Microbial metabolomics: essential definitions and the importance of cultivation conditions for utilizingBacillusspecies as bionematicides

Microbial natural compounds and secondary metabolites as Immunomodulators: A review

Immunomodulatory therapies are beneficial strategies for the improvement of immune system function. Today, due to the increasing prevalence of immune disorders, cancer, and new viral diseases, there is a greater need to introduce immunomodulatory compounds with more efficiency and fewer side effects. Microbial derivatives are fertile and attractive grounds for discovering lots of novel compounds with various medical properties. The discovery of many natural compounds derived from bacterial sources, such as secondary metabolites with promising immunomodulating activities, represents the importance of this topic in drug discovery and emphasizes the necessity for a coherent source of study in this area. Considering this need, in this review, we aim to focus on the current information about the immunomodulatory effects of bacterial secondary metabolites and natural immunomodulators derived from microorganisms.

Towards Reducing Food Wastage: Analysis of Degradation Products Formed during Meat Spoilage under Different Conditions

Foodstuffs, particularly perishable ones such as meat, are frequently discarded once the best-before date has been reached, despite the possibility of their continued suitability for human consumption. The implementation of intelligent packaging has the potential to contribute to a reduction in food wastage by enabling the monitoring of meat freshness during storage time independently of the best-before date. The process of meat spoilage is associated with the formation of specific degradation products, some of which can be potentially utilized as spoilage indicators in intelligent packaging. The aim of the review is to identify degradation products whose concentration correlates with meat shelf life and to evaluate their potential use as spoilage indicators in intelligent packaging. To this end, a comprehensive literature research was conducted to identify the factors influencing meat spoilage and the eight key degradation products (carboxylic acids, biogenic amines, total volatile basic nitrogen, aldehydes, alcohols, ketones, sulfur compounds, and esters) associated with this process. These degradation products were analyzed for their correlation with meat shelf life at different temperatures, atmospheres, and meat types and for their applicability in intelligent packaging. The review provides an overview of these degradation products, comparing their potential to indicate spoilage across different meat types and storage conditions. The findings suggest that while no single degradation product universally indicates spoilage across all meat types and conditions, compounds like carboxylic acids, biogenic amines, and volatile basic nitrogen warrant further investigation. The review elucidates the intricacies inherent in identifying a singular spoilage indicator but underscores the potential of combining specific degradation products to expand the scope of applications in intelligent packaging. Further research (e.g., storage tests in which the concentrations of these substances are specifically examined or research on which indicator substance responds to these degradation products) is recommended to explore these combinations with a view to broadening their applicability.

Biocontrol manufacturing and agricultural applications of Bacillus velezensis

Many microorganisms have been reported as bioagents for producing ecofriendly, cost-effective, and safe products. Some Bacillus species of bacteria can be used in agricultural applications. Bacillus velezensis in particular has shown promising results for controlling destructive phytopathogens and in biofungicide manufacturing. Some B. velezensis strains can promote plant growth and display antibiotic activities against plant pathogen agents. In this review, we focus on the often-overlooked potential properties of B. velezensis as a bioagent for applications that will extend beyond the traditional agricultural uses. We delve into its versatility and future prospects, the challenges such uses may encounter, and some drawbacks associated with B. velezensis-based products.

Biocontrol of plant parasitic nematodes by bacteria and fungi: a multi-omics approach for the exploration of novel nematicides in sustainable agriculture

Plant parasitic nematodes (PPNs) pose a significant threat to global crop productivity, causing an estimated annual loss of US $157 billion in the agriculture industry. While synthetic chemical nematicides can effectively control PPNs, their overuse has detrimental effects on human health and the environment. Biocontrol agents (BCAs), such as bacteria and fungi in the rhizosphere, are safe and promising alternatives for PPNs control. These BCAs interact with plant roots and produce extracellular enzymes, secondary metabolites, toxins, and volatile organic compounds (VOCs) to suppress nematodes. Plant root exudates also play a crucial role in attracting beneficial microbes toward infested roots. The complex interaction between plants and microbes in the rhizosphere against PPNs is mostly untapped which opens new avenues for discovering novel nematicides through multi-omics techniques. Advanced omics approaches, including metagenomics, transcriptomics, proteomics, and metabolomics, have led to the discovery of nematicidal compounds. This review summarizes the status of bacterial and fungal biocontrol strategies and their mechanisms for PPNs control. The importance of omics-based approaches for the exploration of novel nematicides and future directions in the biocontrol of PPNs are also addressed. The review highlighted the potential significance of multi-omics techniques in biocontrol of PPNs to ensure sustainable agriculture.

Complete genome sequence of Bacillus velezensis strain Ag109, a biocontrol agent against plant-parasitic nematodes and Sclerotinia sclerotiorum

Soybean is the main oilseed cultivated worldwide. Even though Brazil is the world's largest producer and exporter of soybean, its production is severely limited by biotic factors. Soil borne diseases are the most damaging biotic stressors since they significantly reduce yield and are challenging to manage. In this context, the present study aimed to evaluate the potential of a bacterial strain (Ag109) as a biocontrol agent for different soil pathogens (nematodes and fungi) of soybean. In addition, the genome of Ag109 was wholly sequenced and genes related to secondary metabolite production and plant growth promotion were mined. Ag109 showed nematode control in soybean and controlled 69 and 45% of the populations of Meloidogyne javanica and Pratylenchus brachyurus, respectively. Regarding antifungal activity, these strains showed activity against Macrophomia phaseolina, Rhizoctonia solani, and Sclerotinia sclerotiorum. For S. sclerotiorum, this strain increased the number of healthy plants and root dry mass compared to the control (with inoculation). Based on the average nucleotide identity and digital DNA-DNA hybridization, this strain was identified as Bacillus velezensis. Diverse clusters of specific genes related to secondary metabolite biosynthesis and root growth promotion were identified, highlighting the potential of this strain to be used as a multifunctional microbial inoculant that acts as a biological control agent while promoting plant growth in soybean.

Redefining bioactive small molecules from microbial metabolites as revolutionary anticancer agents

Cancer treatment remains a significant challenge due to issues such as acquired resistance to conventional therapies and the occurrence of adverse treatment-related toxicities. In recent years, researchers have turned their attention to the microbial world in search of novel and effective drugs to combat this devastating disease. Microbial derived secondary metabolites have proven to be a valuable source of biologically active compounds, which exhibit diverse functions and have demonstrated potential as treatments for various human diseases. The exploration of these compounds has provided valuable insights into their mechanisms of action against cancer cells. In-depth studies have been conducted on clinically established microbial metabolites, unraveling their anticancer properties, and shedding light on their therapeutic potential. This review aims to comprehensively examine the anticancer mechanisms of these established microbial metabolites. Additionally, it highlights the emerging therapies derived from these metabolites, offering a glimpse into the immense potential they hold for anticancer drug discovery. Furthermore, this review delves into approved treatments and major drug candidates currently undergoing clinical trials, focusing on specific molecular targets. It also addresses the challenges and issues encountered in the field of anticancer drug research and development. It also presents a comprehensive exposition of the contemporary panorama concerning microbial metabolites serving as a reservoir for anticancer agents, thereby illuminating their auspicious prospects and the prospect of forthcoming strides in the domain of cancer therapeutics.

Influence of medium modifications (optimization) on high nematicidal activity of the fermentation broth of Clostridium beijerinckii

Introduction: The nematode species Meloidogyne incognita has been responsible for significant financial losses within the agricultural sector. Nematophagous bacteria, characterised by their extensive distribution and broad spectrum of hosts, exhibit remarkable efficacy as natural antagonists against nematodes. Sneb518 (Clostridium beijerinckii) fermentation broth displayed substantial biocontrol activity against M. incognita in previous research. Optimizing fermentation conditions is a fundamental technique for dramatically enhancing end product performance. There has been no such study conducted yet on enhancing the nematicidal activities of Sneb518 (Clostridium beijerinckii) fermentation using response surface methodology (RSM). Methods: The influence of strain Sneb518 fermentation media and conditions on nematicidal activity was examined using the three-factor technique and a Plackett-Burman design, and the interaction between various fermentation factors was examined using a Box-Behnken design. The present study employed response surface methodology (RSM) to examine and enhance the nematicidal activity of Sneb518 culture filtrates by identifying and optimising the influential components. Results: Glucose, peanut cake flour, and potassium chloride as carbon, nitrogen, and inorganic salts displayed considerably increased nematicidal potential in the present study. Furthermore, the corrected mortality of J2 ranged from 52.24% to 91.15% when utilizing the Box-Behnken design. These findings clearly support the application of RSM for medium optimization. Moreover, the outcomes of the validation experiment corresponded to the model predictions. Discussion: This research has enhanced the biocontrol ability of C. beijerinckii to control M. incognita and this research has led to the advancement of new biocontrol agents.

Biocontrol Efficacy of Bacillus methylotrophicus TA-1 Against Meloidogyne incognita in Tomato

Root-knot nematodes (RKNs) are harmful plant-parasitic nematodes of tomatoes which can cause significant yield losses. Therefore, there is increasing interest in exploring the application of bacterial nematicides. The bacterium Bacillus methylotrophicus TA-1 is a broad-spectrum biological control agent; however, its effect on RKNs control remains largely unclear. In this study, the toxicity of B. methylotrophicus TA-1 against Meloidogyne incognita was investigated in vitro, and the potential of B. methylotrophicus TA-1 to decrease infection of RKNs in tomato were evaluated in pot and field trials. Results showed that B. methylotrophicus TA-1 exhibited high nematicidal activity against second-stage juveniles (J2s) and eggs of M. incognita with 50% lethal concentration (LC50) values of 5.80 and 7.00 × 108 colony forming units (CFU)/ml, respectively. In the pot experiments and field trials conducted in 2020 and 2021, tomato plants treated with B. methylotrophicus TA-1 soil drench applied once at 3, 6, and 9 × 108 CFU/plant had significantly higher plant height and greater yield compared with the untreated control. Tomato yields of the treated plots with B. methylotrophicus TA-1 in 2 consecutive years' field trials were between 53.4 to 66.1 and 52.8 to 61.5 t/ha, while they were 49.7 and 48.2 t/ha in the untreated control for each year, respectively. The lowest population densities of M. incognita at 30 and 60 days after treatment were 119 and 135 J2s per 100 g soil in 2020 and 43 and 118 J2s in 2021 in TA-1-treated plots. The lowest gall index of 4.7 and 3.3 in 2020 and 2021, respectively, and the highest yield were all observed in the TA-1 at 9 × 108 CFU/plant treated plants, with no significant differences with the commercial control abamectin. These results provided a basis for further studies of B. methylotrophicus TA-1 formulations, application doses, frequencies, and mechanisms of action, which are necessary before it could be used as a component of integrated management programs to manage RKNs in tomato production.

Native Bacillus paralicheniformis isolate as a potential agent for phytopathogenic nematodes control

Phytopathogenic nematodes (PPNs) are responsible for substantial damages within agricultural crops worldwide which can be controlled employing beneficial microorganisms and/or their metabolites in an ecofriendly way. Nevertheless, the success of the control regards not only on the virulence of the strains or the toxicity of their metabolites but also on their ability to colonize and remain in the rhizospheric environment, particularly in those crops affected by abiotic stresses promoted by the climate change. Consequently, the bioprospection of beneficial microorganisms able to control PPNs and to thrive in adverse conditions has attracted attention. On this way, deserts are perfect ecological niches to isolate microorganisms adapted to harsh enviroments. The purpose of this research was to isolate and characterize bacteria from rhizospheric soil samples collected in the Northwestern Desert of Mexico with potential for PPNs control. As first screening, secretomes of each isolate were tested in vitro for nematicidal activity (NA). Then, activities from secretomes and endospores from the selected isolate were confirmed in vivo assays. From 100 thermotolerant isolates, the secretome of the isolate identified as Bacillus paralicheniformis TB197 showed the highest NA (>95%) against Meloidogyne incognita, both in vitro and in vivo tests, suppressing infections caused by M. enterolobii in tomato crops, too. In open field tests, the endospores of TB197 strain showed a reduction of 81% in the infection severity caused by M. enterolobii (p ≤ 0.05), while the galling index (GI) was reduced 84% (p ≤ 0.05) in tomato greenhouse-tests. Also, a reduction of the root necrosis (81%) caused by Radopholus similis in banana plantations (p ≤ 0.05), compared to the control was observed. Owing to their efficacy in controlling PPNs infections, the endospores and secondary metabolites of B. paralicheniformis TB197 strain could be used in bionematicidal formulations.

Antibacterial activity of epsilon-poly-l-lysine produced by Stenotrophomonas maltophilia HS4 and Paenibacillus polymyxa HS5, alone and in combination with bacteriophages

Over the past decades, antibiotic resistance has become a major clinical problem, and searching for new therapeutic strategies seems to be necessary. Using novel natural compounds, antimicrobial peptides, and bacteriophages is the most promising solution. In this study, various cationic metabolite-producer bacteria were isolated from different soil samples. Two isolates were identified as Stenotrophomonas maltophilia HS4 (accession number: MW791428) and Paenibacillus polymyxa HS5 (accession number: MW791430) based on biochemical characteristics and phylogenetic analysis using 16S rRNA gene sequences. The cationic compound in the fermentation broth was precipitated and purified with sodium tetraphenylborate salt. The purified cationic peptide was confirmed to be epsilon-poly-l-lysine by structural and molecular analysis using High-Performance Liquid Chromatography, Sodium dodecyl-sulfate-polyacrylamide gel electrophoresis, and Fourier-transform infrared spectroscopy. The antibacterial activity of epsilon-poly-l-lysine was evaluated against Staphylococcus aureus ATCC 25923, Escherichia coli ATCC 25922, Enterococcus faecalis ATCC 29212, Serratia marcescens ATCC 13880, and Klebsiella pneumoniae ATCC 13883 by microdilution method. Furthermore, the antibacterial effects of purified epsilon-poly-l-lysine in combination with two long non-contractile tail bacteriophages against vancomycin-resistant Enterococcus faecalis and colistin-resistant Klebsiella pneumoniae were investigated. The results indicated great antibacterial activity of epsilon-poly-l-lysine which was produced by two novel bacteria. The epsilon-poly-l-lysine as a potent cationic antimicrobial peptide is demonstrated to possess great antimicrobial activity against pathogenic and also antibiotic-resistant bacteria.

Multi-omics approach reveals elevated potential of bacteria for biodegradation of imidacloprid

The residual imidacloprid, a widely used insecticide is causing serious environmental concerns. Knowledge of its biodegradation will help in assessing its residual mass in soil. In view of this, a soil microcosm-based study was performed to test the biodegradation potential of Agrobacterium sp. InxBP2. It achieved ∼88% degradation in 20 days and followed the pseudo-first-order kinetics (k = 0.0511 day^-1 and t_1/2=7 days). Whole genome sequencing of Agrobacterium sp. InxBP2 revealed a genome size of 5.44 Mbp with 5179 genes. Imidacloprid degrading genes at loci K7A42_07110 (ABC transporter substrate-binding protein), K7A42_07270 (amidohydrolase family protein), K7A42_07385 (ABC transporter ATP-binding protein), K7A42_16,845 (nitronate monooxygenase family protein), and K7A42_20,660 (FAD-dependent monooxygenase) having sequence and functional similarity with known counterparts were identified. Molecular docking of proteins encoded by identified genes with their respective degradation pathway intermediates exhibited significant binding energies (-6.56 to -4.14 kcal/mol). Molecular dynamic simulation discovered consistent interactions and binding depicting high stability of docked complexes. Proteome analysis revealed differential protein expression in imidacloprid treated versus untreated samples which corroborated with the in-silico findings. Further, the detection of metabolites proved the bacterial degradation of imidacloprid. Thus, results provided a mechanistic link between imidacloprid and associated degradative genes/enzymes of Agrobacterium sp. InxBP2. These findings will be of immense significance in carrying out the lifecycle analysis and formulating strategies for the bioremediation of soils contaminated with insecticides like imidacloprid.

Nematicidal lipopeptides from Bacillus paralicheniformis and Bacillus subtilis: A comparative study

The aim of this work was to develop a comparative study between Bacillus paralicheniformis TB197 and B. subtilis ATCC 21332 strains in terms of growth, cyclic lipopeptide production, nematicidal activity, and active lipopeptide characteristics. Crude lipopeptide extracts (CLEs) from their fermentation broths were obtained, and their nematicidal activity (NA) was estimated as the mean lethal dose (LD₅₀), employing Caenorhabditis elegans. Using a bioguided approach, CLE components were fractionated by semipreparative thin layer chromatography, and active lipopeptides were characterized by mass spectrometry. Both strains produced similar concentrations of CLEs (p ≥ 0.05) (0.99 ± 0.11 and 1.14 ± 0.15 mg/mL by TB197 and ATCC 21332, respectively). The estimated LD₅₀ values of CLEs from the TB197 and ATCC 21332 strains were 3.88 and 8.15 mg/mL, respectively, showing that the NA of the TB197 strain CLE was 2.1-fold higher (p ≤ 0.05). Mass spectrometry revealed that strain TB197 synthesizes several families of lipopeptides, namely, fengycin A (C₁₄-C₁₇), fengycin B (C₁₆-C₁₇), surfactin (C₁₅-C₁₇), and lichenysin (C₁₂, C₁₃, C₁₄, and C₁₆), from which fengycins and lichenysins possess the highest NA (100 and 60% mortality in C. elegans larvae, respectively), while the ATCC 21332 strain produces mainly surfactin (C₁₃-C₁₇) (NA 63% mortality). The main differences found in this study were that the TB197 strain has a higher tolerance to inhibition by the product, and the lipopeptides they synthesize have a higher nematicidal activity due to the diversity of families compared to ATCC 21332. Likewise, it was shown that more polar lipopeptides (fengycins) are more effective at causing mortality in C. elegans larvae. KEY POINTS: • The nematicidal activity of lipopeptides from TB197 is higher than from ATCC 21332 • TB197 produces surfactin, lichenysin, and fengycin, while ATCC 21332 mainly produces surfactin • The most polar lipopeptides (fengycins) cause more mortality in C. elegans L2.

Sample Preparation in Microbial Metabolomics: Advances and Challenges

Microbial metabolomics has gained significant interest as it reflects the physiological state of microorganisms. Due to the great variability of biological organisms, in terms of physicochemical characteristics and variable range of concentration of metabolites, the choice of sample preparation methods is a crucial step in the metabolomics workflow and will reflect on the quality and reliability of the results generated. The procedures applied to the preparation of microbial samples will vary according to the type of microorganism studied, the metabolomics approach (untargeted or targeted), and the analytical platform of choice. This chapter aims to provide an overview of the sample preparation workflow for microbial metabolomics, highlighting the pre-analytical factors associated with cultivation, harvesting, metabolic quenching, and extraction. Discussions focus on obtaining intracellular and extracellular metabolites. Finally, we introduced advanced sample preparation methods based on automated systems.

Making "Sense" of Ecology from a Genetic Perspective: Caenorhabditis elegans, Microbes and Behavior

Our knowledge of animal and behavior in the natural ecology is based on over a century's worth of valuable field studies. In this post-genome era, however, we recognize that genes are the underpinning of ecological interactions between two organisms. Understanding how genes contribute to animal ecology, which is essentially the intersection of two genomes, is a tremendous challenge. The bacterivorous nematode Caenorhabditis elegans, one of the most well-known genetic animal model experimental systems, experiences a complex microbial world in its natural habitat, providing us with a window into the interplay of genes and molecules that result in an animal-microbial ecology. In this review, we will discuss C. elegans natural ecology, how the worm uses its sensory system to detect the microbes and metabolites that it encounters, and then discuss some of the fascinating ecological dances, including behaviors, that have evolved between the nematode and the microbes in its environment.

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

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

Metabolites derived from fungi and bacteria suppress in vitro growth of Gnomoniopsis smithogilvyi, a major threat to the global chestnut industry

INTRODUCTION

Chestnut rot caused by the fungus Gnomoniopsis smithogilvyi is a disease present in the world's major chestnut growing regions. The disease is considered a significant threat to the global production of nuts from the sweet chestnut (Castanea sativa). Conventional fungicides provide some control, but little is known about the potential of biological control agents (BCAs) as alternatives to manage the disease.

OBJECTIVE

Evaluate whether formulated BCAs and their secreted metabolites inhibit the in vitro growth of G. smithogilvyi.

METHODS

The antifungal potential of BCAs was assessed against the pathogen through an inverted plate assay for volatile compounds (VOCs), a diffusion assay for non-volatile compounds (nVOCs) and in dual culture. Methanolic extracts of nVOCs from the solid medium were further evaluated for their effect on conidia germination and were screened through an LC-MS-based approach for antifungal metabolites.

RESULTS

Isolates of Trichoderma spp., derived from the BCAs, significantly suppressed the pathogen through the production of VOCs and nVOCs. The BCA from which Bacillus subtilis was isolated was more effective in growth inhibition through the production of nVOCs. The LC-MS based metabolomics on the nVOCs derived from the BCAs showed the presence of several antifungal compounds.

CONCLUSION

The results show that G. smithogilvyi can be effectively controlled by the BCAs tested and that their use may provide a more ecological alternative for managing chestnut rot. The in vitro analysis should now be expanded to the field to assess the effectiveness of these alternatives for chestnut rot management.

Spaceflight Changes the Production and Bioactivity of Secondary Metabolites in Beauveria bassiana

Studies on microorganism response spaceflight date back to 1960. However, nothing conclusive is known concerning the effects of spaceflight on virulence and environmental tolerance of entomopathogenic fungi; thus, this area of research remains open to further exploration. In this study, the entomopathogenic fungus Beauveria bassiana (strain SB010) was exposed to spaceflight (ChangZheng 5 space shuttle during 5 May 2020 to 8 May 2020) as a part of the Key Research and Development Program of Guangdong Province, China, in collaboration with the China Space Program. The study revealed significant differences between the secondary metabolite profiles of the wild isolate (SB010) and the spaceflight-exposed isolate (BHT021, BH030, BHT098) of B. bassiana. Some of the secondary metabolites/toxins, including enniatin A2, brevianamide F, macrosporin, aphidicolin, and diacetoxyscirpenol, were only produced by the spaceflight-exposed isolate (BHT021, BHT030). The study revealed increased insecticidal activities for of crude protein extracts of B. bassiana spaceflight mutants (BHT021 and BH030, respectively) against Megalurothrips usitatus 5 days post application when compared crude protein extracts of the wild isolate (SB010). The data obtained support the idea of using space mutation as a tool for development/screening of fungal strains producing higher quantities of secondary metabolites, ultimately leading to increased toxicity/virulence against the target insect host.

Potential of rhizobacteria native to Argentina for the control of Meloidogyne javanica

Biocontrol of the nematode Meloidogyne javanica was studied using the Argentinean strains Pseudomonas fluorescens MME3, TAE4, TAR5 and ZME4 and Bacillus sp. B7S, B9T and B19S. Pseudomonas protegens CHA0 was used as a positive control. Egg hatching and juvenile mortality were evaluated in vitro by exposure of nematodes to bacterial suspensions or their cell-free supernatants (CFS). The effect of bacteria on nematode infestation of lettuce was also studied. results showed that most of the tested strains and CFS reduced egg hatching and juvenile survival in vitro. The bacterial suspension of Bacillus sp. B9T produced the lowest hatching of eggs. Juvenile mortality was higher when M. javanica was exposed to Bacillus sp. than to Pseudomonas spp. suspensions. Except for CFS of B9T, all filtrates inhibited hatching at levels similar to or higher than the biocontrol strain P. protegens CHA0. The CFS of CHA0 showed the highest level of juvenile mortality followed by Bacillus sp. strains and P. fluorescens TAE4. None of the inoculated rhizobacteria reverted the negative effect of infestation on the aerial dry weight of lettuce plants. However, inoculation impacted on reproduction of M. javanica by reducing the development of galls and egg masses on roots and diminishing the number of individuals both on roots and in the substrate, as well as the reproduction factor. These results show that most of the analyzed native strains can control the nematode M. javanica. Among them, P. fluorescens TAE4 and Bacillus sp. B9T showed the most promising performances for the biocontrol of this pathogen and have a potential use in the formulation of commercial products.

The Impacts of Microgravity on Bacterial Metabolism

The inside of a space-faring vehicle provides a set of conditions unlike anything experienced by bacteria on Earth. The low-shear, diffusion-limited microenvironment with accompanying high levels of ionizing radiation create high stress in bacterial cells, and results in many physiological adaptations. This review gives an overview of the effect spaceflight in general, and real or simulated microgravity in particular, has on primary and secondary metabolism. Some broad trends in primary metabolic responses can be identified. These include increases in carbohydrate metabolism, changes in carbon substrate utilization range, and changes in amino acid metabolism that reflect increased oxidative stress. However, another important trend is that there is no universal bacterial response to microgravity, as different bacteria often have contradictory responses to the same stress. This is exemplified in many of the observed secondary metabolite responses where secondary metabolites may have increased, decreased, or unchanged production in microgravity. Different secondary metabolites in the same organism can even show drastically different production responses. Microgravity can also impact the production profile and localization of secondary metabolites. The inconsistency of bacterial responses to real or simulated microgravity underscores the importance of further research in this area to better understand how microbes can impact the people and systems aboard spacecraft.

Bacterial Metabolomics: Sample Preparation Methods

Metabolomics is a comprehensive analysis of metabolites existing in biological systems. As one of the important "omics" tools, the approach has been widely employed in various fields in helping to better understand the complex cellular metabolic states and changes. Bacterial metabolomics has gained a significant interest as bacteria serve to provide a better subject or model at systems level. The approach in metabolomics is categorized into untargeted and targeted which serves different paradigms of interest. Nevertheless, the bottleneck in metabolomics has been the sample or metabolite preparation method. A custom-made method and design for a particular species or strain of bacteria might be necessary as most studies generally refer to other bacteria or even yeast and fungi that may lead to unreliable analysis. The paramount aspect of metabolomics design comprises sample harvesting, quenching, and metabolite extraction procedures. Depending on the type of samples and research objective, each step must be at optimal conditions which are significantly important in determining the final output. To date, there are no standardized nor single designated protocols that have been established for a specific bacteria strain for untargeted and targeted approaches. In this paper, the existing and current developments of sample preparation methods of bacterial metabolomics used in both approaches are reviewed. The review also highlights previous literature of optimized conditions used to propose the most ideal methods for metabolite preparation, particularly for bacterial cells. Advantages and limitations of methods are discussed for future improvement of bacterial metabolomics.

Biotechnological formation of dairy flavor inducing δ-lactones from vegetable oil

Agroscope Culture Collection was screened to identify bacterial strains effective in production of dairy flavor inducing lactones using grapeseed oil as a substrate. Lentilactobacillus parafarraginis FAM-1079, Lactococcus lactis subsp. lactis FAM-17918, and L. lactis subsp. lactis biovar diacetylactis FAM-22003 showed the most efficient formation of targeted δ-lactones. The application of sublethal heat stress significantly increased target lactone production. The most profound improvement was for L. lactis subsp. lactis biovar diacetylactis where δ-octadecalactone generation was improved by factor of 9. The pre-fermentation step as well as growth phase in which bacteria are harvested did not have a significant impact on lactones yield. The lactone production process from vegetable oil developed in this study offers a new way of developing a natural flavor ingredient for incorporation into plant-based products.

Pyoluteorin Produced by the Biocontrol Agent Pseudomonas protegens Is Involved in the Inhibition of Heterobasidion Species Present in Europe

Pseudomonas protegens (strain DSMZ 13134) is a biocontrol agent with promising antagonistic activity hinging on antibiosis against the fungal forest pathogens Heterobasidion spp. Here, by using High-Performance Liquid Chromatography coupled to Mass Spectrometry (HPLC-MS), we assessed whether monocultures of P. protegens (strain DSMZ 13134) produce the three major determinants of biocontrol activity known for the genus Pseudomonas: 2,4-diacetylphloroglucinol (2,4-DAPG), pyoluteorin (PLT), and pyrrolnitrin (PRN). At the tested culture conditions, we observed the production of PLT at concentrations ranging from 0.01 to 10.21 mg/L and 2,4-DAPG at a concentration not exceeding 0.5 mg/L. Variations of culture conditions involving culture medium, incubation temperature, and incubation period had no consistent influence on PLT production by the bacterium. Assays using culture medium amended with PLT at the same concentration of that present in cell-free filtrate of the bacterium, i.e., 3.77 mg/L, previously documented as effective against Heterobasidion spp., showed a remarkable activity of PLT against genotypes of all the four Heterobasidion species present in Europe, including the non-native invasive H. irregulare. However, such antifungal activity decreased over time, and this may be a constraint for using this molecule as a pesticide against Heterobasidion spp. When the bacterium was co-cultured in liquid medium with genotypes of the different Heterobasidion species, an increased production of PLT was observed at 4 °C, suggesting the bacterium may perform better as a PLT producer in field applications under similar environmental conditions, i.e., at low temperatures. Our results demonstrated the role of PLT in the inhibition of Heterobasidion spp., although all lines of evidence suggest that antibiosis does not rely on a single constitutively produced metabolite, but rather on a plethora of secondary metabolites. Findings presented in this study will help to optimize treatments based on Pseudomonas protegens (strain DSMZ 13134) against Heterobasidion spp.

Inhibition of the phytopathogenic fungi Curvularia lunata BM and Ganoderma sp. TB4 by antifungal compounds produced by Bacillus siamensis LDR grown on hanjeli (Coix lacryma-jobi L.) starch

Bacillus siamensis LDR was tested for its potential as a biocontrol agent against the phytopathogenic fungi Curvularia lunata BM and Ganoderma sp. TB4. Fermentation of B. siamensis LDR for the production of antifungal compound was performed in modified Czapex-Dox broth using hanjeli (Coix lacryma-jobi L.) starch as carbon source. The Bacillus siamensis LDR inoculum was 105 CFU/ mL, and fermentation was conducted for up to 16 days. Antibiosis assay conducted to test the antifungal activity of filtrate medium. The results showed inhibition of C. lunata BM and Ganoderma sp. TB4 were 47.08% and 85.99%, respectively on 14th day of fermentation. Antifungal assay of the crude extract from filtrate medium revealed growth inhibition of C. lunata BM (60.70%) and Ganoderma sp. TB4 (65.25%). Thin layer chromatography of the crude extract revealed pink-colored spots indicative of lipopeptide compounds. Analysis of the crude extract by ultraperformance liquid chromatography-mass spectrometry was tentatively identified as iturin A, bacillomycin F, and surfactin.

The secondary metabolites from Beauveria bassiana PQ2 inhibit the growth and spore germination of Gibberella moniliformis LIA

Fungal secondary metabolites with antimicrobial properties are used for biological pest control. Their production is influenced by several factors as environment, host, and culture conditions. In the present work, the secondary metabolites from fermented extracts of Beauveria bassiana PQ2 were tested as antifungal agents against Gibberella moniliformis LIA. The L18 (21 × 37) orthogonal array from Taguchi methodology was used to assess 8 parameters (pH, agitation, sucrose, yeast extract, KH2PO4, MgSO4, NH4NO3, and CaCl2) in B. bassiana PQ2 submerged fermentation. The ability of the fermented extracts to slow down the growth rate of G. moniliformis LIA was evaluated. The results from 18 trials were analyzed by Statistica 7 software by evaluating the signal-to-noise ratio (S/N) to find the lower-the-better condition. Optimal culture conditions were pH, 5; agitation, 250 rpm; sucrose, 37.5 g/L-1; yeast extract, 10 g/L-1; KH2PO4, 0.8 g/L-1; MgSO4, 1.2 g/L-1; NH4NO3, 0.1 g/L-1; and CaCl2, 0.4 g/L-1, being the agitation at the highest level the most significant factor. The optimal conditions were validated in a sparged bottle bioreactor resulting in a higher S/N value (12.48) compared to the estimate. The extract obtained has the capacity to inhibit the germination of G. moniliformis spores at 24 h. HPLC-ESI-MS2 allowed to identify the water-soluble red pigment as oosporein (m/z 304.9). The secondary metabolites from B. bassiana PQ2 are a suitable alternative to control the growth and sporulation of G. moniliformis.

Bacillusvelezensis Strains for Protecting Cucumber Plants from Root-Knot Nematode Meloidogyne incognita in a Greenhouse

Meloidogyne incognita Kofoid et White is one of the most dangerous root-knot nematodes in greenhouses. In this study, we evaluated two Bacillus strains (Bacillus velezensis BZR 86 and Bacillus velezensis BZR 277) as promising microbiological agents for protecting cucumber plants from the root-knot nematode M. incognita Kof. The morphological and cultural characteristics and enzymatic activity of the strains have been studied and the optimal conditions for its cultivation have been developed. We have shown the nematicidal activity of these strains against M. incognita. Experiments with the cucumber variety Courage were conducted under greenhouse conditions in 2016-2018. We determined the effect of plant damage with M. incognita to plants on the biometric parameters of underground and aboveground parts of cucumber plants, as well as on the gall formation index and yield. It was found that the treatment of plants with Bacillus strains contributed to an increase in the height of cucumber plants by 7.4-43.1%, an increase in leaf area by 2.7-17.8%, and an increase in root mass by 3.2-16.1% compared with the control plants without treatment. The application of these strains was proved to contribute to an increase in yield by 4.6-45.8% compared to control. Our experiments suggest that the treatment of cucumber plants with two Bacillus strains improved plant health and crop productivity in the greenhouse. B. velezensis BZR 86 and B. velezensis BZR 277 may form the basis for bionematicides to protect cucumber plants from the root-knot nematode M. incognita.

Acid tolerant bacterium Bacillus amyloliquefaciens MBNC retains biocontrol efficiency against fungal phytopathogens in low pH

Soil pH conditions have important consequences for microbial community structure, their dynamics, ecosystem processes, and interactions with plants. Low soil pH affects the growth and functional activity of bacterial biocontrol agents which may experience a paradigm shift in their ability to act antagonistically against fungal phytopathogens. In this study, the antifungal activity of an acid-tolerant soil bacterium Bacillus amyloliquefaciens MBNC was evaluated under low pH and compared to its activity in neutral pH conditions. Bacterial supernatant from 3-day-old culture (approximately 11.2 × 10⁸ cells/mL) grown in low pH conditions was found more effective against fungal pathogens. B. amyloliquefaciens MBNC harboured genes involved in the synthesis of secondary metabolites of which surfactin homologues, with varying chain length (C11-C15), were identified through High-Resolution Mass Spectroscopy. The pH of the medium influenced the production of these metabolites. Surfactin C15 was exclusive to the extract of pH 4.5; production of iturinA and surfactin C11 was detected only in pH 7.0, while surfactin C12, C13 and C14 were detected in extracts of both the pH conditions. The secretion of phytohormones viz. indole acetic acid and gibberellic acid by B. amyloliquefaciens MBNC was detected in higher amounts in neutral condition compared to acidic condition. Although, secretion of metabolites and phytohormones in B. amyloliquefaciens MBNC was influenced by the pH condition of the medium, the isolate retained its antagonistic efficiency against several fungal phyto-pathogens under acidic condition.

Antioxidant and antimutagenic properties of probiotic Lactobacilli determined using LUX-biosensors

The initial screening of probiotic strains in vitro, carried out by different methods, may omit strains that are promising from the point of view of biotechnology or, conversely, mark as promising strains those that will lose activity when transferred in vivo. It is known that the release of metabolites by probiotic bacteria, in particular, lactobacilli, is highly dependent on the biochemical context. In this work, we modified the method that was previously successfully used for the selection of probiotics for poultry, based on their antioxidant and DNA-protective properties. A comparison was made of this activity on standard media and on an artificial intestinal medium that mimics the intestines of a bird. As a result, three Lactobacillus strains were selected, which not only exhibit antioxidant and DNA-protective properties but also do not lose these activities in an artificial intestinal medium.

Evaluation of the antifungal activity of marine actinomycetes isolates against the phytopathogenic fungi Colletotrichum siamense KA: A preliminary study for new antifungal compound discovery

Marine actinomycetes are being explored to discover potential actinomycetes that produce antifungal compounds. In a previous study, marine actinomycetes isolates from the mangrove ecosystem were found to inhibit growth of the phytopathogenic fungi Colletotrichum siamense KA. In this study, the three of these isolates with the highest antagonistic activity—SM11, SM14, and SM15—were evaluated for their antifungal activity using antibiosis assay. The fermentation was performed in SCB:PDB medium (1:1) for 6, 9, and 12 days. The results showed that SM14 was the strongest potential isolate; it inhibited the growth of C. siamense KA on average up to 64.90% for 12 days on PDA filtrate medium. Molecular identification showed SM14 was closely related to Streptomyces sanyensis, but had differences in morphological and biochemical characteristics compared to SM11 or SM15. This indicated that the three isolates were different strains and may challenge further research on identifying and analyzing their antifungal compounds.

Effect of cultivation media and temperature on metabolite profiles of three nematicidal Bacillus species

Globally, root-knot nematode (RKN) infestations cause great financial losses. Although agrochemicals are used to manage these pests, there is increased interest in using biocontrol agents based on natural antagonistic microorganisms, such as Bacillus. These nematicidal bacteria demonstrate antagonism towards RKN through different modes of action, including specialised metabolite production. The aim of this study was to compare metabolite profiles of nematicidal Bacillus species and assess the influence of cultivation conditions on these profiles. Two hyphenated metabolomics platforms, gas chromatography-mass spectrometry (GC-MS) and liquid chromatography coupled to quadrupole time-of-flight mass spectrometry (LC-QTOF-MS), were employed to profile and compare metabolite features produced during the cultivation of three nematicidal Bacillus species (Bacillus firmus, B. cereus and B. soli) in complex Luria-Bertani broth (LB) and a simpler minimal broth (MB), at three different temperatures (25, 30 and 37°C). Cultivation in complex LB as opposed to simpler MB resulted in the production of more statistically significant metabolite features. Selected temperatures in this study did not have a significant influence on metabolite profiles. Moreover, media-specific influences outweighed temperature-specific influences on metabolite profiles. Results from this study are a valuable first step in establishing suitable cultivation conditions for the production of Bacillus metabolites of interest.

Screening of Rhizosphere Bacteria and Nematode Populations Associated with Soybean Roots in the Mpumalanga Highveld of South Africa

Soybean is among South Africa’s top crops in terms of production figures. Over the past few years there has been increasingly more damage caused to local soybean by plant-parasitic nematode infections. The presence of Meloidogyne (root-knot nematodes) and Pratylenchus spp. (root lesion nematodes) in soybean fields can cripple the country’s production, however, little is known about the soil microbial communities associated with soybean in relation to different levels of Meloidogyne and Pratylenchus infestations, as well as the interaction(s) between them. Therefore, this study aimed to identify the nematode population assemblages and endemic rhizosphere bacteria associated with soybean using Next Generation Sequencing (NGS). The abundance of bacterial genera that were then identified as being significant using linear discriminant analysis (LDA) Effect Size (LEfSe) was compared to the abundance of the most prevalent plant-parasitic nematode genera found across all sampled sites, viz. Meloidogyne and Pratylenchus. While several bacterial genera were identified as significant using LEfSe, only two with increased abundance were associated with decreased abundance of Meloidogyne and Pratylenchus. However, six bacterial genera were associated with decreased Pratylenchus abundance. It is therefore possible that endemic bacterial strains can serve as an alternative method for reducing densities of plant-parasitic nematode genera and in this way reduce the damages caused to this economically important crop.

Mass spectrometry based metabolomics approach on the elucidation of volatile metabolites formation in fermented foods: A mini review

Metabolomics can be applied for comparative and quantitative analyses of the metabolic changes induced by microorganisms during fermentation. In particular, mass spectrometry (MS) is a powerful tool for metabolomics that is widely used for elucidating biomarkers and patterns of metabolic changes. Fermentation involves the production of volatile metabolites via diverse and complex metabolic pathways by the activities of microbial enzymes. These metabolites can greatly affect the organoleptic properties of fermented foods. This review provides an overview of the MS-based metabolomics techniques applied in studies of fermented foods, and the major metabolic pathways and metabolites (e.g., sugars, amino acids, and fatty acids) derived from their metabolism. In addition, we suggest an efficient tool for understanding the metabolic patterns and for identifying novel markers in fermented foods.

Selection of Bacterial Strains for Control of Root-Knot Disease Caused by Meloidogyne incognita

Root-knot disease caused by Meloidogyne incognita leads to significant crop yield losses that may be aggravated by the association with pathogenic fungi and bacteria. Biological agents can be effectively used against the complex disease of root-knot nematode and pathogenic fungi. In this study, 35 bacterial strains were analyzed for their in vitro nematicidal, antagonistic and growth stimulation activities. Based on results from the in vitro assays, grow-box experiments on tomato and cucumber were carried out with the strain BZR 86 of Bacillus velezensis applied at different concentrations. Effects of B. velezensis BZR 86 on the development of root-knot disease were evaluated by recording root gall index, number of galls and number of eggs in egg masses. Application of B. velezensis BZR 86 noticeably decreased the development of root-knot disease on tomato and cucumber plants, as well as significantly increased growth and biomass of cucumber plants in accordance with bacterial concentration. This study seems to demonstrate that strain B. velezensis BZR 86 could be an additional tool for an environmentally safe control of root-knot disease on horticultural crops.

Soil Organic Matter Characterization by Fourier Transform Ion Cyclotron Resonance Mass Spectrometry (FTICR MS): A Critical Review of Sample Preparation, Analysis, and Data Interpretation

The biogeochemical cycling of soil organic matter (SOM) plays a central role in regulating soil health, water quality, carbon storage, and greenhouse gas emissions. Thus, many studies have been conducted to reveal how anthropogenic and climate variables affect carbon sequestration and nutrient cycling. Among the analytical techniques used to better understand the speciation and transformation of SOM, Fourier transform ion cyclotron resonance mass spectrometry (FTICR MS) is the only technique that has sufficient mass resolving power to separate and accurately assign elemental compositions to individual SOM molecules. The global increase in the application of FTICR MS to address SOM complexity has highlighted the many challenges and opportunities associated with SOM sample preparation, FTICR MS analysis, and mass spectral interpretation. Here, we provide a critical review of recent strategies for SOM characterization by FTICR MS with emphasis on SOM sample collection, preparation, analysis, and data interpretation. Data processing and visualization methods are presented with suggested workflows that detail the considerations needed for the application of molecular information derived from FTICR MS. Finally, we highlight current research gaps, biases, and future directions needed to improve our understanding of organic matter chemistry and cycling within terrestrial ecosystems.

Bacteria as Biocontrol Tool against Phytoparasitic Nematodes

Phytoparasitic nematodes cause severe damage and yield losses to numerous agricultural crops. Considering the revision of the EU legislation on the use of pesticides on agricultural crops, control strategies with low environmental impact are required. The approach based on the use of bacteria seems particularly promising as it also helps to reduce the applied amounts of chemicals and stabilize ecological changes. This paper gives an overview of the main types of bacteria that can be used as biological control agents against plant parasitic nematodes and their interrelationships with plants and other organisms. Many experiments have given positive results of phytoparasitic nematode control by bacteria, showing possible prospects for their application. In vitro, greenhouse and field experiments have shown that bacteria can regulate the development of ecto- and endoparasitic nematodes by different modes of action. Triggering the induction of plant defense mechanisms by bacteria is seen as the optimum tool because the efficacy of bacterial treatment can be higher than that of chemical pesticides or at least close to it. Moreover, bacterial application produces additional positive effects on growth stimulation, raises yields and suppresses other pathogenic microorganisms. Commercial formulations, both as single bacterial strains and bacterial complexes, are examined.

Optimizing and purifying extracellular amylase from soil bacteria to inhibit clinical biofilm-forming bacteria

BACKGROUND

Bacterial biofilms have become a major threat to human health. The objective of this study was to isolate amylase-producing bacteria from soil to determine the overall inhibition of certain pathogenic bacterial biofilms.

METHODS

We used serial dilution and the streaking method to obtain a total of 75 positive amylase isolates. The starch-agar plate method was used to screen the amylolytic activities of these isolates, and we used morphological and biochemical methods to characterize the isolates. Optimal conditions for amylase production and purification using Sephadex G-200 and SDS-PAGE were monitored. We screened these isolates' antagonistic activities and the purified amylase against pathogenic and multi-drug-resistant human bacteria using the agar disk diffusion method. Some standard antibiotics were controlled according to their degree of sensitivity. Finally, we used spectrophotometric methods to screen the antibiofilm 24 and 48 h after application of filtering and purifying enzymes in order to determine its efficacy at human pathogenic bacteria.

RESULTS

The isolated Bacillus species were Bacillus megaterium (26.7%), Bacillus subtilis (16%), Bacillus cereus (13.3%), Bacillus thuringiesis (10.7%), Bacillus lentus (10.7%), Bacillus mycoides (5.3%), Bacillus alvei (5.3%), Bacillus polymyxa (4%), Bacillus circulans (4%), and Micrococcus roseus (4%). Interestingly, all isolates showed a high antagonism to target pathogens. B. alevi had the highest recorded activity (48 mm) and B. polymyxa had the lowest recorded activity (12 mm) against Staphylococcus aureus (MRSA) and Escherichia coli, respectively. On the other hand, we detected no antibacterial activity for purified amylase. The supernatant of the isolated amylase-producing bacteria and its purified amylase showed significant inhibition for biofilm: 93.7% and 78.8%, respectively. This suggests that supernatant and purified amylase may be effective for clinical and environmental biofilm control.

DISCUSSION

Our results showed that soil bacterial isolates such as Bacillus sp. supernatant and its purified amylase are good antibiofilm tools that can inhibit multidrug-resistant former strains. They could be beneficial for pharmaceutical use. While purified amylase was effective as an antibiofilm, the isolated supernatant showed better results.