Linking Comparative Genomics of Nine Potato-Associated Pseudomonas Isolates With Their Differing Biocontrol Potential Against Late Blight

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.

Biological hydrogen cyanide emission globally impacts the physiology of both HCN-emitting and HCN-perceiving Pseudomonas

IMPORTANCE

Bacteria communicate by exchanging chemical signals, some of which are volatile and can remotely reach other organisms. HCN was one of the first volatiles discovered to severely impact exposed organisms by inhibiting their respiration. Using HCN-deficient mutants in two Pseudomonas strains, we demonstrate that HCN's impact goes beyond the sole inhibition of respiration and affects both emitting and receiving bacteria in a global way, modulating their motility, biofilm formation, and production of antimicrobial compounds. Our data suggest that bacteria could use HCN not only to control their own cellular functions, but also to remotely influence the behavior of other bacteria sharing the same environment. Since HCN emission occurs in both clinically and environmentally relevant Pseudomonas, these findings are important to better understand or even modulate the expression of bacterial traits involved in both virulence of opportunistic pathogens and in biocontrol efficacy of plant-beneficial strains.

Detection of Known and Novel Small Proteins in Pseudomonas stutzeri Using a Combination of Bottom-Up and Digest-Free Proteomics and Proteogenomics

Small proteins of around 50 aa in length have been largely overlooked in genetic and biochemical assays due to the inherent challenges with detecting and characterizing them. Recent discoveries of their critical roles in many biological processes have led to an increased recognition of the importance of small proteins for basic research and as potential new drug targets. One example is CcoM, a 36 aa subunit of the cbb3-type oxidase that plays an essential role in adaptation to oxygen-limited conditions in Pseudomonas stutzeri (P. stutzeri), a model for the clinically relevant, opportunistic pathogen Pseudomonas aeruginosa. However, as no comprehensive data were available in P. stutzeri, we devised an integrated, generic approach to study small proteins more systematically. Using the first complete genome as basis, we conducted bottom-up proteomics analyses and established a digest-free, direct-sequencing proteomics approach to study cells grown under aerobic and oxygen-limiting conditions. Finally, we also applied a proteogenomics pipeline to identify missed protein-coding genes. Overall, we identified 2921 known and 29 novel proteins, many of which were differentially regulated. Among 176 small proteins 16 were novel. Direct sequencing, featuring a specialized precursor acquisition scheme, exhibited advantages in the detection of small proteins with higher (up to 100%) sequence coverage and more spectral counts, including sequences with high proline content. Three novel small proteins, uniquely identified by direct sequencing and not conserved beyond P. stutzeri, were predicted to form an operon with a conserved protein and may represent de novo genes. These data demonstrate the power of this combined approach to study small proteins in P. stutzeri and show its potential for other prokaryotes.

A Novel Robust Screening Assay Identifies Pseudomonas Strains as Reliable Antagonists of the Root-Knot Nematode Meloidogyne incognita

Forty-four bacterial strains isolated from greenhouse soil and beetroots were tested for their antagonistic activity against the plant-parasitic root-knot nematode (RKN) Meloidogyne incognita, which causes significant yield losses in a number of important crops worldwide. Through a novel combination of in vitro and on planta screening assays, Pseudomonas spp. 105 and 108 were identified as the most promising bacterial isolates. Both strains were evaluated for their potential to control different RKN population densities and as root protectants against nematode infestation. Regardless of the application method, both strains significantly reduced root galling caused by M. incognita. These two strains were subjected to whole genome sequencing and de novo genome assembly as a basis for phylogenetic and future functional characterization. Phylogenetic analysis revealed that both Pseudomonas strains cluster within the Pseudomonas fluorescens clade among previously characterized RKN antagonists and Pseudomonas-based biocontrol agents of plant diseases.

Identification and characterization of siderophilic biocontrol strain SL-44 combined with whole genome

Using rhizobacteria as biological fertilizer is gradually expanding in agriculture as excellent substitutes for chemical fertilizers. Bacillus subtilis SL-44 is a plant growth-promoting rhizobacteria screened from the severely salinized cotton rhizosphere soil in Xinjiang. Study showed that indole-3-acetic acid, organic acid production, nitrogen fixation, and other beneficial secondary metabolite secretion can be synthesized by stain SL-44. At the same time, fencyclin, lipopeptide, chitinase, and other antifungal substances were also detected from the secretion of Bacillus subtilis SL-44, which can effectively control plant diseases. Siderophore separated from SL-44 was verified by HPLC, and results showed it was likely bacillibactin. This study also verified that SL-44 has high antifungal activity against Rhizoctonia solani through in vitro antifungal experiments. The B. subtilis SL-44 whole genome was sequenced and annotated to further explore the biotechnological potential of SL-44. And a large number of genes involved in the synthesis of anti-oxidative stress, antibiotic, and toxins were found. Genome-wide analysis provides clear evidence to support the great potential of B. subtilis SL-44 strain to produce multiple bioantagonistic natural products and growth-promoting metabolites, which may facilitate further research into effective therapies for harmful diseases.

Biological Control of Oomycete Soilborne Diseases Caused by Phytophthora capsici, Phytophthora infestans, and Phytophthora nicotianae in Solanaceous Crops

Oomycete pathogens that belong to the genus Phytophthora cause devastating diseases in solanaceous crops such as pepper, potato, and tobacco, resulting in crop production losses worldwide. Although the application of fungicides efficiently controls these diseases, it has been shown to trigger negative side effects such as environmental pollution, phytotoxicity, and fungicide resistance in plant pathogens. Therefore, biological control of Phytophthora-induced diseases was proposed as an environmentally sound alternative to conventional chemical control. In this review, progress on biological control of the soilborne oomycete plant pathogens, Phytophthora capsici, Phytophthora infestans, and Phytophthora nicotianae, infecting pepper, potato, and tobacco is described. Bacterial (e.g., Acinetobacter, Bacillus, Chryseobacterium, Paenibacillus, Pseudomonas, and Streptomyces) and fungal (e.g., Trichoderma and arbuscular mycorrhizal fungi) agents, and yeasts (e.g., Aureobasidium, Curvibasidium, and Metschnikowia) have been reported as successful biocontrol agents of Phytophthora pathogens. These microorganisms antagonize Phytophthora spp. via antimicrobial compounds with inhibitory activities against mycelial growth, sporulation, and zoospore germination. They also trigger plant immunity-inducing systemic resistance via several pathways, resulting in enhanced defense responses in their hosts. Along with plant protection, some of the microorganisms promote plant growth, thereby enhancing their beneficial relations with host plants. Although the beneficial effects of the biocontrol microorganisms are acceptable, single applications of antagonistic microorganisms tend to lack consistent efficacy compared with chemical analogues. Therefore, strategies to improve the biocontrol performance of these prominent antagonists are also discussed in this review.

Disease Inhibiting Effect of Strain Bacillus subtilis EG21 and Its Metabolites Against Potato Pathogens Phytophthora infestans and Rhizoctonia solani

Potato production worldwide is plagued by several disease-causing pathogens that result in crop and economic losses estimated to billions of dollars each year. To this day, synthetic chemical applications remain the most widespread control strategy despite their negative effects on human and environmental health. Therefore, obtainment of superior biocontrol agents or their naturally produced metabolites to replace fungicides or to be integrated into practical pest management strategies has become one of the main targets in modern agriculture. Our main focus in the present study was to elucidate the antagonistic potential of a new strain identified as Bacillus subtilis EG21 against potato pathogens Phytophthora infestans and Rhizoctonia solani using several in vitro screening assays. Microscopic examination of the interaction between EG21 and R. solani showed extended damage in fungal mycelium, while EG21 metabolites displayed strong anti-oomycete and zoosporecidal effect on P. infestans. Mass spectrometry (MS) analysis revealed that EG21 produced antifungal and anti-oomycete cyclic lipopeptides surfactins (C₁₂ to C₁₉). Further characterization of EG21 confirmed its ability to produce siderophores and the extracellular lytic enzymes cellulase, pectinase and chitinase. The antifungal activity of EG21 cell-free culture filtrate (CF) was found to be stable at high-temperature/pressure treatment and extreme pH values and was not affected by proteinase K treatment. Disease-inhibiting effect of EG21 CF against P. infestans and R. solani infection was confirmed using potato leaves and tubers, respectively. Biotechnological applications of using microbial agents and their bioproducts for crop protection hold great promise to develop into effective, environment-friendly and sustainable biocontrol strategies. [Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Bacteria as Biological Control Agents of Plant Diseases

Biological control is an effective and sustainable alternative or complement to conventional pesticides for fungal and bacterial plant disease management. Some of the most intensively studied biological control agents are bacteria that can use multiple mechanisms implicated in the limitation of plant disease development, and several bacterial-based products have been already registered and marketed as biopesticides. However, efforts are still required to increase the commercially available microbial biopesticides. The inconsistency in the performance of bacterial biocontrol agents in the biological control has limited their extensive use in commercial agriculture. Pathosystem factors and environmental conditions have been shown to be key factors involved in the final levels of disease control achieved by bacteria. Several biotic and abiotic factors can influence the performance of the biocontrol agents, affecting their mechanisms of action or the multitrophic interaction between the plant, the pathogen, and the bacteria. This review shows some relevant examples of known bacterial biocontrol agents, with especial emphasis on research carried out by Spanish groups. In addition, the importance of the screening process and of the key steps in the development of bacterial biocontrol agents is highlighted. Besides, some improvement approaches and future trends are considered.

Combating biotic stresses in plants by synthetic microbial communities: Principles, applications, and challenges

Presently, agriculture worldwide is facing the major challenge of feeding the increasing population sustainably. The conventional practices have not only failed to meet the projected needs, but also led to tremendous environmental consequences. Hence, to ensure a food-secure and environmentally sound future, the major thrust is on sustainable alternatives. Due to challenges associated with conventional means of application of biocontrol agents in the management of biotic stresses in agro-ecosystems, significant transformations in this context is needed. The crucial role played by soil microbiomes in efficiently and sustainably managing the agricultural production has unfolded a newer approach of rhizospheric engineering that shows immense promise in mitigating biotic stresses in an eco-friendly manner. The strategy of generating synthetic microbial communities (SynCom), by integrating omics approaches with traditional techniques of enumeration and in-depth analysis of plant-microbe interactions, is encouraging. The review discusses the significance of the rhizospheric microbiome in plant's fitness, and its manipulation for enhancing plant attributes. The focus of the review is to critically analyze the potential tools for the design and utilization of SynCom as a sustainable approach for rhizospheric engineering to ameliorate biotic stresses in plants. Further, based on the synthesis of reports in the area, we have put forth possible solutions to some of the critical issues that impair the large-scale application of SynComs in agriculture.

Agronomic efficiency and genome mining analysis of the wheat-biostimulant rhizospheric bacterium Pseudomonas pergaminensis sp. nov. strain 1008T

Pseudomonas sp. strain 1008 was isolated from the rhizosphere of field grown wheat plants at the tillering stage in an agricultural plot near Pergamino city, Argentina. Based on its in vitro phosphate solubilizing capacity and the production of IAA, strain 1008 was formulated as an inoculant for bacterization of wheat seeds and subjected to multiple field assays within the period 2010-2017. Pseudomonas sp. strain 1008 showed a robust positive impact on the grain yield (+8% on average) across a number of campaigns, soil properties, seed genotypes, and with no significant influence of the simultaneous seed treatment with a fungicide, strongly supporting the use of this biostimulant bacterium as an agricultural input for promoting the yield of wheat. Full genome sequencing revealed that strain 1008 has the capacity to access a number of sources of inorganic and organic phosphorus, to compete for iron scavenging, to produce auxin, 2,3-butanediol and acetoin, and to metabolize GABA. Additionally, the genome of strain 1008 harbors several loci related to rhizosphere competitiveness, but it is devoid of biosynthetic gene clusters for production of typical secondary metabolites of biocontrol representatives of the Pseudomonas genus. Finally, the phylogenomic, phenotypic, and chemotaxonomic comparative analysis of strain 1008 with related taxa strongly suggests that this wheat rhizospheric biostimulant isolate is a representative of a novel species within the genus Pseudomonas, for which the name Pseudomonas pergaminensis sp. nov. (type strain 1008T = DSM 113453T = ATCC TSD-287T) is proposed.

Bacterial Volatiles Known to Inhibit Phytophthora infestans Are Emitted on Potato Leaves by Pseudomonas Strains

Bacterial volatiles play important roles in mediating beneficial interactions between plants and their associated microbiota. Despite their relevance, bacterial volatiles are mostly studied under laboratory conditions, although these strongly differ from the natural environment bacteria encounter when colonizing plant roots or shoots. In this work, we ask the question whether plant-associated bacteria also emit bioactive volatiles when growing on plant leaves rather than on artificial media. Using four potato-associated Pseudomonas, we demonstrate that potato leaves offer sufficient nutrients for the four strains to grow and emit volatiles, among which 1-undecene and Sulfur compounds have previously demonstrated the ability to inhibit the development of the oomycete Phytophthora infestans, the causative agent of potato late blight. Our results bring the proof of concept that bacterial volatiles with known plant health-promoting properties can be emitted on the surface of leaves and warrant further studies to test the bacterial emission of bioactive volatiles in greenhouse and field-grown plants.

Evaluating the Antagonistic Potential of Actinomycete Strains Isolated From Sudan’s Soils Against Phytophthora infestans

Soil microorganisms play crucial roles in soil fertility, e.g., through decomposing organic matter, cycling nutrients or through beneficial interactions with plants. Actinomycetes are a major component of soil inhabitants; they are prolific producers of specialized metabolites, among which many antibiotics. Here we report the isolation and characterization of 175 Actinomycetes from rhizosphere and bulk soil samples collected in 18 locations in Sudan. We evaluated the strains’ metabolic potential for plant protection by testing their ability to inhibit the mycelial growth of the oomycete Phytophthora infestans, which is one of the most devastating plant pathogens worldwide. Most strains significantly reduced the oomycete’s growth in direct confrontational in vitro assays. A significant proportion of the tested strains (15%) were able to inhibit P. infestans to more than 80%, 23% to 50%–80%, while the remaining 62% had inhibition percentages lesser than 50%. Different morphologies of P. infestans mycelial growth and sporangia formation were observed upon co-inoculation with some of the Actinomycetes isolates, such as the production of fewer, thinner hyphae without sporangia leading to a faint growth morphology, or on the contrary, of clusters of thick-walled hyphae leading to a bushy, or “frozen” morphology. These morphologies were caused by strains differing in activity levels but phylogenetically closely related with each other. To evaluate whether the isolated Actinomycetes could also inhibit the pathogen’s growth in planta, the most active strains were tested for their ability to restrict disease progress in leaf disc and full plant assays. Five of the active strains showed highly significant protection of potato leaves against the pathogen in leaf disc assays, as well as substantial reduction of disease progress in full plants assays. Using cell-free filtrates instead of the bacterial spores also led to full protection against disease on leaf discs, which highlights the strong crop protective potential of the secreted metabolites that could be applied as leaf spray. This study demonstrates the strong anti-oomycete activity of soil- and rhizosphere-borne Actinomycetes and highlights their significant potential for the development of sustainable solutions based on either cell suspensions or cell-free filtrates to safeguard potatoes from their most damaging pathogen.

In Tuber Biocontrol of Potato Late Blight by a Collection of Phenazine-1-Carboxylic Acid-Producing Pseudomonas spp

Phenazine-1-carboxylic acid (PCA) produced by plant-beneficial Pseudomonas spp. is an antibiotic with antagonistic activities against Phytophthora infestans, the causal agent of potato late blight. In this study, a collection of 23 different PCA-producing Pseudomonas spp. was confronted with P. infestans in potato tuber bioassays to further understand the interaction existing between biocontrol activity and PCA production. Overall, the 23 strains exhibited different levels of biocontrol activity. In general, P. orientalis and P. yamanorum strains showed strong disease reduction, while P. synxantha strains could not effectively inhibit the pathogen’s growth. No correlation was found between the quantities of PCA produced and biocontrol activity, suggesting that PCA cannot alone explain P. infestans’ growth inhibition by phenazine-producing pseudomonads. Other genetic determinants potentially involved in the biocontrol of P. infestans were identified through genome mining in strains displaying strong biocontrol activity, including siderophores, cyclic lipopeptides and non-ribosomal peptide synthase and polyketide synthase hybrid clusters. This study represents a step forward towards better understanding the biocontrol mechanisms of phenazine-producing Pseudomonas spp. against potato late blight.

Mitigation of Pseudomonas syringae virulence by signal inactivation

Pseudomonas syringae is an important plant pathogen of many valuable crops worldwide, with more than 60 identified pathovars. The phytotoxins produced by these organisms were related to the severity of the damage caused to the plant. An emerging strategy to treat bacterial infections relies on interference with their signaling systems. In this study, we investigated P. syringae pv. syringae, which produces the virulence factor mangotoxin that causes bacterial apical necrosis on mango leaves. A previously unknown signaling molecule named leudiazen was identified, determined to be unstable and volatile, and responsible for mangotoxin production. A strategy using potassium permanganate, compatible with organic farming, was developed to degrade leudiazen and thus to attenuate the pathogenicity of P. syringae pv. syringae.

A biofoundry workflow for the identification of genetic determinants of microbial growth inhibition

Biofoundries integrate high-throughput software and hardware platforms with synthetic biology approaches to enable the design, execution and analyses of large-scale experiments. The unique and powerful combination of laboratory infrastructure and expertise in molecular biology and automation programming, provide flexible resources for a wide range of workflows and research areas. Here, we demonstrate the applicability of biofoundries to molecular microbiology, describing the development and application of automated workflows to identify the genetic basis of growth inhibition of the plant pathogen Streptomyces scabies by a Pseudomonas strain isolated from a potato field. Combining transposon mutagenesis with automated high-throughput antagonistic assays, the workflow accelerated the screening of 2880 mutants to correlate growth inhibition with a biosynthetic gene cluster within 2 weeks.

An integrated model system to gain mechanistic insights into biofilm-associated antimicrobial resistance in Pseudomonas aeruginosa MPAO1

Pseudomonas aeruginosa MPAO1 is the parental strain of the widely utilized transposon mutant collection for this important clinical pathogen. Here, we validate a model system to identify genes involved in biofilm growth and biofilm-associated antibiotic resistance. Our model employs a genomics-driven workflow to assemble the complete MPAO1 genome, identify unique and conserved genes by comparative genomics with the PAO1 reference strain and genes missed within existing assemblies by proteogenomics. Among over 200 unique MPAO1 genes, we identified six general essential genes that were overlooked when mapping public Tn-seq data sets against PAO1, including an antitoxin. Genomic data were integrated with phenotypic data from an experimental workflow using a user-friendly, soft lithography-based microfluidic flow chamber for biofilm growth and a screen with the Tn-mutant library in microtiter plates. The screen identified hitherto unknown genes involved in biofilm growth and antibiotic resistance. Experiments conducted with the flow chamber across three laboratories delivered reproducible data on P. aeruginosa biofilms and validated the function of both known genes and genes identified in the Tn-mutant screens. Differential protein abundance data from planktonic cells versus biofilm confirmed the upregulation of candidates known to affect biofilm formation, of structural and secreted proteins of type VI secretion systems, and provided proteogenomic evidence for some missed MPAO1 genes. This integrated, broadly applicable model promises to improve the mechanistic understanding of biofilm formation, antimicrobial tolerance, and resistance evolution in biofilms.

Harnessing the Microbiomes of Suppressive Composts for Plant Protection: From Metagenomes to Beneficial Microorganisms and Reliable Diagnostics

Soil-borne diseases cause significant yield losses worldwide, are difficult to treat and often only limited options for disease management are available. It has long been known that compost amendments, which are routinely applied in organic and integrated farming as a part of good agricultural practice to close nutrient cycles, can convey a protective effect. Yet, the targeted use of composts against soil-borne diseases is hampered by the unpredictability of the efficacy. Several studies have identified and/or isolated beneficial microorganisms (i.e., bacteria, oomycetes, and fungi) from disease suppressive composts capable of suppressing pathogens (e.g., Pythium and Fusarium) in various crops (e.g., tomato, lettuce, and cucumber), and some of them have been developed into commercial products. Yet, there is growing evidence that synthetic or complex microbial consortia can be more effective in controlling diseases than single strains, but the underlying molecular mechanisms are poorly understood. Currently, a major bottleneck concerns the lack of functional assays to identify the most potent beneficial microorganisms and/or key microbial consortia from complex soil and compost microbiomes, which can harbor tens of thousands of species. This focused review describes microorganisms, which have been isolated from, amended to or found to be abundant in disease-suppressive composts and for which a beneficial effect has been documented. We point out opportunities to increasingly harness compost microbiomes for plant protection through an integrated systems approach that combines the power of functional assays to isolate biocontrol and plant growth promoting strains and further prioritize them, with functional genomics approaches that have been successfully applied in other fields of microbiome research. These include detailed metagenomics studies (i.e., amplicon and shotgun sequencing) to achieve a better understanding of the complex system compost and to identify members of taxa enriched in suppressive composts. Whole-genome sequencing and complete assembly of key isolates and their subsequent functional profiling can elucidate the mechanisms of action of biocontrol strains. Integrating the benefits of these approaches will bring the long-term goals of employing microorganisms for a sustainable control of plant pathogens and developing reliable diagnostic assays to assess the suppressiveness of composts within reach.

Contribution of Hydrogen Cyanide to the Antagonistic Activity of Pseudomonas Strains Against Phytophthora infestans

Plants face many biotic and abiotic challenges in nature; one of them is attack by disease-causing microbes. Phytophthora infestans, the causal agent of late blight is one of the most prominent pathogens of the potato responsible for multi-billion-dollar losses every year. We have previously reported that potato-associated Pseudomonas strains inhibited P. infestans at various developmental stages. A comparative genomics approach identified several factors putatively involved in this anti-oomycete activity, among which was the production of hydrogen cyanide (HCN). Here, we report the relative contribution of HCN emission to the overall anti-Phytophthora activity of two cyanogenic Pseudomonas strains, P. putida R32 and P. chlororaphis R47. To quantify this contribution, we generated HCN-negative mutants (Δhcn) and compared their activities to those of their respective wild types in different experiments assessing P. infestans mycelial growth, zoospore germination, and infection of potato leaf disks. Using in vitro experiments allowing only volatile-mediated interactions, we observed that HCN accounted for most of the mycelial growth inhibition (57% in R47 and 80% in R32). However, when allowing both volatile and diffusible compound-mediated interactions, HCN only accounted for 1% (R47) and 18% (R32) of mycelial growth inhibition. Likewise, both mutants inhibited zoospore germination in a similar way as their respective wild types. More importantly, leaf disk experiments showed that both wild-type and Δhcn strains of R47 and R32 were able to limit P. infestans infection to a similar extent. Our results suggest that while HCN is a major contributor to the in vitro volatile-mediated restriction of P. infestans mycelial growth, it does not play a major role in the inhibition of other disease-related features such as zoospore germination or infection of plant tissues.

Complete genome sequence and epigenetic profile of Bacillus velezensis UCMB5140 used for plant and crop protection in comparison with other plant-associated Bacillus strains

The application of biocontrol biopesticides based on plant growth-promoting rhizobacteria (PGPR), particularly members of the genus Bacillus, is considered a promising perspective to make agricultural practices sustainable and ecologically safe. Recent advances in genome sequencing by third-generation sequencing technologies, e.g., Pacific Biosciences' Single Molecule Real-Time (PacBio SMRT) platform, have allowed researchers to gain deeper insights into the molecular and genetic mechanisms of PGPR activities, and to compare whole genome sequences and global patterns of epigenetic modifications. In the current work, this approach was used to sequence and compare four Bacillus strains that exhibited various PGPR activities including the strain UCMB5140, which is used in the commercial biopesticide Phytosubtil. Whole genome comparison and phylogenomic inference assigned the strain UCMB5140 to the species Bacillus velezensis. Strong biocontrol activities of this strain were confirmed in several bioassays. Several factors that affect the evolution of active PGPR B. velezensis strains were identified: (1) horizontal acquisition of novel non-ribosomal peptide synthetases (NRPS) and adhesion genes; (2) rearrangements of functional modules of NRPS genes leading to strain specific combinations of their encoded products; (3) gain and loss of methyltransferases that can cause global alterations in DNA methylation patterns, which eventually may affect gene expression and regulate transcription. Notably, we identified a horizontally transferred NRPS operon encoding an uncharacterized polypeptide antibiotic in B. velezensis UCMB5140. Other horizontally acquired genes comprised a possible adhesin and a methyltransferase, which may explain the strain-specific methylation pattern of the chromosomal DNA of UCMB5140. KEY POINTS: • Whole genome sequence of the active PGPR Bacillus velezensis UCMB5140. • Identification of genetic determinants responsible for PGPR activities. • Role of methyltransferases and epigenetic mechanisms in evolution of bacteria.