Biosynthesis, Chemical Structure, and Structure-Activity Relationship of Orfamide Lipopeptides Produced by Pseudomonas protegens and Related Species

Effect of Pseudomonas protegens EMM-1 Against Rhizopus oryzae in Interactions with Mexican Autochthonous Red Maize

In the present study, the strain Rhizopus oryzae EMM was isolated from germinated autochthonous red maize seeds, which were harvested in a region of San Diego-Buenavista, Papalotla, Tlaxcala, Mexico, where cobs with fungal infections have been observed. This fungal strain caused wilting in the maize seedlings. Pseudomonas protegens EMM-1 was tested for its ability to inhibit R. oryzae EMM, both in culture media and in association with maize plantlets. P. protegens EMM-1 inhibited the growth of R. oryzae EMM under all culture media conditions explored. The ability of P. protegens EMM-1 to inhibit the growth of R. oryzae EMM associated with plants was evaluated in both a hydroponic system and in vermiculite. In both systems, P. protegens EMM-1 strongly inhibited the growth of R. oryzae EMM. The dry weight of root plants infected with R. oryzae EMM and inoculated with P. protegens EMM-1 increased to 0.43 g, while that of plants infected only with R. oryzae EMM reached just 0.19 g under hydroponic conditions. However, no differences were observed under vermiculite conditions. The dry weight of the aerial region of plants infected with R. oryzae EMM and inoculated with P. protegens EMM-1 was greater than that of plants infected only with R. oryzae EMM, both under hydroponic and vermiculite conditions. These results indicate that P. protegens EMM-1 inhibits the infection caused by R. oryzae EMM, thereby improving plant growth. Moreover, the genome analysis of P. protegens EMM-1 revealed the presence of several genes that potentially encode for antimicrobial compounds, which could strengthen the potential use of P. protegens EMM-1 as a biocontrol agent in maize plants.

Natural Cyclic Peptides: Synthetic Strategies and Biomedical Applications

Natural cyclic peptides, a diverse class of bioactive compounds, have been isolated from various natural sources and are renowned for their extensive structural variability and broad spectrum of medicinal properties. Over 40 cyclic peptides or their derivatives are currently approved as medicines, underscoring their significant therapeutic potential. These compounds are employed in diverse roles, including antibiotics, antifungals, antiparasitics, immune modulators, and anti-inflammatory agents. Their unique ability to combine high specificity with desirable pharmacokinetic properties makes them valuable tools in addressing unmet medical needs, such as combating drug-resistant pathogens and targeting challenging biological pathways. Due to the typically low concentrations of cyclic peptides in nature, effective synthetic strategies are indispensable for their acquisition, characterization, and biological evaluation. Cyclization, a critical step in their synthesis, enhances metabolic stability, bioavailability, and receptor binding affinity. Advances in synthetic methodologies-such as solid-phase peptide synthesis (SPPS), chemoenzymatic approaches, and orthogonal protection strategies-have transformed cyclic peptide production, enabling greater structural complexity and precision. This review compiles recent progress in the total synthesis and biological evaluation of natural cyclic peptides from 2017 onward, categorized by cyclization strategies: head-to-tail; head-to-side-chain; tail-to-side-chain; and side-chain-to-side-chain strategies. Each account includes retrosynthetic analyses, synthetic advancements, and biological data to illustrate their therapeutic relevance and innovative methodologies. Looking ahead, the future of cyclic peptides in drug discovery is bright. Emerging trends, including integrating computational tools for rational design, novel cyclization techniques to improve pharmacokinetic profiles, and interdisciplinary collaboration among chemists, biologists, and computational scientists, promise to expand the scope of cyclic peptide-based therapeutics. These advancements can potentially address complex diseases and advance the broader field of biological drug development.

Pseudomonas fungipugnans sp. nov., a potently antifungal bacterium isolated from moss

A novel strain, 681, was isolated from a moss sample taken from the Chrutzelried woods in Canton Zürich, Switzerland. The strain showed potent activity against several fungi and oomycetes. It was affiliated to the Pseudomonas genus by 16S rRNA gene sequence phylogeny. Genome sequencing showed a G+C content of 59.9 mol%. The highest average nucleotide identity was 86.63%, and the highest digital DNA-DNA hybridization value was 32.2% (with Pseudomonas nunensis ln5), considerably below the thresholds for species delineation. Multi-locus phylogeny using 81 concatenated sequences indicated that the strain represented a new species within the Pseudomonas mandelii subgroup. This study details its characterization as a new species. The 681 genome was screened in silico using antiSMASH to reveal candidate secondary metabolite clusters for the strong antifungal activity exhibited by 681. Of the 15 clusters identified, we disrupted the seven best and tested for activity against Fusarium solani. The pyrrolnitrin, rhizoxin, novel PKS-NRPS and acaterin gene clusters contributed significantly to the observed antifungal activity. Phenotypic analyses found that strain 681 cells were aerobic, Gram-negative, motile rods (mean length 2.60 µm and mean width of 0.67 µm) with one to three polar flagella. Optimal growth was at 30 °C, but growth also occurred at 8 °C. The pH range was 6-7, with some growth at pH 8. Robust growth occurred at 0-3% (w/v) NaCl and weak growth at 4% (w/v) NaCl, with the optimum at 1% (w/v) NaCl. Strain 681 was oxidase positive, hydrolysed arginine under anaerobic conditions, showed intense fluorescence on King's medium B and produced a hypersensitive response in tobacco leaves. Following our investigations, we propose the designation Pseudomonas fungipugnans sp. nov. for this new species. The type strain, 681, is available from the DSMZ and LMG/BCCM culture collections under the designations DSM 115721 and LMG 33039, respectively.

Pyoluteorin-deficient Pseudomonas protegens improves cooperation with Bacillus velezensis, biofilm formation, co-colonizing, and reshapes rhizosphere microbiome

Plant-beneficial Pseudomonas and Bacillus have been extensively studied and applied in biocontrol of plant diseases. However, there is less known about their interaction within two-strain synthetic communities (SynCom). Our study revealed that Pseudomonas protegens Pf-5 inhibits the growth of several Bacillus species, including Bacillus velezensis. We established a two-strain combination of Pf-5 and DMW1 to elucidate the interaction. In this combination, pyoluteorin conferred the competitive advantage of Pf-5. Noteworthy, pyoluteorin-deficient Pf-5 cooperated with DMW1 in biofilm formation, production of metabolites, root colonization, tomato bacterial wilt disease control, as well as in cooperation with beneficial bacteria in tomato rhizosphere, such as Bacillus spp. RNA-seq analysis and RT-qPCR also proved the pyoluteorin-deficient Pf-5 mutant improved cell motility and metabolite production. This study suggests that the cooperative effect of Bacillus-Pseudomonas consortia depends on the balance of pyoluteorin. Our finding needs to be considered in developing efficient SynCom in sustainable agriculture.

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.

A review on mechanisms and prospects of endophytic bacteria in biocontrol of plant pathogenic fungi and their plant growth-promoting activities

Endophytic bacteria, living inside plants, are competent plant colonizers, capable of enhancing immune responses in plants and establishing a symbiotic relationship with them. Endophytic bacteria are able to control phytopathogenic fungi while exhibiting plant growth-promoting activity. Here, we discussed the mechanisms of phytopathogenic fungi control and plant growth-promoting actions discovered in some major groups of beneficial endophytic bacteria such as Bacillus, Paenibacillus, and Pseudomonas. Most of the studied strains in these genera were isolated from the rhizosphere and soils, and a more extensive study of these endophytic bacteria is needed. It is essential to understand the underlying biocontrol and plant growth-promoting mechanisms and to develop an effective screening approach for selecting potential endophytic bacteria for various applications. We have suggested a screening strategy to identify potentially useful endophytic bacteria based on mechanistic phenomena. The discovery of endophytic bacteria with useful biocontrol and plant growth-promoting characteristics is essential for developing sustainable agriculture.

Does regulation hold the key to optimizing lipopeptide production in Pseudomonas for biotechnology?

Lipopeptides (LPs) produced by Pseudomonas spp. are specialized metabolites with diverse structures and functions, including powerful biosurfactant and antimicrobial properties. Despite their enormous potential in environmental and industrial biotechnology, low yield and high production cost limit their practical use. While genome mining and functional genomics have identified a multitude of LP biosynthetic gene clusters, the regulatory mechanisms underlying their biosynthesis remain poorly understood. We propose that regulation holds the key to unlocking LP production in Pseudomonas for biotechnology. In this review, we summarize the structure and function of Pseudomonas-derived LPs and describe the molecular basis for their biosynthesis and regulation. We examine the global and specific regulator-driven mechanisms controlling LP synthesis including the influence of environmental signals. Understanding LP regulation is key to modulating production of these valuable compounds, both quantitatively and qualitatively, for industrial and environmental biotechnology.

Resistance towards and biotransformation of a Pseudomonas-produced secondary metabolite during community invasion

The role of antagonistic secondary metabolites produced by Pseudomonas protegens in suppression of soil-borne phytopathogens has been clearly documented. However, their contribution to the ability of P. protegens to establish in soil and rhizosphere microbiomes remains less clear. Here, we use a four-species synthetic community (SynCom) in which individual members are sensitive towards key P. protegens antimicrobial metabolites (DAPG, pyoluteorin, and orfamide A) to determine how antibiotic production contributes to P. protegens community invasion and to identify community traits that counteract the antimicrobial effects. We show that P. protegens readily invades and alters the SynCom composition over time, and that P. protegens establishment requires production of DAPG and pyoluteorin. An orfamide A-deficient mutant of P. protegens invades the community as efficiently as wildtype, and both cause similar perturbations to community composition. Here, we identify the microbial interactions underlying the absence of an orfamide A mediated impact on the otherwise antibiotic-sensitive SynCom member, and show that the cyclic lipopeptide is inactivated and degraded by the combined action of Rhodococcus globerulus D757 and Stenotrophomonas indicatrix D763. Altogether, the demonstration that the synthetic community constrains P. protegens invasion by detoxifying its antibiotics may provide a mechanistic explanation to inconsistencies in biocontrol effectiveness in situ.

The genome of a steinernematid-associated Pseudomonas piscis bacterium encodes the biosynthesis of insect toxins

Several species of soil-dwelling Steinernema nematodes are used in the biocontrol of crop pests, due to their natural capacity to kill diverse lepidopteran species. Although this insect-killing trait is known to be augmented by the nematodes' Xenorhabdus endosymbionts, the role of other steinernematid-associated bacterial genera in the nematode lifecycle remains unclear. This genomic study aimed to determine the potential of Pseudomonas piscis to contribute to the entomopathogenicity of its Steinernema host. Insect larvae were infected with three separate Steinernema cultures. From each of the three treatments, the prevalent bacteria in the haemocoel of cadavers, four days post-infection, were isolated. These three bacterial isolates were morphologically characterised. DNA was extracted from each of the three bacterial isolates and used for long-read genome sequencing and assembly. Assemblies were used to delineate species and identify genes that encode insect toxins, antimicrobials, and confer antibiotic resistance. We assembled three complete genomes. Through digital DNA-DNA hybridisation analyses, we ascertained that the haemocoels of insect cadavers previously infected with Steinernema sp. Kalro, Steinernema sp. 75, and Steinernema sp. 97 were dominated by Xenorhabdus griffiniae Kalro, Pseudomonas piscis 75, and X. griffiniae 97, respectively. X. griffiniae Kalro and X. griffiniae 97 formed a subspecies with other X. griffiniae symbionts of steinernematids from Kenya. P. piscis 75 phylogenetically clustered with pseudomonads that are characterised by high insecticidal activity. The P. piscis 75 genome encoded the production pathway of insect toxins such as orfamides and rhizoxins, antifungals such as pyrrolnitrin and pyoluteorin, and the broad-spectrum antimicrobial 2,4-diacetylphloroglucinol. The P. piscis 75 genome encoded resistance to over ten classes of antibiotics, including cationic lipopeptides. Steinernematid-associated P. piscis bacteria hence have the biosynthetic potential to contribute to nematode entomopathogenicity.

Stereomeric Lipopeptides from a Single Non-Ribosomal Peptide Synthetase as an Additional Source of Structural and Functional Diversification in Pseudomonas Lipopeptide Biosynthesis

In Pseudomonas lipopeptides, the D-configuration of amino acids is generated by dedicated, dual-function epimerization/condensation (E/C) domains. The increasing attention to stereochemistry in lipopeptide structure elucidation efforts has revealed multiple examples where epimerization does not occur, even though an E/C-type domain is present. While the origin of the idle epimerization in those E/C-domains remains elusive, epimerization activity has so far shown a binary profile: it is either 'on' (active) or 'off' (inactive). Here, we report the unprecedented observation of an E/C-domain that acts 'on and off', giving rise to the production of two diastereoisomeric lipopeptides by a single non-ribosomal peptide synthetase system. Using dereplication based on solid-phase peptide synthesis and NMR fingerprinting, we first show that the two cyclic lipopeptides produced by Pseudomonas entomophila COR5 correspond to entolysin A and B originally described for P. entomophila L48. Next, we prove that both are diastereoisomeric homologues differing only in the configuration of a single amino acid. This configurational variability is maintained in multiple Pseudomonas strains and typically occurs in a 3:2 ratio. Bioinformatic analysis reveals a possible correlation with the composition of the flanking sequence of the N-terminal secondary histidine motif characteristic for dual-function E/C-type domains. In permeabilization assays, using propidium iodide entolysin B has a higher antifungal activity compared to entolysin A against Botrytis cinerea and Pyricularia oryzae spores. The fact that configurational homologues are produced by the same NRPS system in a Pseudomonas strain adds a new level of structural and functional diversification to those already known from substrate flexibility during the recruitment of the amino acids and fatty acids and underscores the importance of complete stereochemical elucidation of non-ribosomal lipopeptide structures.

Relation of pest insect-killing and soilborne pathogen-inhibition abilities to species diversification in environmental Pseudomonas protegens

Strains belonging to the Pseudomonas protegens phylogenomic subgroup have long been known for their beneficial association with plant roots, notably antagonising soilborne phytopathogens. Interestingly, they can also infect and kill pest insects, emphasising their interest as biocontrol agents. In the present study, we used all available Pseudomonas genomes to reassess the phylogeny of this subgroup. Clustering analysis revealed the presence of 12 distinct species, many of which were previously unknown. The differences between these species also extend to the phenotypic level. Most of the species were able to antagonise two soilborne phytopathogens, Fusarium graminearum and Pythium ultimum, and to kill the plant pest insect Pieris brassicae in feeding and systemic infection assays. However, four strains failed to do so, likely as a consequence of adaptation to particular niches. The absence of the insecticidal Fit toxin explained the non-pathogenic behaviour of the four strains towards Pieris brassicae. Further analyses of the Fit toxin genomic island evidence that the loss of this toxin is related to non-insecticidal niche specialisation. This work expands the knowledge on the growing Pseudomonas protegens subgroup and suggests that loss of phytopathogen inhibition and pest insect killing abilities in some of these bacteria may be linked to species diversification processes involving adaptation to particular niches. Our work sheds light on the important ecological consequences of gain and loss dynamics for functions involved in pathogenic host interactions of environmental bacteria.

Charting the Lipopeptidome of Nonpathogenic Pseudomonas

A major source of pseudomonad-specialized metabolites is the nonribosomal peptide synthetases (NRPSs) assembling siderophores and lipopeptides. Cyclic lipopeptides (CLPs) of the Mycin and Peptin families are frequently associated with, but not restricted to, phytopathogenic species. We conducted an in silico analysis of the NRPSs encoded by lipopeptide biosynthetic gene clusters in nonpathogenic Pseudomonas genomes, covering 13 chemically diversified families. This global assessment of lipopeptide production capacity revealed it to be confined to the Pseudomonas fluorescens lineage, with most strains synthesizing a single type of CLP. Whereas certain lipopeptide families are specific for a taxonomic subgroup, others are found in distant groups. NRPS activation domain-guided peptide predictions enabled reliable family assignments, including identification of novel members. Focusing on the two most abundant lipopeptide families (Viscosin and Amphisin), a portion of their uncharted diversity was mapped, including characterization of two novel Amphisin family members (nepenthesin and oakridgin). Using NMR fingerprint matching, known Viscosin-family lipopeptides were identified in 15 (type) species spread across different taxonomic groups. A bifurcate genomic organization predominates among Viscosin-family producers and typifies Xantholysin-, Entolysin-, and Poaeamide-family producers but most families feature a single NRPS gene cluster embedded between cognate regulator and transporter genes. The strong correlation observed between NRPS system phylogeny and rpoD-based taxonomic affiliation indicates that much of the structural diversity is linked to speciation, providing few indications of horizontal gene transfer. The grouping of most NRPS systems in four superfamilies based on activation domain homology suggests extensive module dynamics driven by domain deletions, duplications, and exchanges. IMPORTANCE Pseudomonas species are prominent producers of lipopeptides that support proliferation in a multitude of environments and foster varied lifestyles. By genome mining of biosynthetic gene clusters (BGCs) with lipopeptide-specific organization, we mapped the global Pseudomonas lipopeptidome and linked its staggering diversity to taxonomy of the producers, belonging to different groups within the major Pseudomonas fluorescens lineage. Activation domain phylogeny of newly mined lipopeptide synthetases combined with previously characterized enzymes enabled assignment of predicted BGC products to specific lipopeptide families. In addition, novel peptide sequences were detected, showing the value of substrate specificity analysis for prioritization of BGCs for further characterization. NMR fingerprint matching proved an excellent tool to unequivocally identify multiple lipopeptides bioinformatically assigned to the Viscosin family, by far the most abundant one in Pseudomonas and with stereochemistry of all its current members elucidated. In-depth analysis of activation domains provided insight into mechanisms driving lipopeptide structural diversification.

The Diversity of Lipopeptides in the Pseudomonas syringae Complex Parallels Phylogeny and Sheds Light on Structural Diversification during Evolutionary History

Pseudomonas spp. colonize diverse aquatic and terrestrial habitats and produce a wide variety of secondary metabolites, including lipopeptides. However, previous studies have often examined a limited number of lipopeptide-producing strains. In this study, we performed a systematic analysis of lipopeptide production across a wide data set of strains of the Pseudomonas syringae complex (724) by using a combined bioinformatics, mass spectrometry, and phylogenetics approach. The large P. syringae complex, which is composed of 13 phylogroups, is known to produce factins (including syringafactin-like lipopeptides), mycins (including syringomycin-like lipopeptides), and peptins (such as syringopeptins). We found that 80.8% of P. syringae strains produced lipopeptides and that factins were the most frequently produced (by 96% of the producing strains). P. syringae strains were either factin monoproducers or factin, mycin, and peptin coproducers or lipopeptide nonproducers in relation to their phylogenetic group. Our analyses led to the discovery of 42 new lipopeptides, bringing the number of lipopeptides identified in the P. syringae complex to 75. We also highlighted that factins have high structural resemblance and are widely distributed among the P. syringae complex, while mycins and peptins are highly structurally diverse and patchily distributed. IMPORTANCE This study provides an insight into the P. syringae metabolome that emphasizes the high diversity of lipopeptides produced within the P. syringae complex. The production profiles of strains are closely related to their phylogenetic classification, indicating that structural diversification of lipopeptides parallels the phylogeny of this bacterial complex, thereby further illustrating the inherent importance of lipopeptides in the ecology of this group of bacteria throughout its evolutionary history. Furthermore, this overview of P. syringae lipopeptides led us to propose a refined classification that could be extended to the lipopeptides produced by other bacterial groups.

Sequential interspecies interactions affect production of antimicrobial secondary metabolites in Pseudomonas protegens DTU9.1

Soil and rhizosphere microbiomes play important roles in suppression of plant pathogens through production of antagonistic secondary metabolites, yet mechanisms that determine the strength of pathogen control are not well understood. Many Pseudomonas species are associated with soil and rhizosphere microbiomes, and their ability to suppress pathogens is well documented. Here, we investigate how interactions within the Pseudomonas genus affect their production of antimicrobial metabolites. From a biosensor-based screen, we identify P. capeferrum species as capable of modulating secondary metabolite production in P. protegens. We show that P. capeferrum alters production of pyoluteorin and 2,4-diacetylphloroglucinol (DAPG) in P. protegens via two distinct and sequential mechanisms that depends on spatial proximity of the two species. Specifically, P. capeferrum secretes a diffusible signal that induce pyoluteorin production up to 100-fold in neighboring P. protegens colonies. In contrast, the interaction results in reduced DAPG production, but only within mixed-species colonies. Additionally, we found that increased pyoluteorin production and cell lysis of P. capeferrum is required for inhibition of DAPG production, suggesting that pyoluteorin-facilitated antibiosis of P. protegens on P. capeferrum leads to release of cell-associated metabolites and subsequent inhibition of DAPG production in P. protegens. As the interaction modulates in vitro bioactivity of the species, genus-specific interactions may assist in improving efficacy of biocontrol strains and consortia.

Draft Genome Sequence of Pseudomonas sp. Strains MWU12-2319 and MWU12-2311, Isolated from a Wild Cranberry Bog in the Cape Cod National Seashore

Pseudomonas sp. strains MWU12-2319 and MWU12-2311 were isolated from the soil of a wild cranberry bog in the Cape Cod National Seashore as part of a culture-dependent bacterial population survey. The genomes exceed 7 Mbp and contain putative gene clusters for the biosurfactant orfamides A and C.

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.

An Nuclear Magnetic Resonance Fingerprint Matching Approach for the Identification and Structural Re-Evaluation of Pseudomonas Lipopeptides

Cyclic lipopeptides (CLiPs) are secondary metabolites secreted by a range of bacterial phyla. CLiPs from Pseudomonas in particular, display diverse structural variations in terms of the number of amino acid residues, macrocycle size, amino acid identity, and stereochemistry (e.g., d- versus l-amino acids). Reports detailing the discovery of novel or already characterized CLiPs from new sources appear regularly in literature. Increasingly, however, the lack of detailed characterization threatens to cause considerable confusion, especially if configurational heterogeneity is present for one or more amino acids. Using Pseudomonas CLiPs from the Bananamide, Orfamide, and Xantholysin groups as test cases, we demonstrate and validate that the combined 1H and 13C Nuclear Magnetic Resonance (NMR) chemical shifts of CLiPs constitute a spectral fingerprint that is sufficiently sensitive to differentiate between possible diastereomers of a particular sequence even when they only differ in a single d/l configuration. Rapid screening, involving simple matching of the NMR fingerprint of a newly isolated CLiP with that of a reference CLiP of known stereochemistry, can then be applied to resolve dead-ends in configurational characterization and avoid the much more cumbersome chemical characterization protocols. Even when the stereochemistry of a particular reference CLiP remains to be established, its spectral fingerprint allows to quickly verify whether a newly isolated CLiP is novel or already present in the reference collection. We show NMR fingerprinting leads to a simple approach for early on dereplication which should become more effective as more fingerprints are collected. To benefit research involving CLiPs, we have made a publicly available data repository accompanied by a 'knowledge base' at https://www.rhizoclip.be, where we present an overview of published NMR fingerprint data of characterized CLiPs, together with literature data on the originally determined structures. IMPORTANCE Pseudomonas CLiPs are ubiquitous specialized metabolites, impacting the producer's lifestyle and interactions with the (a)biotic environment. Consequently, they generate interest for agricultural and clinical applications. Establishing structure-activity relationships as a premise to their development is hindered because full structural characterization including stereochemical information requires labor-intensive analyses, without guarantee for success. Moreover, increasing use of superficial comparison with previously characterized CLiPs introduces or propagates erroneous attributions, clouding further scientific progress. We provide a generally applicable characterization methodology based on matching NMR spectral fingerprints of newly isolated CLiPs to natural and synthetic reference compounds with (un)known stereochemistry. In addition, NMR fingerprinting is shown to provide a suitable basis for structural dereplication. A publicly available reference compound repository promises to facilitate participation of the lipopeptide research community in structural assessment and dereplication of newly isolated CLiPs, which should also support further developments in genome mining for novel CLiPs.

The secret life of plant-beneficial rhizosphere bacteria: insects as alternative hosts

Root-colonizing bacteria have been intensively investigated for their intimate relationship with plants and their manifold plant-beneficial activities. They can inhibit growth and activity of pathogens or induce defence responses. In recent years, evidence has emerged that several plant-beneficial rhizosphere bacteria do not only associate with plants but also with insects. Their relationships with insects range from pathogenic to mutualistic and some rhizobacteria can use insects as vectors for dispersal to new host plants. Thus, the interactions of these bacteria with their environment are even more complex than previously thought and can extend far beyond the rhizosphere. The discovery of this secret life of rhizobacteria represents an exciting new field of research that should link the fields of plant-microbe and insect-microbe interactions. In this review, we provide examples of plant-beneficial rhizosphere bacteria that use insects as alternative hosts, and of potentially rhizosphere-competent insect symbionts. We discuss the bacterial traits that may enable a host-switch between plants and insects and further set the multi-host lifestyle of rhizobacteria into an evolutionary and ecological context. Finally, we identify important open research questions and discuss perspectives on the use of these rhizobacteria in agriculture.

Combining in vitro and in vivo screening to identify efficient Pseudomonas biocontrol strains against the phytopathogenic bacterium Ralstonia solanacearum

Although plant pathogens are traditionally controlled using synthetic agrochemicals, the availability of commercial bactericides is still limited. One potential control strategy could be the use of plant growth‐promoting bacteria (PGPB) to suppress pathogens via resource competition or the production of antimicrobial compounds. This study aimed to conduct in vitro and in vivo screening of eight Pseudomonas strains against Ralstonia solanacearum (the causative agent of bacterial wilt) and to investigate underlying mechanisms of potential pathogen suppression. We found that inhibitory effects were Pseudomonas strain‐specific, with strain CHA0 showing the highest pathogen suppression. Genomic screening identified 2,4‐diacetylphloroglucinol, pyoluteorin, and orfamides A and B secondary metabolite clusters in the genomes of the most inhibitory strains, which were investigated further. Although all these compounds suppressed R. solanacearum growth, only orfamide A was produced in the growth media based on mass spectrometry. Moreover, orfamide variants extracted from Pseudomonas cultures showed high pathogen suppression. Using the “Micro‐Tom” tomato cultivar, it was found that CHA0 could reduce bacterial wilt disease incidence with one of the two tested pathogen strains. Together, these findings suggest that a better understanding of Pseudomonas–Ralstonia interactions in the rhizosphere is required to successfully translate in vitro findings into agricultural applications.

Total Synthesis and Structure Correction of the Cyclic Lipodepsipeptide Orfamide A

A total synthesis of the cyclic lipodepsipeptide natural product orfamide A was achieved. By developing a synthesis format using an aminoacid ester building block and SPPS protocol adaptation, a focused library of target compounds was obtained, in high yield and purity. Spectral and LC-HRMS data of all library members with the isolated natural product identified the 5 Leu residue to be d- and the 3'-OH group to be R-configured. The structural correction of orfamide A by chemical synthesis and analysis was confirmed by biological activity comparison in Chlamydomonas reinhardtii, which indicated compound configuration to be important for bioactivity. Acute toxicity was also found against Trypanosoma brucei, the parasite causing African sleeping sickness.

Nonribosomal Peptide Synthesis Definitely Working Out of the Rules

Nonribosomal peptides are microbial secondary metabolites exhibiting a tremendous structural diversity and a broad range of biological activities useful in the medical and agro-ecological fields. They are built up by huge multimodular enzymes called nonribosomal peptide synthetases. These synthetases are organized in modules constituted of adenylation, thiolation, and condensation core domains. As such, each module governs, according to the collinearity rule, the incorporation of a monomer within the growing peptide. The release of the peptide from the assembly chain is finally performed by a terminal core thioesterase domain. Secondary domains with modifying catalytic activities such as epimerization or methylation are sometimes included in the assembly lines as supplementary domains. This assembly line structure is analyzed by bioinformatics tools to predict the sequence and structure of the final peptides according to the sequence of the corresponding synthetases. However, a constantly expanding literature unravels new examples of nonribosomal synthetases exhibiting very rare domains and noncanonical organizations of domains and modules, leading to several amazing strategies developed by microorganisms to synthesize nonribosomal peptides. In this review, through several examples, we aim at highlighting these noncanonical pathways in order for the readers to perceive their complexity.

Pseudomonas bijieensis Strain XL17 within the P. corrugata Subgroup Producing 2,4-Diacetylphloroglucinol and Lipopeptides Controls Bacterial Canker and Gray Mold Pathogens of Kiwifruit

Kiwifruit worldwide suffers from the devastating diseases of bacterial canker caused by Pseudomonas syringae pv. actinidiae (Psa) and gray mold caused by Botrytis cinerea. Here, an endophytic bacterium XL17 isolated from a rape crown gall was screened out for its potent antagonistic activities against Psa and B. cinerea. Strain XL17 and its cell-free culture filtrate (CF) inhibited the growth of Psa and B. cinerea, Psa-associated leaf necrosis, and B. cinerea-associated kiwifruit necrosis. Electron microscopy showed that XL17 CF could damage the cell structures of Psa and B. cinerea. Genome-based taxonomy revealed that strain XL17 belongs to Pseudomonas bijieensis within the P. corrugata subgroup of the P. fluorescens species complex. Among the P. corrugata subgroup containing 31 genomospecies, the presence of the phl operon responsible for the biosynthesis of the phenolic polyketide 2,4-diacetylphloroglucinol (DAPG) and the absence of the lipopeptide/quorum sensing island can serve as the genetic marker for the determination of a plant-protection life style. HPLC detected DAPG in extracts from XL17 CF. MALDI-TOF-MS analysis revealed that strain XL17 produced cyclic lipopeptides of the viscosin family and orfamide family. Together, phenotypic, genomic, and metabolic analyses identified that P. bijieensis XL17 producing DAPG and cyclic lipopeptides can be used to control bacterial canker and gray mold pathogens of kiwifruit.

Environmental structure impacts microbial composition and secondary metabolism

Determining the drivers of microbial community assembly is a central theme of microbial ecology, and chemical ecologists seek to characterize how secondary metabolites mediate these assembly patterns. Environmental structure affects how communities assemble and what metabolic pathways aid in that assembly. Here, we bridged these two perspectives by addressing the chemical drivers of community assembly within a spatially structured landscape with varying oxygen availability. We hypothesized that structured environments would favor higher microbial diversity and metabolite diversity. We anticipated that the production of a compound would be more advantageous in a structured environment (less mixing) compared to an unstructured environment (more mixing), where the molecule would have a diminished local effect. We observed this to be partially true in our experiments: structured environments had similar microbial diversity compared to unstructured environments but differed significantly in the metabolites produced. We also found that structured environments selected for communities with higher evenness, rather than communities with higher richness. This supports the idea that when characterizing the drivers of community assembly, it matters less about who is there and more about what they are doing. Overall, these data contribute to a growing effort to approach microbial community assembly with interdisciplinary tools and perspectives.

Pseudomonas Lipopeptide-Mediated Biocontrol: Chemotaxonomy and Biological Activity

Pseudomonas lipopeptides (Ps-LPs) play crucial roles in bacterial physiology, host-microbe interactions and plant disease control. Beneficial LP producers have mainly been isolated from the rhizosphere, phyllosphere and from bulk soils. Despite their wide geographic distribution and host range, emerging evidence suggests that LP-producing pseudomonads and their corresponding molecules display tight specificity and follow a phylogenetic distribution. About a decade ago, biocontrol LPs were mainly reported from the P. fluorescens group, but this has drastically advanced due to increased LP diversity research. On the one hand, the presence of a close-knit relationship between Pseudomonas taxonomy and the molecule produced may provide a startup toolbox for the delineation of unknown LPs into existing (or novel) LP groups. Furthermore, a taxonomy-molecule match may facilitate decisions regarding antimicrobial activity profiling and subsequent agricultural relevance of such LPs. In this review, we highlight and discuss the production of beneficial Ps-LPs by strains situated within unique taxonomic groups and the lineage-specificity and coevolution of this relationship. We also chronicle the antimicrobial activity demonstrated by these biomolecules in limited plant systems compared with multiple in vitro assays. Our review further stresses the need to systematically elucidate the roles of diverse Ps-LP groups in direct plant-pathogen interactions and in the enhancement of plant innate immunity.

Transporter Gene-mediated Typing for Detection and Genome Mining of Lipopeptide-producing Pseudomonas

Pseudomonas lipopeptides (LPs) are involved in diverse ecological functions and have biotechnological application potential associated with their antimicrobial and/or antiproliferative activities. They are synthesized by multimodular nonribosomal peptide synthetases which, together with transport and regulatory proteins, are encoded by large biosynthetic gene clusters (BGCs). These secondary metabolites are classified in distinct families based on the sequence and length of the oligopeptide and size of the macrocycle, if present. The phylogeny of PleB, the MacB-like transporter that is part of a dedicated ATP-dependent tripartite efflux system driving export of Pseudomonas LPs, revealed a strong correlation with LP chemical diversity. As each LP BGC carries its cognate pleB, PleB is suitable as a diagnostic sequence for genome mining, allowing assignment of the putative metabolite to a particular LP family. In addition, pleB proved to be a suitable target gene for an alternative PCR method for detecting LP-producing Pseudomonas sp. and did not rely on amplification of catalytic domains of the biosynthetic enzymes. Combined with amplicon sequencing, this approach enabled typing of Pseudomonas strains as potential producers of a LP belonging to one of the known LP families, underscoring its value for strain prioritization. This finding was validated by chemical characterization of known LPs from three different families secreted by novel producers isolated from the rice or maize rhizosphere, namely, the type strains of Pseudomonas fulva (putisolvin), Pseudomonas zeae (tensin), and Pseudomonas xantholysinigenes (xantholysin). In addition, a new member of the Bananamide family, prosekin, was discovered in the type strain of Pseudomonas prosekii, which is an Antarctic isolate.

IMPORTANCEPseudomonas spp. are ubiquitous bacteria able to thrive in a wide range of ecological niches, and lipopeptides often support their lifestyle but also their interaction with other micro- and macro-organisms. Therefore, the production of lipopeptides is widespread among Pseudomonas strains. Consequently, Pseudomonas lipopeptide research not only affects chemists and microbiologists but also touches a much broader audience, including biochemists, ecologists, and plant biologists. In this study, we present a reliable transporter gene-guided approach for the detection and/or typing of Pseudomonas lipopeptide producers. Indeed, it allows us to readily assess the lipopeptide diversity among sets of Pseudomonas isolates and differentiate strains likely to produce known lipopeptides from producers of potentially novel lipopeptides. This work provides a valuable tool that can also be integrated in a genome mining strategy and adapted for the typing of other specialized metabolites.

Harnessing Chemical Ecology for Environment-Friendly Crop Protection

Heavy reliance on synthetic pesticides for crop protection has become increasingly unsustainable, calling for robust alternative strategies that do not degrade the environment and vital ecosystem services. There are numerous reports of successful disease control by various microbes used in small-scale trials. However, inconsistent efficacy has hampered their large-scale application. A better understanding of how beneficial microbes interact with plants, other microbes, and the environment and which factors affect disease control efficacy is crucial to deploy microbial agents as effective and reliable pesticide alternatives. Diverse metabolites produced by plants and microbes participate in pathogenesis and defense, regulate the growth and development of themselves and neighboring organisms, help maintain cellular homeostasis under various environmental conditions, and affect the assembly and activity of plant and soil microbiomes. However, research on the metabolites associated with plant health-related processes, except antibiotics, has not received adequate attention. This review highlights several classes of metabolites known or suspected to affect plant health, focusing on those associated with biocontrol and belowground plant-microbe and microbe-microbe interactions. The review also describes how new insights from systematic explorations of the diversity and mechanism of action of bioactive metabolites can be harnessed to develop novel crop protection strategies.

Microbial Toxins in Insect and Nematode Pest Biocontrol

Invertebrate pests, such as insects and nematodes, not only cause or transmit human and livestock diseases but also impose serious crop losses by direct injury as well as vectoring pathogenic microbes. The damage is global but greater in developing countries, where human health and food security are more at risk. Although synthetic pesticides have been in use, biological control measures offer advantages via their biodegradability, environmental safety and precise targeting. This is amply demonstrated by the successful and widespread use of Bacillusthuringiensis to control mosquitos and many plant pests, the latter by the transgenic expression of insecticidal proteins from B. thuringiensis in crop plants. Here, I discuss the prospects of using bacterial and fungal toxins for pest control, including the molecular basis of their biocidal activity.

A review on new aspects of lipopeptide biosurfactant: Types, production, properties and its application in the bioremediation process

Nowadays, the worldwide search regarding renewable products from natural resources is increasing due to the toxicity of chemical counterparts. Biosurfactants are surface-active compounds that contain several physiological functions that are used in industries like food, pharmaceutical, petroleum and agriculture. Microbial lipopeptides have gained more attention among the researchers for their low toxicity, efficient action and good biodegradability when compared with other surfactants. Because of their versatile properties, lipopeptide compounds are utilized in the remediation of organic and inorganic pollutants. This review presented a depth evaluation of lipopeptide surfactants in the bioremediation process and their properties to maintain a sustainable environment. Lipopeptide can acts as a replacement to chemical surfactants only if they meet industrial-scale production and low-cost substrates. This review also demonstrated the production of a lipopeptide biosurfactant from a low-cost substrate and depicted plausible techniques to manage the substrate residues to determine its ability in the different applications particularly in the bioremediation process.

Fungicidal Activity of Volatile Organic Compounds Emitted by Burkholderia gladioli Strain BBB-01

A Burkholderia gladioli strain, named BBB-01, was isolated from rice shoots based on the confrontation plate assay activity against several plant pathogenic fungi. The genome of this bacterial strain consists of two circular chromosomes and one plasmid with 8,201,484 base pairs in total. Pangenome analysis of 23 B. gladioli strains suggests that B. gladioli BBB-01 has the closest evolutionary relationship to B. gladioli pv. gladioli and B. gladioli pv. agaricicola. B. gladioli BBB-01 emitted dimethyl disulfide and 2,5-dimethylfuran when it was cultivated in lysogeny broth and potato dextrose broth, respectively. Dimethyl disulfide is a well-known pesticide, while the bioactivity of 2,5-dimethylfuran has not been reported. In this study, the inhibition activity of the vapor of these two compounds was examined against phytopathogenic fungi, including Magnaporthe oryzae, Gibberella fujikuroi, Sarocladium oryzae, Phellinus noxius and Colletotrichumfructicola, and human pathogen Candida albicans. In general, 2,5-dimethylfuran is more potent than dimethyl disulfide in suppressing the growth of the tested fungi, suggesting that 2,5-dimethylfuran is a potential fumigant to control plant fungal disease.

Identification of the genes controlling biofilm formation in the plant commensal Pseudomonas protegens Pf-5

Determinant genes controlling biofilm formation in a plant commensal bacterium, Pseudomonas protegens Pf-5, were identified by transposon mutagenesis. Comprehensive screening of 7500 transposon-inserted mutants led to the isolation of four mutants exhibiting decreased and five mutants exhibiting increased biofilm formation. Mutations in the genes encoding MFS drug resistance transporter, LapA adhesive protein, RetS sensor histidine kinase/response regulator, and HecA adhesin/hemagglutinin led to decreased biofilm formation, indicating that these genes are necessary for biofilm formation in Pf-5. The mutants exhibiting increased biofilm formation had transposon insertions in the genes coding for an outer membrane protein, a GGDEF domain-containing protein, AraC transcriptional regulator, non-ribosomal peptide synthetase OfaB, and the intergenic region of a DNA-binding protein and the Aer aerotaxis receptor, suggesting that these genes are negative regulators of biofilm formation. Some of these mutants also showed altered swimming and swarming motilities, and a negative correlation between biofilm formation and swarming motility was observed. Thus, sessile-motile lifestyle is regulated by divergent regulatory genes in Pf-5.

Diversity of Antibiotic Biosynthesis Gene-possessing Rhizospheric Fluorescent Pseudomonads in Japan and Their Biocontrol Efficacy

More than 3,000 isolates of fluorescent pseudomonads have been collected from plant roots in Japan and screened for the presence of antibiotic-synthesizing genes. In total, 927 hydrogen cyanide (HCN)-, 47 2,4-diacetylphloroglucinol (PHL)-, 6 pyoluteorin (PLT)-, 14 pyrrolnitrin (PRN)-, and 8 phenazine (PHZ)-producing isolates have been detected. A cluster analysis (≥99% identity) identified 10 operational taxonomic units (OTUs) in antibiotic biosynthesis gene-possessing pseudomonads. OTU HLR (PHL, PLT, and PRN) contained four antibiotics: HCN, PHL, PLT, and PRN, while OTU RZ (PRN and PHZ) contained three: HCN, PRN, and PHZ. OTU H1, H2, H3, H4, H5, H6, and H7 (PHL1-7) contained two antibiotics: HCN and PHL, while OTU H8 (PHL8) contained one: PHL. Isolates belonging to OTU HLR and RZ suppressed damping-off disease in cabbage seedlings caused by Rhizoctonia solani. Effective strains belonging to OTU HLR and RZ were related to Pseudomonas protegens and Pseudomonas chlororaphis, respectively. Antibiotic biosynthesis gene-possessing fluorescent pseudomonads are distributed among different geographical sites in Japan and plant species.

Isolation and characterization of a new cyclic lipopeptide surfactin from a marine-derived Bacillus velezensis SH-B74

A marine-sediment-derived bacterium Bacillus velezensis SH-B74 can produce cyclic lipopeptides (CLPs). This study presented the isolation, characterization, and activity evaluation of a new CLP from the bacterial cultures of the strain SH-B74. Multiple chromatographic methods (solid-phase extraction and reversed-phase high-performance liquid chromatography) were applied to the purifying procedure of CLP, and the structural characterization of the new CLP was conducted by various spectroscopy (1D and 2D nuclear magnetic resonance together with Fourier transform infrared spectroscopy) and spectrometry (liquid chromatography-mass spectrometry, high-resolution mass spectrometry and tandem mass spectrometry) techniques as well as Marfey's method. The results displayed that the new CLP (anteiso-C₁₅ Ile_2,7 surfactin, 1) consists of a peptidic backbone of L-Glu₁, L-Ile₂, D-Leu₃, L-Val₄, L-Asp₅, D-Leu₆, L-Ile₇, and an anteiso-C₁₅ type saturated fatty acid chain. Further activity assay showed that the new CLP displays activity on the inhibition of the appressoria formation of rice blast causal pathogen Magnaporthe oryzae. To sum up, the results presented the perspective of potential application of the new CLP as a green agrichemical to control M. oryzae.

Pseudomonas sp. COW3 Produces New Bananamide-Type Cyclic Lipopeptides with Antimicrobial Activity against Pythium myriotylum and Pyricularia oryzae

Pseudomonas species are metabolically robust, with capacity to produce secondary metabolites including cyclic lipopeptides (CLPs). Herein we conducted a chemical analysis of a crude CLP extract from the cocoyam rhizosphere-derived biocontrol strain Pseudomonas sp. COW3. We performed in silico analyses on its whole genome, and conducted in vitro antagonistic assay using the strain and purified CLPs. Via LC-MS and NMR, we elucidated the structures of four novel members of the bananamide group, named bananamides D-G. Besides variability in fatty acid length, bananamides D-G differ from previously described bananamides A-C and MD-0066 by the presence of a serine and aspartic acid at position 6 and 2, respectively. In addition, bananamide G has valine instead of isoleucine at position 8. Kendrick mass defect (KMD) allowed the assignment of molecular formulae to bananamides D and E. We unraveled a non-ribosomal peptide synthetase cluster banA, banB and banC which encodes the novel bananamide derivatives. Furthermore, COW3 displayed antagonistic activity and mycophagy against Pythium myriotylum, while it mainly showed mycophagy on Pyricularia oryzae. Purified bananamides D-G inhibited the growth of P. myriotylum and P. oryzae and caused hyphal distortion. Our study shows the complementarity of chemical analyses and genome mining in the discovery and elucidation of novel CLPs. In addition, structurally diverse bananamides differ in their antimicrobial activity.

Root-associated microbes in sustainable agriculture: models, metabolites and mechanisms

Since the discovery of penicillin in 1928 and throughout the 'age of antibiotics' from the 1940s until the 1980s, the detection of novel antibiotics was restricted by lack of knowledge about the distribution and ecology of antibiotic producers in nature. The discovery that a phenazine compound produced by Pseudomonas bacteria could suppress soilborne plant pathogens, and its recovery from rhizosphere soil in 1990, provided the first incontrovertible evidence that natural metabolites could control plant pathogens in the environment and opened a new era in biological control by root-associated rhizobacteria. More recently, the advent of genomics, the availability of highly sensitive bioanalytical instrumentation, and the discovery of protective endophytes have accelerated progress toward overcoming many of the impediments that until now have limited the exploitation of beneficial plant-associated microbes to enhance agricultural sustainability. Here, we present key developments that have established the importance of these microbes in the control of pathogens, discuss concepts resulting from the exploration of classical model systems, and highlight advances emerging from ongoing investigations. © 2019 Society of Chemical Industry.

Pseudomonas Cyclic Lipopeptides Suppress the Rice Blast Fungus Magnaporthe oryzae by Induced Resistance and Direct Antagonism

Beneficial Pseudomonas spp. produce an array of antimicrobial secondary metabolites such as cyclic lipopeptides (CLPs). We investigated the capacity of CLP-producing Pseudomonas strains and their crude CLP extracts to control rice blast caused by Magnaporthe oryzae, both in a direct manner and via induced systemic resistance (ISR). In planta biocontrol assays showed that lokisin-, white line inducing principle (WLIP)-, entolysin- and N3-producing strains successfully induced resistance to M. oryzae VT5M1. Furthermore, crude extracts of lokisin, WLIP and entolysin gave similar ISR results when tested in planta. In contrast, a xantholysin-producing strain and crude extracts of N3, xantholysin and orfamide did not induce resistance against the rice blast disease. The role of WLIP in triggering ISR was further confirmed by using WLIP-deficient mutants. The severity of rice blast disease was significantly reduced when M. oryzae spores were pre-treated with crude extracts of N3, lokisin, WLIP, entolysin or orfamide prior to inoculation. In vitro microscopic assays further revealed the capacity of crude N3, lokisin, WLIP, entolysin, xantholysin and orfamide to significantly inhibit appressoria formation by M. oryzae. In addition, the lokisin and WLIP biosynthetic gene clusters in the producing strains are described. In short, our study demonstrates the biological activity of structurally diverse CLPs in the control of the rice blast disease caused by M. oryzae. Furthermore, we provide insight into the non-ribosomal peptide synthetase genes encoding the WLIP and lokisin biosynthetic machineries.

Antimicrobial activity and carbohydrate metabolism in the bacterial metagenome of the soil-living invertebrate Folsomia candida

The microbiome associated with an animal's gut and other organs is considered an integral part of its ecological functions and adaptive capacity. To better understand how microbial communities influence activities and capacities of the host, we need more information on the functions that are encoded in a microbiome. Until now, the information about soil invertebrate microbiomes is mostly based on taxonomic characterization, achieved through culturing and amplicon sequencing. Using shotgun sequencing and various bioinformatics approaches we explored functions in the bacterial metagenome associated with the soil invertebrate Folsomia candida, an established model organism in soil ecology with a fully sequenced, high-quality genome assembly. Our metagenome analysis revealed a remarkable diversity of genes associated with antimicrobial activity and carbohydrate metabolism. The microbiome also contains several homologs to F. candida genes that were previously identified as candidates for horizontal gene transfer (HGT). We suggest that the carbohydrate- and antimicrobial-related functions encoded by Folsomia's metagenome play a role in the digestion of recalcitrant soil-born polysaccharides and the defense against pathogens, thereby significantly contributing to the adaptation of these animals to life in the soil. Furthermore, the transfer of genes from the microbiome may constitute an important source of new functions for the springtail.

Fluorescent Pseudomonas and cyclic lipopeptide diversity in the rhizosphere of cocoyam (Xanthosoma sagittifolium)

Cocoyam (Xanthosoma sagittifolium (L.)), an important tuber crop in the tropics, is severely affected by the cocoyam root rot disease (CRRD) caused by Pythium myriotylum. The white cocoyam genotype is very susceptible while the red cocoyam has some field tolerance to CRRD. Fluorescent Pseudomonas isolates obtained from the rhizosphere of healthy red and white cocoyams from three different fields in Cameroon were taxonomically characterized. The cocoyam rhizosphere was enriched with P. fluorescens complex and P. putida isolates independent of the plant genotype. LC-MS and NMR analyses revealed that 50% of the Pseudomonas isolates produced cyclic lipopeptides (CLPs) including entolysin, lokisin, WLIP, putisolvin and xantholysin together with eight novel CLPs. In general, CLP types were linked to specific taxonomic groups within the fluorescent pseudomonads. Representative CLP-producing bacteria showed effective control against CRRD while purified CLPs caused hyphal branching or hyphal leakage in P. myriotylum. The structure of cocoyamide A, a CLP which is predominantly produced by P. koreensis group isolates within the P. fluorescens complex is described. Compared with the white cocoyam, the red cocoyam rhizosphere appeared to support a more diverse CLP spectrum. It remains to be investigated whether this contributes to the field tolerance displayed by the red cocoyam.

Cyclic Lipodepsipeptides From Pseudomonas spp. - Biological Swiss-Army Knives

Cyclic lipodepsipeptides produced by Pseudomonas spp. (Ps-CLPs) are biosurfactants that constitute a diverse class of versatile bioactive natural compounds with promising application potential. While chemically diverse, they obey a common structural blue-print, allowing the definition of 14 distinct groups with multiple structurally homologous members. In addition to antibacterial and antifungal properties the reported activity profile of Ps-CLPs includes their effect on bacterial motility, biofilm formation, induced defense responses in plants, their insecticidal activity and anti-proliferation effects on human cancer cell-lines. To further validate their status of potential bioactive substances, we assessed the results of 775 biological tests on 51 Ps-CLPs available from literature. From this, a fragmented view emerges. Taken as a group, Ps-CLPs present a broad activity profile. However, reports on individual Ps-CLPs are often much more limited in the scope of organisms that are challenged or activities that are explored. As a result, our analysis shows that the available data is currently too sparse to allow biological function to be correlated to a particular group of Ps-CLPs. Consequently, certain generalizations that appear in literature with respect to the biological activities of Ps-CLPs should be nuanced. This notwithstanding, the data for the two most extensively studied Ps-CLPs does indicate they can display activities against various biological targets. As the discovery of novel Ps-CLPs accelerates, current challenges to complete and maintain a useful overview of biological activity are discussed.

Gram-negative bacilli-derived peptide antibiotics developed since 2000

Gram-negative bacilli such as Pseudomonas spp., Pseudoalteromonas sp., Angiococcus sp., Archangium sp., Burkholderia spp., Chromobacterium sp., Chondromyces sp., Cystobacter sp., Jahnella sp., Janthinobacterium sp., Lysobacter spp., Paraliomyxa sp., Photobacterium spp., Photorhabdus sp., Pontibacter sp., Ruegeria sp., Serratia sp., Sorangium sp., Sphingomonas sp., and Xenorhabdus spp. produce an enormous array of short peptides of 30 residues or fewer that are potential pharmaceutical drugs and/or biocontrol agents. The need for novel lead antibiotic compounds is urgent due to increasing drug resistance, and this review summarises 150 Gram-negative bacilli-derived compounds reported since 2000, including 40 cyclic lipopeptides from Pseudomonas spp.; nine aromatic peptides; eight glycopeptides; 45 different cyclic lipopeptides; 24 linear lipopeptides; eight thiopeptides; one lasso peptide; ten typical cyclic peptides; and five standard linear peptides. The current and potential therapeutic applications of these peptides, including structures and antituberculotic, anti-cyanobacterial, antifungal, antibacterial, antiviral, insecticidal, and antiprotozoal activities are discussed.

Synthetic Rhamnolipid Bolaforms trigger an innate immune response in Arabidopsis thaliana

Stimulation of plant innate immunity by natural and synthetic elicitors is a promising alternative to conventional pesticides for a more sustainable agriculture. Sugar-based bolaamphiphiles are known for their biocompatibility, biodegradability and low toxicity. In this work, we show that Synthetic Rhamnolipid Bolaforms (SRBs) that have been synthesized by green chemistry trigger Arabidopsis innate immunity. Using structure-function analysis, we demonstrate that SRBs, depending on the acyl chain length, differentially activate early and late immunity-related plant defense responses and provide local increase in resistance to plant pathogenic bacteria. Our biophysical data suggest that SRBs can interact with plant biomimetic plasma membrane and open the possibility of a lipid driven process for plant-triggered immunity by SRBs.

Identification of Pseudomonas mosselii BS011 gene clusters required for suppression of Rice Blast Fungus Magnaporthe oryzae

Pseudomonas is a Gram-negative, rod-shaped bacteria. Many members of this genus displayed remarkable physiological and metabolic activity against different plant pathogens. However, Pseudomonas mosselii has not yet been characterized in biocontrol against plant disease. Here we isolated a strain of P. mosselii BS011 from the rhizosphere soil of rice plants, and the isolate showed strong inhibitory activity against the rice blast fungus Magnaporthe oryzae. Further we sequenced the complete genome of BS011, which consist of 5.75 Mb with a circular chromosome, 5,170 protein-coding genes, 23 rRNA and 78 tRNA operons. Bioinformatic analysis revealed that seven gene clusters may be involved in the biosynthesis of metabolites. Gene deletion experiments demonstrated that the gene cluster c-xtl is required for inhibitory activity against M. oryzae. Bioassay showed that the crude extract from BS011 fermentation sample significantly inhibited the development of M. oryzae at a concentration of 10 μg/ml. Besides, we illustrated that the crude extract of BS011 impaired the appressorial formation in a dose dependent manner. Collectively our results revealed that P. mosselii BS011 is a promising biocontrol agent and the gene cluster c-xtl is essential for inhibiting the development of M. oryzae.

Plipastatin A1 produced by a marine sediment-derived Bacillus amyloliquefaciens SH-B74 contributes to the control of gray mold disease in tomato

Certain Bacillus species have the capacity to produce cyclic lipopeptides and these lipopeptides are promising determinants contributing to the biocontrol of plant diseases. In the current study, a cyclic lipopeptide plipastatin A1 was isolated from the fermentation broth of a marine sediment-derived Bacillus amyloliquefaciens SH-B74 by the combination of solid-phase extraction and reversed-phase high-performance liquid chromatography, and its structure was identified by tandem mass spectrometry, high-resolution electro-spray ionization mass spectrometry, and gas chromatography-mass spectrometry together with nuclear magnetic resonance analysis. Moreover, data from activity evaluation revealed that plipastatin A1 has excellent in vitro activity on the suppression of the conidia germination of B. cinerea, the causal agent of gray mold disease in tomato. Furthermore, plipastatin A1 can successfully decrease the incidence of gray mold disease on tomato leaves at 50 µM concentration. This study indicates that B. amyloliquefaciens SH-B74 appears to be a potentially sustainable pesticide to control gray mold disease in tomato plants, and its cyclic lipopeptide plipastatin A1 plays an important role in the in vitro and in planta biocontrol of B. cinerea.

Antagonistic bacteria disrupt calcium homeostasis and immobilize algal cells

Photosynthetic unicellular organisms, known as microalgae, are key contributors to carbon fixation on Earth. Their biotic interactions with other microbes shape aquatic microbial communities and influence the global photosynthetic capacity. So far, limited information is available on molecular factors that govern these interactions. We show that the bacterium Pseudomonas protegens strongly inhibits the growth and alters the morphology of the biflagellated green alga Chlamydomonas reinhardtii. This antagonistic effect is decreased in a bacterial mutant lacking orfamides, demonstrating that these secreted cyclic lipopeptides play an important role in the algal-bacterial interaction. Using an aequorin Ca²⁺-reporter assay, we show that orfamide A triggers an increase in cytosolic Ca²⁺ in C. reinhardtii and causes deflagellation of algal cells. These effects of orfamide A, which are specific to the algal class of Chlorophyceae and appear to target a Ca²⁺ channel in the plasma membrane, represent a novel biological activity for cyclic lipopeptides.

The cyclic lipopeptide orfamide induces systemic resistance in rice to Cochliobolus miyabeanus but not to Magnaporthe oryzae

The Pseudomonas- derived cyclic lipopeptide orfamide can induce resistance to Cochliobolus miyabeanus but not to Magnaporthe oryzae in rice. Abscisic acid signaling is involved in the induced systemic resistance response triggered by orfamide. Diverse natural products produced by beneficial Pseudomonas species have the potential to trigger induced systemic resistance (ISR) in plants, and thus may contribute to control of diseases in crops. Some beneficial Pseudomonas spp. can produce cyclic lipopeptides (CLPs), amphiphilic molecules composed of a fatty acid tail linked to an oligopeptide which is cyclized. CLPs can have versatile biological functions, but the capacity of Pseudomonas-derived CLPs in triggering ISR responses has barely been studied. Pseudomonas protegens and related species can produce orfamide-type CLPs. Here we show that in rice, orfamides can act as ISR elicitors against the necrotrophic fungus Cochliobolus miyabeanus, the causal agent of brown spot disease, but are not active against the blast fungus Magnaporthe oryzae. Orfamide A can trigger early defensive events and activate transcripts of defense-related genes in rice cell suspension cultures, but does not cause cell death. Further testing in rice cell suspension cultures and rice plants showed that abscisic acid signaling, the transcriptional activator OsWRKY4 and pathogenesis-related protein PR1b are triggered by orfamide A and may play a role in the ISR response against C. miyabeanus.

A matter of hierarchy: activation of orfamide production by the post-transcriptional Gac-Rsm cascade of Pseudomonas protegens CHA0 through expression upregulation of the two dedicated transcriptional regulators

In this work, we surveyed the genome of P. protegens CHA0 in order to identify novel mRNAs possibly under the control of the Gac-Rsm cascade that might, for their part, serve to elucidate as-yet-unknown functions involved in the biocontrol of plant pathogens and/or in cellular processes required for fitness in natural environments. In view of the experimental evidence from former studies on the Gac-Rsm cascade, we developed a computational screen supported by a combination of sequence, structural and evolutionary constraints that led to a dataset of 43 potential novel mRNA targets. We then confirmed several mRNA targets experimentally and next focused on two of the respective genes that are physically linked to the orfamide biosynthetic gene cluster and whose predicted open-reading frames resembled cognate LuxR-type transcriptional regulators of cyclic lipopeptide clusters in related pseudomonads. In this report, we demonstrate that in strain CHA0, orfamide production is stringently dependent on a functional Gac-Rsm cascade and that both mRNAs encoding transcriptional regulatory proteins are under direct translational control of the RsmA/E proteins. Our results have thus revealed a hierarchical control over the expression of orfamide biosynthetic genes with the final transcriptional control subordinated to the global Gac-Rsm post-transcriptional regulatory system.

Let the Core Microbiota Be Functional

The microbial community that is systematically associated with a given host plant is called the core microbiota. The definition of the core microbiota was so far based on its taxonomic composition, but we argue that it should also be based on its functions. This so-called functional core microbiota encompasses microbial vehicles carrying replicators (genes) with essential functions for holobiont (i.e., plant plus microbiota) fitness. It builds up from enhanced horizontal transfers of replicators as well as from ecological enrichment of their vehicles. The transmission pathways of this functional core microbiota vary over plant generations according to environmental constraints and its added value for holobiont fitness.

Coregulation of the cyclic lipopeptides orfamide and sessilin in the biocontrol strain Pseudomonas sp. CMR12a

Cyclic lipopeptides (CLPs) are synthesized by nonribosomal peptide synthetases (NRPS), which are often flanked by LuxR‐type transcriptional regulators. Pseudomonas sp. CMR12a, an effective biocontrol strain, produces two different classes of CLPs namely sessilins and orfamides. The orfamide biosynthesis gene cluster is flanked up‐ and downstream by LuxR‐type regulatory genes designated ofaR1 and ofaR2, respectively, whereas the sessilin biosynthesis gene cluster has one LuxR‐type regulatory gene which is situated upstream of the cluster and is designated sesR. Our study investigated the role of these three regulators in the biosynthesis of orfamides and sessilins. Phylogenetic analyses positioned OfaR1 and OfaR2 with LuxR regulatory proteins of similar orfamide‐producing Pseudomonas strains and the SesR with that of the tolaasin producer, Pseudomonas tolaasii. LC‐ESI‐MS analyses revealed that sessilins and orfamides are coproduced and that production starts in the late exponential phase. However, sessilins are secreted earlier and in large amounts, while orfamides are predominantly retained in the cell. Deletion mutants in ofaR1 and ofaR2 lost the capacity to produce both orfamides and sessilins, whereas the sesR mutant showed no clear phenotype. Additionally, RT‐PCR analysis showed that in the sessilin cluster, a mutation in either ofaR1 or ofaR2 led to weaker transcripts of the biosynthesis genes, sesABC, and putative transporter genes, macA1B1. In the orfamide cluster, mainly the biosynthesis genes ofaBC were affected, while the first biosynthesis gene ofaA and putative macA2B2 transport genes were still transcribed. A mutation in either ofaR1, ofaR2, or sesR genes did not abolish the transcription of any of the other two.

Antimicrobial and Insecticidal: Cyclic Lipopeptides and Hydrogen Cyanide Produced by Plant-Beneficial Pseudomonas Strains CHA0, CMR12a, and PCL1391 Contribute to Insect Killing

Particular groups of plant-beneficial fluorescent pseudomonads are not only root colonizers that provide plant disease suppression, but in addition are able to infect and kill insect larvae. The mechanisms by which the bacteria manage to infest this alternative host, to overcome its immune system, and to ultimately kill the insect are still largely unknown. However, the investigation of the few virulence factors discovered so far, points to a highly multifactorial nature of insecticidal activity. Antimicrobial compounds produced by fluorescent pseudomonads are effective weapons against a vast diversity of organisms such as fungi, oomycetes, nematodes, and protozoa. Here, we investigated whether these compounds also contribute to insecticidal activity. We tested mutants of the highly insecticidal strains Pseudomonas protegens CHA0, Pseudomonas chlororaphis PCL1391, and Pseudomonas sp. CMR12a, defective for individual or multiple antimicrobial compounds, for injectable and oral activity against lepidopteran insect larvae. Moreover, we studied expression of biosynthesis genes for these antimicrobial compounds for the first time in insects. Our survey revealed that hydrogen cyanide and different types of cyclic lipopeptides contribute to insecticidal activity. Hydrogen cyanide was essential to full virulence of CHA0 and PCL1391 directly injected into the hemolymph. The cyclic lipopeptide orfamide produced by CHA0 and CMR12a was mainly important in oral infections. Mutants of CMR12a and PCL1391 impaired in the production of the cyclic lipopeptides sessilin and clp1391, respectively, showed reduced virulence in injection and feeding experiments. Although virulence of mutants lacking one or several of the other antimicrobial compounds, i.e., 2,4-diacetylphloroglucinol, phenazines, pyrrolnitrin, or pyoluteorin, was not reduced, these metabolites might still play a role in an insect background since all investigated biosynthetic genes for antimicrobial compounds of strain CHA0 were expressed at some point during insect infection. In summary, our study identified new factors contributing to insecticidal activity and extends the diverse functions of antimicrobial compounds produced by fluorescent pseudomonads from the plant environment to the insect host.