Mass Spectrometry Uncovers the Role of Surfactin as an Interspecies Recruitment Factor

Bacillus lipopeptides as key players in rhizosphere chemical ecology

Microbial natural products are widely explored for their therapeutic potential. Understanding the underlying evolutionary and adaptive forces driving their production remains a fundamental question in biology. Amphiphilic cyclic lipopeptides (CLPs), a prominent category of bacterial specialized metabolites, show strong antimicrobial activity, particularly against phytopathogens. It is thus assumed that these compounds are deployed by soil- or rhizosphere-dwelling bacteria as microbial weapons in competitive natural environments. Here, we challenge this reductionist perspective and present evidence that Bacillus CLPs are prominent chemical mediators of ecological interactions. They help Bacillus to communicate, compete, defend against predators, or cooperate and establish mutualistic relationships with other (micro)organisms. Additional parallel examples are highlighted in other genera, such as Pseudomonas. This broader perspective underscores the need for further investigation into the role of CLPs in shaping the adaptive strategies of key rhizobacterial species.

Optimisation of surfactin yield in Bacillus using data-efficient active learning and high-throughput mass spectrometry

Integration of machine learning and high throughput measurements are essential to drive the next generation of the design-build-test-learn (DBTL) cycle in synthetic biology. Here, we report the use of active learning in combination with metabolomics for optimising production of surfactin, a complex lipopeptide resulting from a non-ribosomal assembly pathway. We designed a media optimisation algorithm that iteratively learns the yield landscape and steers the media composition toward maximal production. The algorithm led to a 160 % yield increase after three DBTL runs as compared to an M9 baseline. Metabolomics data helped to elucidate the underpinning biochemistry for yield improvement and revealed Pareto-like trade-offs in production of other lipopeptides from related pathways. We found positive associations between organic acids and surfactin, suggesting a key role of central carbon metabolism, as well as system-wide anisotropies in how metabolism reacts to shifts in carbon and nitrogen levels. Our framework offers a novel data-driven approach to improve yield of biological products with complex synthesis pathways that are not amenable to traditional yield optimisation strategies.

Common operational issues and possible solutions for sustainable biosurfactant production from lignocellulosic feedstock

Surfactants are compounds with high surface activity and emulsifying property. These compounds find application in food, medical, pharmaceutical, and petroleum industries, as well as in agriculture, bioremediation, cleaning, cosmetics, and personal care product formulations. Due to their widespread use and environmental persistence, ensuring biodegradability and sustainability is necessary so as not to harm the environment. Biosurfactants, i.e., surfactants of plant or microbial origin produced from lignocellulosic feedstock, perform better than their petrochemically derived counterparts on the scale of net-carbon-negativity. Although many biosurfactants are commercially available, their high cost of production justifies their application only in expensive pharmaceuticals and cosmetics. Besides, the annual number of new biosurfactant compounds reported is less, compared to that of chemical surfactants. Multiple operational issues persist in the biosurfactant value chain. In this review, we have categorized some of these issues based on their relative position in the value chain - hurdles occurring during planning, upstream processes, production stage, and downstream processes - alongside plausible solutions. Moreover, we have presented the available paths forward for this industry in terms of process development and integrated pretreatment, combining conventional tried-and-tested strategies, such as reactor designing and statistical optimization with cutting-edge technologies including metabolic modeling and artificial intelligence. The development of techno-economically feasible biosurfactant production processes would be instrumental in the complete substitution of petrochemical surfactants, rather than mere supplementation.

Lipopeptides as rhizosphere public goods for microbial cooperation

IMPORTANCE

Here, we provide new insights into the possible fate of cyclic lipopeptides as prominent specialized metabolites from beneficial bacilli and pseudomonads once released in the soil. Our data illustrate how the B. velezensis lipopeptidome may be enzymatically remodeled by Streptomyces as important members of the soil bacterial community. The enzymatic arsenal of S. venezuelae enables an unsuspected extensive degradation of these compounds, allowing the bacterium to feed on these exogenous products via a mechanism going beyond linearization, which was previously reported as a detoxification strategy. As soils are carbon-rich and nitrogen-poor environments, we propose a new role for cyclic lipopeptides in interspecies interactions, which is to fuel the nitrogen metabolism of a part of the rhizosphere microbial community. Streptomyces and other actinomycetes, producing numerous peptidases and displaying several traits of beneficial bacteria, should be at the front line to directly benefit from these metabolites as "public goods" for microbial cooperation.

MALDI Mass Spectrometry Imaging: A Potential Game-Changer in a Modern Microbiology

Nowadays, matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS) is routinely implemented as the reference method for the swift and straightforward identification of microorganisms. However, this method is not flawless and there is a need to upgrade the current methodology in order to free the routine lab from incubation time and shift from a culture-dependent to an even faster independent culture system. Over the last two decades, mass spectrometry imaging (MSI) gained tremendous popularity in life sciences, including microbiology, due to its ability to simultaneously detect biomolecules, as well as their spatial distribution, in complex samples. Through this literature review, we summarize the latest applications of MALDI-MSI in microbiology. In addition, we discuss the challenges and avenues of exploration for applying MSI to solve current MALDI-TOF MS limits in routine and research laboratories.

The Exploration of Microbial Natural Products and Metabolic Interaction Guided by Mass Spectrometry Imaging

As an impressive mass spectrometry technology, mass spectrometric imaging (MSI) can provide mass spectra data and spatial distribution of analytes simultaneously. MSI has been widely used in diverse fields such as clinical diagnosis, the pharmaceutical industry and environmental study due to its accuracy, high resolution and developing reproducibility. Natural products (NPs) have been a critical source of leading drugs; almost half of marketed drugs are derived from NPs or their derivatives. The continuous search for bioactive NPs from microorganisms or microbiomes has always been attractive. MSI allows us to analyze and characterize NPs directly in monocultured microorganisms or a microbial community. In this review, we briefly introduce current mainstream ionization technologies for microbial samples and the key issue of sample preparation, and then summarize some applications of MSI in the exploration of microbial NPs and metabolic interaction, especially NPs from marine microbes. Additionally, remaining challenges and future prospects are discussed.

Bacillus for Plant Growth Promotion and Stress Resilience: What Have We Learned?

The rhizosphere is a thin film of soil that surrounds plant roots and the primary location of nutrient uptake, and is where important physiological, chemical, and biological activities are occurring. Many microbes invade the rhizosphere and have the capacity to promote plant growth and health. Bacillus spp. is the most prominent plant growth promoting rhizobacteria due to its ability to form long-lived, stress-tolerant spores. Bacillus-plant interactions are driven by chemical languages constructed by a wide spectrum of metabolites and lead to enhanced plant growth and defenses. Thus, this review is a synthesis and a critical assessment of the current literature on the application of Bacillus spp. in agriculture, highlighting gaps that remain to be explored to improve and expand on the Bacillus-based biostimulants. Furthermore, we suggest that omics sciences, with a focus on metabolomics, offer unique opportunities to illuminate the chemical intercommunications between Bacillus and plants, to elucidate biochemical and molecular details on modes of action of Bacillus-based formulations, to generate more actionable insights on cellular and molecular events that explain the Bacillus-induced growth promotion and stress resilience in plants.

Extracts from Environmental Strains of Pseudomonas spp. Effectively Control Fungal Plant Diseases

The use of synthetic chemical products in agriculture is causing severe damage to the environment and human health, but agrochemicals are still widely used to protect our crops. To counteract this trend, we have been looking for alternative strategies to control plant diseases without causing harm to the environment or damage to our health. However, these alternatives are still far from completely replacing chemical products. Microorganisms have been widely known as a biological tool to control plant diseases, but their use is still limited due to the high variability in their efficacy, together with issues in product registration. However, the metabolites produced by these microorganisms can represent a novel tool for the environment-friendly management of plant diseases, while reducing the issues mentioned above. In this study, we explore the soil microbial diversity in natural systems to look for microorganisms with the potential to be used in pre- and post-harvest protection against fungal plant pathogens. Using a simple workflow, we isolated 22 bacterial strains that were tested both in vitro and in vivo for their ability to counteract the growth of common plant pathogens. The three best isolates, identified as members of the bacterial genus Pseudomonas, were used to produce a series of alcoholic extracts, which were then tested for their action against plant pathogens in simulated real-world applications. Results show that extracts from these isolates have an exceptional biocontrol activity and can be successfully used to control plant pathogens in operational setups. Thus, this study shows that the environmental microbiome is an important source of microorganisms producing metabolites that might provide an alternative strategy to synthetic chemical products.

Mass Spectral Molecular Networking to Profile the Metabolome of Biostimulant Bacillus Strains

Beneficial soil microbes like plant growth-promoting rhizobacteria (PGPR) significantly contribute to plant growth and development through various mechanisms activated by plant-PGPR interactions. However, a complete understanding of the biochemistry of the PGPR and microbial intraspecific interactions within the consortia is still enigmatic. Such complexities constrain the design and use of PGPR formulations for sustainable agriculture. Therefore, we report the application of mass spectrometry (MS)-based untargeted metabolomics and molecular networking (MN) to interrogate and profile the intracellular chemical space of PGPR Bacillus strains: B. laterosporus, B. amyloliquefaciens, B. licheniformis 1001, and B. licheniformis M017 and their consortium. The results revealed differential and diverse chemistries in the four Bacillus strains when grown separately, and also differing from when grown as a consortium. MolNetEnhancer networks revealed 11 differential molecular families that are comprised of lipids and lipid-like molecules, benzenoids, nucleotide-like molecules, and organic acids and derivatives. Consortium and B. amyloliquefaciens metabolite profiles were characterized by the high abundance of surfactins, whereas B. licheniformis strains were characterized by the unique presence of lichenysins. Thus, this work, applying metabolome mining tools, maps the microbial chemical space of isolates and their consortium, thus providing valuable insights into molecular information of microbial systems. Such fundamental knowledge is essential for the innovative design and use of PGPR-based biostimulants.

Lipopeptide Interplay Mediates Molecular Interactions between Soil Bacilli and Pseudomonads

Some Bacillus species, such as B. velezensis, are important members of the plant-associated microbiome, conferring protection against phytopathogens. However, our knowledge about multitrophic interactions determining the ecological fitness of these biocontrol bacteria in the competitive rhizosphere niche is still limited. Here, we investigated molecular mechanisms underlying interactions between B. velezensis and Pseudomonas as a soil-dwelling competitor. Upon their contact-independent in vitro confrontation, a multifaceted macroscopic outcome was observed and characterized by Bacillus growth inhibition, white line formation in the interaction zone, and enhanced motility. We correlated these phenotypes with the production of bioactive secondary metabolites and identified specific lipopeptides as key compounds involved in the interference interaction and motile response. Bacillus mobilizes its lipopeptide surfactin not only to enhance motility but also to act as a chemical trap to reduce the toxicity of lipopeptides formed by Pseudomonas. We demonstrated the relevance of these unsuspected roles of lipopeptides in the context of competitive tomato root colonization by the two bacterial genera.

IMPORTANCE Plant-associated Bacillus velezensis and Pseudomonas spp. represent excellent model species as strong producers of bioactive metabolites involved in phytopathogen inhibition and the elicitation of plant immunity. However, the ecological role of these metabolites during microbial interspecies interactions and the way their expression may be modulated under naturally competitive soil conditions has been poorly investigated. Through this work, we report various phenotypic outcomes from the interactions between B. velezensis and 10 Pseudomonas strains used as competitors and correlate them with the production of specific metabolites called lipopeptides from both species. More precisely, Bacillus overproduces surfactin to enhance motility, which also, by acting as a chemical trap, reduces the toxicity of other lipopeptides formed by Pseudomonas. Based on data from interspecies competition on plant roots, we assume this would allow Bacillus to gain fitness and persistence in its natural rhizosphere niche. The discovery of new ecological functions for Bacillus and Pseudomonas secondary metabolites is crucial to rationally design compatible consortia, more efficient than single-species inoculants, to promote plant health and growth by fighting economically important pathogens in sustainable agriculture.

Reproducible molecular networking of untargeted mass spectrometry data using GNPS

Global Natural Product Social Molecular Networking (GNPS) is an interactive online small molecule-focused tandem mass spectrometry (MS2) data curation and analysis infrastructure. It is intended to provide as much chemical insight as possible into an untargeted MS2 dataset and to connect this chemical insight to the user's underlying biological questions. This can be performed within one liquid chromatography (LC)-MS2 experiment or at the repository scale. GNPS-MassIVE is a public data repository for untargeted MS2 data with sample information (metadata) and annotated MS2 spectra. These publicly accessible data can be annotated and updated with the GNPS infrastructure keeping a continuous record of all changes. This knowledge is disseminated across all public data; it is a living dataset. Molecular networking-one of the main analysis tools used within the GNPS platform-creates a structured data table that reflects the molecular diversity captured in tandem mass spectrometry experiments by computing the relationships of the MS2 spectra as spectral similarity. This protocol provides step-by-step instructions for creating reproducible, high-quality molecular networks. For training purposes, the reader is led through a 90- to 120-min procedure that starts by recalling an example public dataset and its sample information and proceeds to creating and interpreting a molecular network. Each data analysis job can be shared or cloned to disseminate the knowledge gained, thus propagating information that can lead to the discovery of molecules, metabolic pathways, and ecosystem/community interactions.

Structure, properties, and biological functions of nonribosomal lipopeptides from pseudomonads

Bacteria of the genusPseudomonasdisplay a fascinating metabolic diversity. In this review, we focus our attention on the natural product class of nonribosomal lipopeptides, which help pseudomonads to colonize a wide range of ecological niches.

Crossroads of Antibiotic Resistance and Biosynthesis

The biosynthesis of antibiotics and self-protection mechanisms employed by antibiotic producers are an integral part of the growing antibiotic resistance threat. The origins of clinically relevant antibiotic resistance genes found in human pathogens have been traced to ancient microbial producers of antibiotics in natural environments. Widespread and frequent antibiotic use amplifies environmental pools of antibiotic resistance genes and increases the likelihood for the selection of a resistance event in human pathogens. This perspective will provide an overview of the origins of antibiotic resistance to highlight the crossroads of antibiotic biosynthesis and producer self-protection that result in clinically relevant resistance mechanisms. Some case studies of synergistic antibiotic combinations, adjuvants, and hybrid antibiotics will also be presented to show how native antibiotic producers manage the emergence of antibiotic resistance.