cucumber, and potato) are being carried out, with preliminary results that make B. cabrialesii a promising biological control agent, inhibiting the growth of phytopathogens. However, research into this bacterium has not only been reported in our country; there are many studies around the world in which promising native Bacillus strains end up being identified as B. cabrialesii, which reaffirms the fact that this bacterial species can promote plant growth and combat phytopathogens, showing great agrobiotechnological potential.

Unraveling the functional genes present in rhizosphere microbiomes of Solanum lycopersicum

The microbiomes living in the rhizosphere soil of the tomato plant contribute immensely to the state of health of the tomato plant alongside improving sustainable agriculture. With the aid of shotgun metagenomics sequencing, we characterized the putative functional genes (plant-growth-promoting and disease-resistant genes) produced by the microbial communities dwelling in the rhizosphere soil of healthy and powdery mildew-diseased tomato plants. The results identified twenty-one (21) plant growth promotion (PGP) genes in the microbiomes inhabiting the healthy rhizosphere (HR) which are more predomiant as compared to diseased rhizosphere (DR) that has nine (9) genes and four (4) genes in bulk soil (BR). Likewise, we identified some disease-resistant genes which include nucleotide binding genes and antimicrobial genes. Our study revealed fifteen (15) genes in HR which made it greater in comparison to DR that has three (3) genes and three (3) genes in bulk soil. Further studies should be conducted by isolating these microorganisms and introduce them to field experiments for cultivation of tomatoes.

Lysinibacillus capsici 38,328 isolated from agricultural soils as a promising probiotic candidate for intestinal health

There is an increasing interest in the use of spore-forming Bacillus spp. as probiotic ingredients on the market. However, probiotics Bacillus species are insufficient, and more safe Bacillus species were required. In the study, traditional fermented foods and soil samples were collected from more than ten provinces in China, and 506 Bacillus were selected from 109 samples. Using the optimized procedure, we screened nine strains, which successfully passed the acid, alkali, bile salt, and trypsin resistance test. Drug sensitivity test results showed that three Bacillus out of the nine isolates exhibited antibiotic sensitivity to more than 29 antibiotics. The three strains sensitive to antibiotics were identified by 16S ribosomal RNA, recA, and gyrB gene analysis, two isolates (38,327 and 38,328) belong to the species Lysinibacillus capsici and one isolate (37,326) belong to Bacillus halotolerans. Moreover, the three strains were confirmed safe through animal experiments. Finally, L. capsici 38,327 and 38,328 showed protections in the Salmonella typhimurium infection mouse model, which slowed down weight loss, reduced bacterial load, and improved antioxidant capacity. Altogether, our data demonstrated that selected L. capsici strains can be used as novel probiotics for intestinal health.

Frenemies of the soil: Bacillus and Pseudomonas interspecies interactions

Bacillus and Pseudomonas ubiquitously occur in natural environments and are two of the most intensively studied bacterial genera in the soil. They are often coisolated from environmental samples, and as a result, several studies have experimentally cocultured bacilli and pseudomonads to obtain emergent properties. Even so, the general interaction between members of these genera is virtually unknown. In the past decade, data on interspecies interactions between natural isolates of Bacillus and Pseudomonas has become more detailed, and now, molecular studies permit mapping of the mechanisms behind their pairwise ecology. This review addresses the current knowledge about microbe-microbe interactions between strains of Bacillus and Pseudomonas and discusses how we can attempt to generalize the interaction on a taxonomic and molecular level.

Prenylated notoamide-type alkaloids isolated from the fungus Aspergillus sclerotiorum and their inhibition of NLRP3 inflammasome activation and antibacterial activities

Notoamides are a family of prenylated indole alkaloids with unusual ring systems and possessing a range of significant pharmaceutical activities. Based on LC-MS/MS and genome orientations, ten undescribed notoamide-type alkaloids namely sclerotiamides I-R were isolated from a marine gorgonian-derived fungus Aspergillus sclerotiorum LZDX-33-4. Their structures were determined by extensive spectroscopic data, in association with ECD data and single-crystal X-ray diffraction for configurational assignments. Bioassays resulted in sclerotiamide J along with five analogs possessing inhibitory effects against LDH and IL-1β expression in BV-2 cells. Further investigation revealed that sclerotiamide J significantly inhibited NLRP3 inflammasome activation and blocked NLRP3 inflammasome-induced pyroptosis via amelioration of mitochondria damage. In addition, sclerotiamide L exhibited potent inhibition against pathogenic Staphylococcus aureus ATCC 29213 with MIC value of 4.0 μM and the growth of MRSA T144 and Enterococcus faecalis ATCC 29212. This study extends the chemical diversity of notoamide-type alkaloids, and provides potential anti-inflammasome and antibacterial lead compounds for further structure optimization.

Genome mining reveals polysaccharide-degrading potential and new antimicrobial gene clusters of novel intestinal bacterium Paenibacillus jilinensis sp. nov

Background

Drug-resistant bacteria have posed a great threat to animal breeding and human health. It is obviously urgent to develop new antibiotics that can effectively combat drug-resistant bacteria. The commensal flora inhabited in the intestines become potential candidates owing to the production of a wide range of antimicrobial substances. In addition, host genomes do not encode most of the enzymes needed to degrade dietary structural polysaccharides. The decomposition of these polysaccharides mainly depends on gut commensal-derived CAZymes.

Results

We report a novel species isolated from the chicken intestine, designated as Paenibacillus jilinensis sp. nov. and with YPG26^T (= CCTCC M2020899^T) as the type strain. The complete genome of P. jilinensis YPG26^T is made up of a single circular chromosome measuring 3.97 Mb in length and containing 49.34% (mol%) G + C. It carries 33 rRNA genes, 89 tRNA genes, and 3871 protein-coding genes, among which abundant carbohydrate-degrading enzymes (CAZymes) are encoded. Moreover, this strain has the capability to antagonize multiple pathogens in vitro. We identified putative 6 BGCs encoding bacteriocin, NRPs, PKs, terpenes, and protcusin by genome mining. In addition, antibiotic susceptibility testing showed sensitivity to all antibiotics tested.

Conclusions

This study highlights the varieties of CAZymes genes and BGCs in the genome of Paenibacillus jilinensis. These findings confirm the beneficial function of the gut microbiota and also provide a promising candidate for the development of new carbohydrate degrading enzymes and antibacterial agents.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08623-4.

Plant Health Status Affects the Functional Diversity of the Rhizosphere Microbiome Associated With Solanum lycopersicum

The microorganisms inhabiting soil perform unique functions in the growth and development of plants. However, little is known about how plant health status affects their potential functions. We examined the functional diversity of the microbiome inhabiting the rhizosphere of powdery mildew diseased and healthy tomato plants alongside the bulk soils in South Africa's Northwest Province employing a shotgun metagenomics approach. We envisaged that the functional categories would be abundant in the healthy rhizosphere (HR) of the tomato plant. We collected soil from the rhizosphere of healthy, powdery mildew diseased tomato plants (DR), and bulk soil (BR). After that, their DNA was extracted. The extracted DNA was subjected to shotgun metagenomic sequencing. Our result using the SEED subsystem revealed that a total of fifteen (15) functional categories dominated the healthy rhizosphere, seven (7) functional categories dominated the diseased rhizosphere. At the same time, six (6) functions dominated the bulk soil. Alpha (α) diversity assessment did not reveal a significant difference (p > 0.05) in all the soil samples, but a considerable difference was observed for beta (β) diversity (P = 0.01). The functional categories obtained in this research were highly abundant in HR. Therefore, this study shows that the functions groups of the rhizosphere microbiomes were more abundant in HR samples as compared to others. The high prevalence of functions groups associated with rhizobiomes in the tomato rhizosphere indicates the need for more research to establish the functional genes associated with these rhizosphere microbiomes.

Genomic insights on fighting bacterial wilt by a novel Bacillus amyloliquefaciens strain Cas02

Bacterial wilt, caused by the Ralstonia solanacearum, can infect several economically important crops. However, the management strategies available to control this disease are limited. Plant growth-promoting rhizobacteria (PGPR) have been considered promising biocontrol agents. In this study, Bacillus amyloliquefaciens strain Cas02 was isolated from the rhizosphere soil of healthy tobacco plants and evaluated for its effect on plant growth promotion and bacterial wilt suppression. Strain Cas02 exhibited several growth-promoting-related features including siderophore production, cellulase activity, protease activity, ammonia production and catalase activity. Moreover, strain Cas02 showed a significant inhibitory growth effect on R. solanacearum, and its active substances were separated and identified to be macrolactin A and macrolactin W by HPLC-DAD-ESI-MS/MS. Both greenhouse and field experiments demonstrated a good performance of Cas02 in plant growth promotion and bacterial wilt suppression. To explore the underlying genetic mechanisms, complete genome sequencing was performed and the gene clusters responsible for antibacterial metabolites expression were identified. Overall, these findings suggest that the strain Cas02 could be a potential biocontrol agent in bacterial wilt management and a source of antimicrobial compounds for further exploitation.

Biocontrol properties from phyllospheric bacteria isolated from Solanum lycopersicum and Lactuca sativa and genome mining of antimicrobial gene clusters

BACKGROUND

Biocontrol agents are sustainable eco-friendly alternatives for chemical pesticides that cause adverse effects in the environment and toxicity in animals including humans. An improved understanding of the phyllosphere microbiology is of vital importance for biocontrol development. Most studies have been directed towards beneficial plant-microbe interactions and ignore the pathogens that might affect humans when consuming vegetables. In this study we extended this perspective and investigated potential biocontrol strains isolated from tomato and lettuce phyllosphere that can promote plant growth and potentially antagonize human pathogens as well as plant pathogens. Subsequently, we mined into their genomes for discovery of antimicrobial biosynthetic gene clusters (BGCs), that will be further characterized.

RESULTS

The antimicrobial activity of 69 newly isolated strains from a healthy tomato and lettuce phyllosphere against several plant and human pathogens was screened. Three strains with the highest antimicrobial activity were selected and characterized (Bacillus subtilis STRP31, Bacillus velezensis SPL51, and Paenibacillus sp. PL91). All three strains showed a plant growth promotion effect on tomato and lettuce. In addition, genome mining of the selected isolates showed the presence of a large variety of biosynthetic gene clusters. A total of 35 BGCs were identified, of which several are already known, but also some putative novel ones were identified. Further analysis revealed that among the novel BGCs, one previously unidentified NRPS and two bacteriocins are encoded, the gene clusters of which were analyzed in more depth.

CONCLUSIONS

Three recently isolated strains of the Bacillus genus were identified that have high antagonistic activity against lettuce and tomato plant pathogens. Known and unknown antimicrobial BGCs were identified in these antagonistic bacterial isolates, indicating their potential to be used as biocontrol agents. Our study serves as a strong incentive for subsequent purification and characterization of novel antimicrobial compounds that are important for biocontrol.

Exploring the roles of microbes in facilitating plant adaptation to climate change

Plants benefit from their close association with soil microbes which assist in their response to abiotic and biotic stressors. Yet much of what we know about plant stress responses is based on studies where the microbial partners were uncontrolled and unknown. Under climate change, the soil microbial community will also be sensitive to and respond to abiotic and biotic stressors. Thus, facilitating plant adaptation to climate change will require a systems-based approach that accounts for the multi-dimensional nature of plant-microbe-environment interactions. In this perspective, we highlight some of the key factors influencing plant-microbe interactions under stress as well as new tools to facilitate the controlled study of their molecular complexity, such as fabricated ecosystems and synthetic communities. When paired with genomic and biochemical methods, these tools provide researchers with more precision, reproducibility, and manipulability for exploring plant-microbe-environment interactions under a changing climate.

Exploring the Nature of the Antimicrobial Metabolites Produced by Paenibacillus ehimensis Soil Isolate MZ921932 Using a Metagenomic Nanopore Sequencing Coupled with LC-Mass Analysis

The continuous emergence of multidrug-resistant (MDR) pathogens poses a global threat to public health. Accordingly, global efforts are continuously conducted to find new approaches to infection control by rapidly discovering antibiotics, particularly those that retain activities against MDR pathogens. In this study, metagenomic nanopore sequence analysis coupled with spectroscopic methods has been conducted for rapid exploring of the various active metabolites produced by Paenibacillus ehimensis soil isolate. Preliminary soil screening resulted in selection of a Gram-positive isolate identified via 16S ribosomal RNA gene sequencing as Paenibacillus ehimensis MZ921932. The isolate showed a broad range of activity against MDR Gram-positive, Gram-negative, and Candida spp. A metagenomics sequence analysis of the soil sample harboring Paenibacillus ehimensis isolate MZ921932 (NCBI GenBank accession PRJNA785410) revealed the presence of conserved biosynthetic gene clusters of petrobactin, tridecaptin, locillomycin (β-lactone), polymyxin, and macrobrevin (polyketides). The liquid chromatography/mass (LC/MS) analysis of the Paenibacillus ehimensis metabolites confirmed the presence of petrobactin, locillomycin, and macrobrevin. In conclusion, Paenibacillus ehimensis isolate MZ921932 is a promising rich source for broad spectrum antimicrobial metabolites. The metagenomic nanopore sequence analysis was a rapid, easy, and efficient method for the preliminary detection of the nature of the expected active metabolites. LC/MS spectral analysis was employed for further confirmation of the nature of the respective active metabolites.

Screening and Biocontrol Potential of Rhizobacteria Native to Gangetic Plains and Hilly Regions to Induce Systemic Resistance and Promote Plant Growth in Chilli against Bacterial Wilt Disease

Plant growth-promoting rhizobacteria (PGPR) is a microbial population found in the rhizosphere of plants that can stimulate plant development and restrict the growth of plant diseases directly or indirectly. In this study, 90 rhizospheric soil samples from five agro climatic zones of chilli (Capsicum annuum L.) were collected and rhizobacteria were isolated, screened and characterized at morphological, biochemical and molecular levels. In total, 38% of rhizobacteria exhibited the antagonistic capacity to suppress Ralstonia solanacearum growth and showed PGPR activities such as indole acetic acid production by 67.64% from total screened rhizobacteria isolates, phosphorus solubilization by 79.41%, ammonia by 67.75%, HCN by 58.82% and siderophore by 55.88%. We performed a principal component analysis depicting correlation and significance among plant growth-promoting activities, growth parameters of chilli and rhizobacterial strains. Plant inoculation studies indicated a significant increase in growth parameters and PDS1 strain showed maximum 71.11% biocontrol efficiency against wilt disease. The best five rhizobacterial isolates demonstrating both plant growth-promotion traits and biocontrol potential were characterized and identified as PDS1—Pseudomonas fluorescens (MN368159), BDS1—Bacillus subtilis (MN395039), UK4—Bacillus cereus (MT491099), UK2—Bacillus amyloliquefaciens (MT491100) and KA9—Bacillus subtilis (MT491101). These rhizobacteria have the potential natural elicitors to be used as biopesticides and biofertilizers to improve crop health while warding off soil-borne pathogens. The chilli cv. Pusa Jwala treated with Bacillus subtilis KA9 and Pseudomonas fluorescens PDS1 showed enhancement in the defensive enzymes PO, PPO, SOD and PAL activities in chilli leaf and root tissues, which collectively contributed to induced resistance in chilli plants against Ralstonia solanacearum. The induction of these defense enzymes was found higher in leave tissues (PO—4.87-fold, PP0—9.30-fold, SOD—9.49-fold and PAL—1.04-fold, respectively) in comparison to roots tissue at 48 h after pathogen inoculation. The findings support the view that plant growth-promoting rhizobacteria boost defense-related enzymes and limit pathogen growth in chilli plants, respectively, hence managing the chilli bacterial wilt.

Biocontrol Ability and Mechanism of a Broad-Spectrum Antifungal Strain Bacillus safensis sp. QN1NO-4 Against Strawberry Anthracnose Caused by Colletotrichum fragariae

Strawberry is a very popular fruit with a special taste, color, and nutritional value. Anthracnose caused by Colletotrichum fragariae severely limits fruit shelf life during post-harvest storage. Use of traditional chemical fungicides leads to serious environment pollution and threatens food safety. Biocontrol is considered as a promising strategy to manage the post-harvest fruit diseases. Here, strain QN1NO-4 isolated from noni (Morinda citrifolia L.) fruit exhibited a high antifungal activity against C. fragariae. Based on its physicochemical profiles and phylogenetic tree of the 16S rRNA sequence, strain QN1NO-4 belonged to the genus Bacillus. The average nucleotide identity (ANI) calculated by comparing two standard strain genomes was below 95-96%, suggesting that the strain might be a novel species of the genus Bacillus and named as Bacillus safensis sp. QN1NO-4. Its extract effectively reduced the incidence of strawberry anthracnose of harvested fruit. Fruit weight and TSS contents were also maintained significantly. The antifungal mechanism assays indicated that the extract of the test antagonist inhibited mycelial growth and spore germination of C. fragariae in vitro. Cells of strain QN1NO-4 demonstrated the cytoplasmic heterogeneity, disappeared organelles, and ruptured ultrastructure. Notably, the strain extract also had a broad-spectrum antifungal activity. Compared with the whole genome of strain QN1NO-4, several functional gene clusters involved in the biosynthesis of active secondary metabolites were observed. Fifteen compounds were identified by gas chromatography-mass spectrometry (GC-MS). Hence, the fruit endophyte B. safensis sp. QN1NO-4 is a potential bio-agent identified for the management of post-harvest disease of strawberry fruit.

Bacillus cabrialesii BH5 Protects Tomato Plants Against Botrytis cinerea by Production of Specific Antifungal Compounds

The gray mold caused by the phytopathogen Botrytis cinerea presents a threat to global food security. For the biological regulation of several plant diseases, Bacillus species have been extensively studied. In this work, we explore the ability of a bacterial strain, Bacillus cabrialesii BH5, that was isolated from tomato rhizosphere soil, to control the fungal pathogen B. cinerea. Strain B. cabrialesii BH5 showed a strong antifungal activity against B. cinerea. A compound was isolated and identified as a cyclic lipopeptide of the fengycin family by high-performance liquid chromatography and tandem mass spectrometry (ESI-MS/MS) that we named fengycin H. The fengycin H-treated hyphae of B. cinerea displayed stronger red fluorescence than the control, which is clearly indicating that fengycin H triggered the hyphal cell membrane defects. Moreover, root inoculation of tomato seedlings with BH5 effectively promoted the growth of tomato plants. Transcription analysis revealed that both BH5 and fengycin H stimulate induced systemic resistance of tomato plants via the jasmonic acid signaling pathway and provide a strong biocontrol effect in vivo. Therefore, the strain BH5 and fengycin H are very promising candidates for biological control of B. cinerea and the associated gray mold.

Identification, Isolation, and Characterization of Medipeptins, Antimicrobial Peptides From Pseudomonas mediterranea EDOX

The plant microbiome is a vastly underutilized resource for identifying new genes and bioactive compounds. Here, we used Pseudomonas sp. EDOX, isolated from the leaf endosphere of a tomato plant grown on a small farm in the Netherlands. To get more insight into its biosynthetic potential, the genome of Pseudomonas sp. EDOX was sequenced and subjected to bioinformatic analyses. The genome sequencing analysis identified strain EDOX as a member of the Pseudomonas mediterranea. In silico analysis for secondary metabolites identified a total of five non-ribosomally synthesized peptides synthetase (NRPS) gene clusters, related to the biosynthesis of syringomycin, syringopeptin, anikasin, crochelin A, and fragin. Subsequently, we purified and characterized several cyclic lipopeptides (CLPs) produced by NRPS, including some of the already known ones, which have biological activity against several plant and human pathogens. Most notably, mass spectrometric analysis led to the discovery of two yet unknown CLPs, designated medipeptins, consisting of a 22 amino acid peptide moiety with varying degrees of activity against Gram-positive and Gram-negative pathogens. Furthermore, we investigated the mode of action of medipeptin A. The results show that medipeptin A acts as a bactericidal antibiotic against Gram-positive pathogens, but as a bacteriostatic antibiotic against Gram-negative pathogens. Medipeptin A exerts its potent antimicrobial activity against Gram-positive bacteria via binding to both lipoteichoic acid (LTA) and lipid II as well as by forming pores in membranes. Collectively, our study provides important insights into the biosynthesis and mode of action of these novel medipeptins from P. mediterranea EDOX.