Bacillibactins E and F from a Marine Sponge-Associated Bacillus sp

Ion Mobility-Coupled Mass Spectrometry for Metallophore Detection

Metal chelating small molecules (metallophores) play significant roles in microbial interactions and bacterial survival; however, current methods to identify metallophores are limited by low sensitivity, a lack of metal selectivity, and/or complicated data analysis. To overcome these limitations, we developed a novel approach for detecting metallophores in natural product extracts using ion mobility-coupled mass spectrometry (IM-MS). As a proof of concept, marine bacterial extracts containing known metallophores were analyzed by IM-MS with and without added metals, and the data were compared between conditions to identify metal-binding metabolites. Ions with changes in both mass and mobility were specific to metallophores, enabling their identification within these complex extracts. Additionally, we compared the use of direct infusion (DI) and liquid chromatography (LC) separation with IM-MS. For most samples, DI outperformed LC by minimizing the time required for data collection and simplifying analysis. However, for some samples, LC improved the detection of metallophores likely by reducing ion suppression. IM-MS was then used to identify 10 metallophores in an extract from a marine Micromonospora sp. Overall, incorporating IM-MS facilitated the rapid detection of metal-binding natural products in complex bacterial extracts through the comparison of mass and mobility data in the presence and absence of metals.

Bacillus safensis APC 4099 has broad-spectrum antimicrobial activity against both bacteria and fungi and produces several antimicrobial peptides, including the novel circular bacteriocin safencin E

Bacillus safensis APC 4099, isolated from bees' gut, has been identified as a promising candidate for food biopreservation. Antimicrobial activity screening revealed a broad-spectrum inhibition potential, ranging from gram-positive pathogenic bacteria to fungi responsible for food spoilage. Genomic analysis identified biosynthetic gene clusters coding for several antimicrobial peptides and secondary metabolites. Specifically, a novel, anionic, 6 kDa circular bacteriocin, named safencin E, was detected, showing 52.5% similarity to butyrivibriocin AR10. Additionally, gene clusters coding for the biosynthesis of bacteriocins such as pumilarin and plantazolicin and biosynthetic pathways for secondary metabolites, including pumilacidin A, bacilysin, and bacillibactin, were identified. Matrix-assisted laser desorption ionization-time of flight mass spectrometry analysis detected molecular masses correlating to safencin E, plantazolicin, pumilarin, and pumilacidin A from the cell-free supernatant, cell extracts, or both. Overall, the broad-spectrum antimicrobial activity of B. safensis APC 4099 indicates that this strain is a promising candidate for the biological control of food ecosystems and thus has the potential to enhance food safety.

IMPORTANCE

The present article highlights the importance of the strain Bacillus safensis APC 4099 as a potential biocontrol agent. The strain possesses biosynthetic gene clusters coding for various antimicrobial peptides and secondary metabolites, including a novel circular bacteriocin, safencin E, and the bacteriocins pumilarin and plantazolicin. This diversity in the production of antimicrobial peptides renders the producer with broad-spectrum antimicrobial activity, ranging from gram-positive pathogenic and spoilage bacteria to spoilage molds. Considering that 1.3 billion tons of food appropriate for human consumption is lost or wasted annually, identifying strains or novel antimicrobial peptides capable of biopreservation is highly relevant. This strain and its bioactive compounds offer a solution to this global problem as biocontrol agents for food ecosystems against spoilage and pathogenic microbes.

Cyclic natural product oligomers: diversity and (bio)synthesis of macrocycles

Cyclic compounds are generally preferred over linear compounds for functional studies due to their enhanced bioavailability, stability towards metabolic degradation, and selective receptor binding. This has led to a need for effective cyclization strategies for compound synthesis and hence increased interest in macrocyclization mediated by thioesterase (TE) domains, which naturally boost the chemical diversity and bioactivities of cyclic natural products. Many non-ribosomal peptide synthetase (NRPS) and polyketide synthase (PKS) derived natural products are assembled to form cyclodimeric compounds, with these molecules possessing diverse structures and biological activities. There is significant interest in identifying the biosynthetic pathways that produce such molecules given the challenge that cyclodimerization represents from a biosynthetic perspective. In the last decade, many groups have pursued the characterization of TE domains and have provided new insights into this biocatalytic machinery: however, the enzymes involved in formation of cyclodimeric compounds have proven far more elusive. In this review we focus on natural products that involve macrocyclization in their biosynthesis and chemical synthesis, with an emphasis on the function and biosynthetic investigation on the special family of TE domains responsible for forming cyclodimeric natural products. We also introduce additional macrocyclization catalysts, including butelase and the CT-mediated cyclization of peptides, alongside the formation of cyclodipeptides mediated by cyclodipeptide synthases (CDPS) and single-module NRPSs. Due to the interdisciplinary nature of biosynthetic research, we anticipate that this review will prove valuable to synthetic chemists, drug discovery groups, enzymologists, and the biosynthetic community in general, and inspire further efforts to identify and exploit these biocatalysts for the formation of novel bioactive molecules.

Whole genome sequence and LC-Mass for identifying antimicrobial metabolites of Bacillus licheniformis endophyte

Antimicrobial resistance (AMR) represents a critical public health issue that requiring immediate action. Wild halophytic plants can be the solution for the AMR crisis because they harbor unique endophytes capable of producing potent antimicrobial metabolites. This study aimed at identifying promising and antimicrobial metabolites produced by endophytic/epiphytic bacteria recovered from the wild Bassia scoparia plant. Standard methods were employed for the isolation of endophytes/epiphytes. Whole genome sequence (WGS) using Oxford Nanopore technology followed by antiSMASH analysis coupled with advanced LC-MS spectroscopic analysis were used for identification of the active antimicrobial metabolites. This study identified Bacillus licheniformis strain CCASU-B18 as a promising endophytic bacterium from the Bassia scoparia plant. In addition, the strain showed broad-spectrum antibacterial activity against three standard and five MDR clinical Gram-positive and Gram-negative isolates, and antifungal activity against the standard C. albicans strain. Six main antimicrobial metabolites-thermoactinoamide A, bacillibactins, lichenysins, lichenicidins, fengycin, and bacillomycin-were verified to exist by whole genome sequencing for identifying the respective conserved biosynthetic gene clusters in conjunction with LC/MS-MS analysis. The complete genomic DNA (4125835) and associated plasmid (205548 bp) of the promising endophytic isolate were sequenced, assembled, annotated, and submitted into the NCBI GenBank database under the accession codes, CP157373. In conclusion, Bacillus licheniformis strain CCASU-B18, a promising endophytic bacterium exhibiting broad-spectrum antimicrobial activities, was isolated. Future research is highly recommended to optimize the culture conditions that will be employed to enhance the production of respective antimicrobial metabolites, as well as testing these compounds against a broader range of MDR-resistant pathogens.

Characterization of Siderophores Produced by Bacillus velezensis YL2021 and Its Application in Controlling Rice Sheath Blight and Rice Blast

Bacillus velezensis YL2021 has extensive antimicrobial activities against phytopathogens, and its genome harbors a catechol-type siderophore biosynthesis gene cluster. Here, we describe the characterization of siderophores produced by strain YL2021 and its antimicrobial activity in vitro and in vivo. A few types of siderophores were detected by chrome azurol S plates coupled with Arnow's test, purified, and identified by reversed-phase high-performance liquid chromatography. We found that strain YL2021 can produce different antimicrobial compounds under low-iron M9 medium or iron-sufficient Luria-Bertani medium, although antimicrobial activities can be easily observed on the two media as described above in vitro. Strain YL2021 can produce at least three catechol-type siderophores in low-iron M9 medium, whereas no siderophores were produced in Luria-Bertani medium. Among them, the main antimicrobial siderophore produced by strain YL2021 was bacillibactin, with m/z 882, based on the liquid chromatography-tandem mass spectrometry analysis, which has broad-spectrum antimicrobial activities against gram-positive and gram-negative bacteria, the oomycete Phytophthora capsici, and phytopathogenic fungi. Moreover, the antifungal activity of siderophores, including bacillibactin, observed in vitro was correlated with control efficacies against rice sheath blight disease caused by Rhizoctonia solani and rice blast disease caused by Magnaporthe oryzae in vivo. Collectively, the results demonstrate that siderophores, including bacillibactin, produced by B. velezensis YL2021 are promising biocontrol agents for application in rice disease control.

A comprehensive review of marine sponge metabolites, with emphasis on Neopetrosia sp

The secondary metabolites that marine sponges create are essential to the advancement of contemporary medicine and are often employed in clinical settings. Over the past five years, microbes associated with sponges have yielded the identification of 140 novel chemicals. Statistics show that most are derived from actinomycetes (bacteria) and ascomycotes (fungi). The aim of this study was to investigate the biological activity of metabolites from marine sponges. Chlocarbazomycins A-D, which are a group of novel chlorinated carbazole alkaloids isolated from the sponge Neopetrosia fennelliae KUFA 0811, exhibit antimicrobial, cytotoxic, and enzyme inhibitory activities. Recently, marine sponges of the genus Neopetrosia have attracted attention due to the unique chemical composition of the compounds they produce, including alkaloids of potential importance in drug discovery. Fridamycin H and fridamycin I are two novel type II polyketides synthesized by sponge-associated bacteria exhibit antitrypanosomal activity. Fintiamin, composed of amino acids and terpenoid moieties, shows affinity for the cannabinoid receptor CB 1. It was found that out of 27 species of Neopetrosia sponges, the chemical composition of only 9 species has been studied. These species mainly produce bioactive substances such as alkaloids, quinones, sterols, and terpenoids. The presence of motuporamines is a marker of the species Neopetrosia exigua. Terpenoids are specific markers of Neopetrosia vanilla species. Although recently discovered, secondary metabolites from marine sponges have been shown to have diverse biological activities, antimicrobial, antiviral, antibacterial, antimicrobial, antioxidant, antimalarial, and anticancer properties, providing many lead compounds for drug development. The data presented in this review on known and future natural products derived from sponges will further clarify the role and importance of microbes in marine sponges and trace the prospects of their applications, especially in medicine, cosmeceuticals, environmental protection, and manufacturing industries.

Genomic Characterization of Bacillus pumilus Sonora, a Strain with Inhibitory Activity against Vibrio parahaemolyticus-AHPND and Probiotic Candidate for Shrimp Aquaculture

Acute hepatopancreatic necrosis disease, caused by Vibrio parahaemolyticus strains carrying the pirA and pirB toxin genes (VpAHPND), has been causing great economic losses in Asia and America in the shrimp farming industry. Numerous strains are resistant to antibiotics. However, supplementation with probiotic antagonists has become a more desirable treatment alternative. Fourteen strains of microorganisms were assessed for their potential to inhibit VpAHPND in vitro activity. The bacteria with the highest activity were challenged with VpAHPND-infected Pacific white shrimp Litopenaeus vannamei. Furthermore, the genomic characteristics of probiotic bacteria were explored by whole-genome sequencing. We identified the Sonora strain as Bacillus pumilus, which possesses positive proteolytic and cellulolytic activities that may improve shrimp nutrient uptake and digestion. Challenge trials showed a low cumulative mortality (11.1%). B. pumilus Son has a genome of 3,512,470 bp and 3734 coding sequences contained in 327 subsystems. Some of these genes are related to the biosynthesis of antimicrobial peptides (surfactins, fengycin, schizokinen, bacilibactin, and bacilysin), nitrogen and phosphorus metabolism, and stress response. Our in vitro and in vivo findings suggest that B. pumilus Sonora has potential as a functional probiotic.

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.

Metabolomics and Molecular Networking-Guided Screening of Bacillus-Derived Bioactive Compounds Against a Highly Lethal Vibrio Species

Microorganisms are important sources of bioactive natural products. However, the complexity of microbial metabolites and the low abundance of active compounds render the isolation and purification process laborious and inefficient. During our search for active substances capable of inhibiting the newly discovered highly lethal Vibrio strain vp-HL, we found that the fermentation broth of multiple Bacillus strains exhibited antibacterial activity. However, the substances responsible for the activity remained unclear. Metabolomics, molecular networking (MN), and the Structural similarity Network Annotation Platform for Mass Spectrometry (SNAP-MS) were employed in conjunction with bioactivity screening to predict the antibacterial compounds from Bacillus strains. The analysis of fractions, and their isolation, NMR-based annotation, and bioactivity evaluation of an amicoumacin compound partially confirmed the prediction from these statistical analyses. This work presents the potential of marine Bacillus in producing active substances against Vibrio species. Additionally, it highlighted the significance and feasibility of metabolomics and MN in the dereplication of compounds and the determination of isolation targets.

Optimization of Siderophore Production in Three Marine Bacterial Isolates along with Their Heavy-Metal Chelation and Seed Germination Potential Determination

Siderophores are low-molecular-weight and high-affinity molecules produced by bacteria under iron-limited conditions. Due to the low iron (III) (Fe+3) levels in surface waters in the marine environment, microbes produce a variety of siderophores. In the current study, halophilic bacteria Bacillus taeanensis SMI_1, Enterobacter sp., AABM_9, and Pseudomonas mendocina AMPPS_5 were isolated from marine surface water of Kalinga beach, Bay of Bengal (Visakhapatnam, Andhra Pradesh, India) and were investigated for siderophore production using the Chrome Azurol S (CAS) assay. The effect of various production parameters was also studied. The optimum production of siderophores for SMI_1 was 93.57% siderophore units (SU) (after 48 h of incubation at 30 °C, pH 8, sucrose as carbon source, sodium nitrate as nitrogen source, 0.4% succinic acid), and for AABM_9, it was 87.18 %SU (after 36 h of incubation period at 30 °C, pH 8, in the presence of sucrose, ammonium sulfate, 0.4% succinic acid). The maximum production of siderophores for AMPPS_5 was 91.17 %SU (after 36 h of incubation at 35 °C, pH 8.5, glucose, ammonium sulfate, 0.4% citric acid). The bacterial isolates SMI_1, AABM_9, and AMPPS_5 showed siderophore production at low Fe+3 concentrations of 0.10 µM, 0.01 µM, and 0.01 µM, respectively. The SMI_1 (73.09 %SU) and AMPPS_5 (68.26 %SU) isolates showed siderophore production in the presence of Zn+2 (10 µM), whereas AABM_9 (50.4 %SU) exhibited siderophore production in the presence of Cu+2 (10 µM). Additionally, these bacterial isolates showed better heavy-metal chelation ability and rapid development in seed germination experiments. Based on these results, the isolates of marine-derived bacteria effectively produced the maximum amount of siderophores, which could be employed in a variety of industrial and environmental applications.

Astellolides R-W, Drimane-Type Sesquiterpenoids from an Aspergillus parasiticus Strain Associated with an Isopod

Sesquiterpenoids with a cage-like multiring frame are rarely found in nature. Mining of the isopod-derived fungus Aspergillus parasiticus SDU001 by the one strain-many compounds (OSMAC) strategy unexpectedly led to the discovery of fungal drimane-type sesquiterpenoids astellolide R (1), featuring an unusual cage-like 6/6/5/6/5 pentacyclic ring system, astellolide S (2), possessing a rare nicotinic acid building block, and astellolides T-W (3-6). Their structures were comprehensively assigned by spectroscopic data analysis, single-crystal X-ray diffraction, and electronic circular dichroism calculations. Furthermore, compounds 3 and 5 exhibited anti-inflammatory activity by inhibiting the lipopolyssacharide-induced NO production in RAW264.7 macrophages with IC₅₀ values of 6.1 ± 0.8 and 6.8 ± 0.8 μM, respectively. A putative biosynthetic pathway for 1 is proposed. Our results enlarge the chemical space of the drimane-type sesquiterpenoids generated from endophytic fungi.

Marine natural products

Covering: January to December 2021This review covers the literature published in 2021 for marine natural products (MNPs), with 736 citations (724 for the period January to December 2021) referring to compounds isolated from marine microorganisms and phytoplankton, green, brown and red algae, sponges, cnidarians, bryozoans, molluscs, tunicates, echinoderms, mangroves and other intertidal plants and microorganisms. The emphasis is on new compounds (1425 in 416 papers for 2021), together with the relevant biological activities, source organisms and country of origin. Pertinent reviews, biosynthetic studies, first syntheses, and syntheses that led to the revision of structures or stereochemistries, have been included. An analysis of the number of authors, their affiliations, domestic and international collection locations, focus of MNP studies, citation metrics and journal choices is discussed.

Microbiome composition modulates secondary metabolism in a multispecies bacterial community

Bacterial secondary metabolites are a major source of antibiotics and other bioactive compounds. In microbial communities, these molecules can mediate interspecies interactions and responses to environmental change. Despite the importance of secondary metabolites in human health and microbial ecology, little is known about their roles and regulation in the context of multispecies communities. In a simplified model of the rhizosphere composed of Bacillus cereus, Flavobacterium johnsoniae, and Pseudomonas koreensis, we show that the dynamics of secondary metabolism depend on community species composition and interspecies interactions. Comparative metatranscriptomics and metametabolomics reveal that the abundance of transcripts of biosynthetic gene clusters (BGCs) and metabolomic molecular features differ between monocultures or dual cultures and a tripartite community. In both two- and three-member cocultures, P. koreensis modified expression of BGCs for zwittermicin, petrobactin, and other secondary metabolites in B. cereus and F. johnsoniae, whereas the BGC transcriptional response to the community in P. koreensis itself was minimal. Pairwise and tripartite cocultures with P. koreensis displayed unique molecular features that appear to be derivatives of lokisin, suggesting metabolic handoffs between species. Deleting the BGC for koreenceine, another P. koreensis metabolite, altered transcript and metabolite profiles across the community, including substantial up-regulation of the petrobactin and bacillibactin BGCs in B. cereus, suggesting that koreenceine represses siderophore production. Results from this model community show that bacterial BGC expression and chemical output depend on the identity and biosynthetic capacity of coculture partners, suggesting community composition and microbiome interactions may shape the regulation of secondary metabolism in nature.

Secondary Metabolites from Marine-Derived Bacillus: A Comprehensive Review of Origins, Structures, and Bioactivities

The marine is a highly complex ecosystem including various microorganisms. Bacillus species is a predominant microbialflora widely distributed in marine ecosystems. This review aims to provide a systematic summary of the newly reported metabolites produced by marine-derived Bacillus species over recent years covering the literature from 2014 to 2021. It describes the structural diversity and biological activities of the reported compounds. Herein, a total of 87 newly reported metabolites are included in this article, among which 49 compounds originated from marine sediments, indicating that marine sediments are majority sources of productive strains of Bacillus species Therefore, marine-derived Bacillus species are a potentially promising source for the discovery of new metabolites.

Natural products from mangrove sediments-derived microbes: Structural diversity, bioactivities, biosynthesis, and total synthesis

The mangrove forests are a complex ecosystem, and the microbial communities in mangrove sediments play a critical role in the biogeochemical cycles of mangrove ecosystems. Mangrove sediments-derived microbes (MSM), as a rich reservoir of natural product diversity, could be utilized in the exploration of new antibiotics or drugs. To understand the structural diversity and bioactivities of the metabolites of MSM, this review for the first time provides a comprehensive overview of 519 natural products isolated from MSM with their bioactivities, up to 2021. Most of the structural types of these compounds are alkaloids, lactones, xanthones, quinones, terpenoids, and steroids. Among them, 210 compounds are obtained from bacteria, most of which are from Streptomyces, while 309 compounds are from fungus, especially genus Aspergillus and Penicillium. The pharmacological mechanisms of some representative lead compounds are well studied, revealing that they have important medicinal potentials, such as piericidins with anti-renal cell cancer effects, azalomycins with anti-MRSA activities, and ophiobolins as antineoplastic agents. The biosynthetic pathways of representative natural products from MSM have also been summarized, especially ikarugamycin, piericidins, divergolides, and azalomycins. In addition, the total synthetic strategies of representative secondary metabolites from MSM are also reviewed, such as piericidin A and borrelidin. This review provides an important reference for the research status of natural products isolated from MSM and the lead compounds worthy of further development, and reveals that MSM have important medicinal values and are worthy of further development.

Bacillimidazoles A-F, Imidazolium-Containing Compounds Isolated from a Marine Bacillus

Chemical investigations of a marine sponge-associated Bacillus revealed six new imidazolium-containing compounds, bacillimidazoles A-F (1-6). Previous reports of related imidazolium-containing natural products are rare. Initially unveiled by timsTOF (trapped ion mobility spectrometry) MS data, extensive HRMS and 1D and 2D NMR analyses enabled the structural elucidation of 1-6. In addition, a plausible biosynthetic pathway to bacillimidazoles is proposed based on isotopic labeling experiments and invokes the highly reactive glycolytic adduct 2,3-butanedione. Combined, the results of structure elucidation efforts, isotopic labeling studies and bioinformatics suggest that 1-6 result from a fascinating intersection of primary and secondary metabolic pathways in Bacillus sp. WMMC1349. Antimicrobial assays revealed that, of 1-6, only compound six displayed discernible antibacterial activity, despite the close structural similarities shared by all six natural products.

Needles in haystacks: reevaluating old paradigms for the discovery of bacterial secondary metabolites

Covering: up to 2021Natural products research is in the midst of a renaissance ushered in by a modern understanding of microbiology and the technological explosions of genomics and metabolomics. As the exploration of uncharted chemical space expands into high-throughput discovery campaigns, it has become increasingly clear how design elements influence success: (bio)geography, habitat, community dynamics, culturing/induction methods, screening methods, dereplication, and more. We explore critical considerations and assumptions in natural products discovery. We revisit previous estimates of chemical rediscovery and discuss their relatedness to study design and producer taxonomy. Through frequency analyses of biosynthetic gene clusters in publicly available genomic data, we highlight phylogenetic biases that influence rediscovery rates. Through selected examples of how study design at each level determines discovery outcomes, we discuss the challenges and opportunities for the future of high-throughput natural product discovery.

The Discovery and Biosynthesis of Nicotinic Myxochelins from an Archangium sp. SDU34

Myxobacteria are a prolific source of structurally diverse natural products, and one of the best-studied myxobacterial products is the siderophore myxochelin. Herein, we report two new compounds, myxochelins N (1) and O (2), that are nicotinic paralogs of myxochelin A, from the terrestrial myxobacterium Archangium sp. SDU34; 2 is functionalized with a rare 2-oxazolidinone. A precursor-feeding experiment implied that the biosynthesis of 1 or 2 was due to altered substrate specificity of the loading module of MxcE, which likely accepts nicotinic acid and benzoic acid instead of more conventional 2,3-dihydroxybenzoic acid. We also employed a phylogenomic approach to map the evolutionary relationships of the myxochelin biosynthetic gene clusters (BGCs) in all the available myxobacterial genomes, to pave the way for the future discovery of potentially hidden myxochelin derivatives. Although the biological function of 1 and 2 is unclear yet, this work underpins that even extensively studied BGCs in myxobacteria can still produce new chemistry.

Expanding the Myxochelin Natural Product Family by Nicotinic Acid Containing Congeners

Myxobacteria represent a viable source of chemically diverse and biologically active secondary metabolites. The myxochelins are a well-studied family of catecholate-type siderophores produced by various myxobacterial strains. Here, we report the discovery, isolation, and structure elucidation of three new myxochelins N1-N3 from the terrestrial myxobacterium Corallococcus sp. MCy9049, featuring an unusual nicotinic acid moiety. Precursor-directed biosynthesis (PDB) experiments and total synthesis were performed in order to confirm structures, improve access to pure compounds for bioactivity testing, and to devise a biosynthesis proposal. The combined evaluation of metabolome and genome data covering myxobacteria supports the notion that the new myxochelin congeners reported here are in fact frequent side products of the known myxochelin A biosynthetic pathway in myxobacteria.