Biology subjects

Jarmusch, S. A.

Publications and source records attributed to Jarmusch, S. A..

15 recordsLinked to original sources

bioRxiv2026

Beyond Antimicrobial Activity: Soil Bacteria Reveal a Biotransformation Fate for the Lanthipeptide Nisin

Natural products are central mediators of microbial interactions. However, once released into the environment, they also become available for neighboring microorganisms capable of degrading and modifying them through biotransformation. These biotransformations may fundamentally reshape metabolomes and influence community behavior, yet our understanding of these processes remains limited. Ribosomally synthesized peptides are particularly compelling in this context because their structural complexity and potent antimicrobial activity coexist with the potential to yield essential nutrients and reduced bioactivity through biotransformation. Identifying the pathways underlying these biotransformations is essential for understanding mechanisms that support microbial coexistence and nutrient recycling in soil microbiomes. Here, we used nisin as a model peptide to investigate biotransformation by soil bacteria. Selective isolation under nisin-rich, carbon-limited conditions yielded two Gram-negative isolates, Burkholderia stabilis and Pseudomonas fragi. Using growth assays and liquid chromatography-mass spectrometry, we found that both isolates grow in the presence of nisin while biotransforming and depleting the peptide. Burkholderia stabilis completely converted nisin through sequential cleavage of the C-terminus, hinge region and lanthionine ring C, whereas Pseudomonas fragi showed more limited processing restricted to the C-terminal region. Although these biotransformations dismantled structural features required for nisins antimicrobial activity, the intrinsic resistance of both isolates suggests a role beyond detoxification. We further detected nisin biosynthetic genes in the source environment, supporting nisins ecological relevance and suggesting that these bacteria may participate in its turnover in soil. Together, these findings reveal extensive microbial processing of nisin and support a role for antimicrobial peptide recycling in soil microbiomes. ImportanceNatural products are often studied through the lens of their biological activities, but much less attention has been paid to what happens to these molecules after they enter complex microbial communities. Using the lantibiotic nisin as a model system, we show that soil bacteria can extensively biotransform and deplete an antimicrobial peptide through extracellular enzymatic activity. The presence of both nisin-producing and nisin-biotransforming microorganisms in the same soil environment suggests that antimicrobial peptides may be continuously produced and recycled in nature. Our findings highlight biotransformation as an important but underexplored process governing the persistence, turnover, and ecological roles of microbial natural products.

microbiology↗

bioRxiv2026

Multi-omics reveals mechanisms behind pathogen inhibition by a microalgal microbiome

Aquaculture is an essential food production sector for meeting the global demand for high-quality protein. However, the sector faces significant challenges from bacterial pathogens, particularly Vibrio anguillarum, which causes vibriosis in numerous commercially important fish species. Current disease management strategies rely heavily on antibiotics, leading to antimicrobial resistance and environmental concerns. Microalgal microbiomes represent promising alternatives for sustainable pathogen control, yet the molecular mechanisms underlying their inhibitory activity remain poorly understood. Here, we employed an integrated multi-omics approach to elucidate the mechanisms by which the microbiome of microalga Isochrysis galbana inhibits the highly virulent fish pathogen V. anguillarum strain 90-11-286. Using a GFP-based inhibition assay, we confirmed potent pathogen suppression by the algal microbiome, achieving complete inhibition at a 1:1000 ratio of pathogen to microbiome. Through 16S rRNA gene amplicon sequencing, metagenomics, metatranscriptomics, and metabolomics, we characterized community composition, genomic potential, gene expression patterns, and metabolite production during pathogen challenge. The inhibitory microbiome was dominated by Alteromonas macleodii and Vreelandella alkaliphila, with high-quality metagenome-assembled genomes revealing substantial secondary metabolite biosynthetic potential. Metatranscriptomic analysis revealed active expression of biosynthetic gene clusters encoding, for example, non-ribosomal peptide synthetases, particularly a siderophore gene cluster in V. alkaliphila. Metabolomic profiling confirmed the production of hydroxamate siderophores in the microbiome, including desferrioxamine analogues, proferrioxamine G1t, and tenacibactin D, which accumulated during pathogen inhibition, as well as 10 putative new compounds. Notably, siderophore production was constitutive rather than pathogen-induced, suggesting iron competition as the primary inhibitory mechanism. Our findings demonstrate that iron sequestration through siderophore production represents a key strategy for pathogen suppression in marine microbial communities. This work provides molecular evidence for microbiome-mediated disease control and establishes a foundation for developing rationally designed multi-strain probiotic consortia for sustainable aquaculture applications, offering an environmentally friendly alternative to antibiotic-based pathogen management strategies.

microbiology↗

bioRxiv2025

Penicillium hordei acidification precipitates Bacillus subtilis lipopeptides to evade inhibition

Interkingdom interactions are crucial for community and ecosystem functioning, however secondary metabolites mediating interactions between plant beneficial bacteria and fungi remain understudied. Penicillium and Bacillus species can individually suppress soilborne phytopathogens and promote plant growth. Here, we showed that Penicillium hordei and Bacillus subtilis co-culture led to precipitation of B. subtilis lipopeptides, observed as white line in agar. Metabolomic analysis revealed B. subtilis triggered enhanced production of fungal terrestric acid and its biosynthetic intermediates, which induced lipopeptide precipitation to prevent P. hordei inhibition by chemical inactivation and physical barrier formation. Besides lipopeptide precipitation, terrestric acid-mediated acidification progressively reduced production of antifungal plipastatins. The lack of lipopeptide production permitted P. hordei to invade and overgrow B. subtilis colony. We demonstrated that the white line phenomenon was conserved among closely related fungi via secretion of terrestric, fulvic or barceloneic acids. Furthermore, terrestric acid at specific concentrations acted as a universal metabolite that drives B. subtilis lipopeptide precipitation even in distantly related fungi. This study provides new insights into acidification as a fungal defensive strategy that may promote co-existence with beneficial bacteria exhibiting strong antagonistic potential, thereby contributing to the formation of a stable rhizosphere community.

microbiology↗

bioRxiv2024

Discovery and Biosynthesis of Nyuzenamides D and E by Genome Mining in Streptomyces hygroscopicus

Nyuzenamides belong to the class of bioactive cinnamoyl moiety containing non-ribosomal peptides (NRPs). However, their biosynthetic gene cluster (BGC) remains unconfirmed. Genome-mining revealed a putative nyu BGC in Streptomyces hygroscopicus DSM 40578. Nyuzenamides D (1) and E (2) were subsequently isolated, and the structures were elucidated by detailed NMR spectroscopic and MS spectrometric data analyses. The absolute configuration of 1 was determined by a single-crystal X-ray diffraction study. Through retro-biosynthesis and CRISPR-genome editing, the non-ribosomal peptide synthetase biosynthetic gene cluster for nyuzenamides was confirmed. Our discovery enriches the diversity of cinnamoyl-containing nonribosomal peptides and validates the biosynthetic gene clusters for future genome-mining research.

microbiology↗

bioRxiv2024

Coupling of secondary metabolite production in Bacillus subtilis

Although not essential for their growth, the production of secondary metabolites increases the fitness of the producing microorganisms in their natural habitat by enhancing establishment, competition and nutrient acquisition. The Gram-positive soil-dwelling bacterium, Bacillus subtilis produces a variety of secondary metabolites. Here, we investigated the regulatory relationship between the non-ribosomal peptide surfactin and the sactipeptide bacteriocin subtilosin A. We discovered that B. subtilis mutants lacking surfactin production exhibited higher production of subtilosin A compared to their parental wild-type strain. Additionally, spatial visualization of B. subtilis production of metabolites demonstrated that surfactin secreted by a wild-type colony could suppress subtilosin A production in an adjacent mutant colony lacking surfactin production. Reporter assays were performed using mutants in specific transcriptional regulators that confirmed the role of ResD as an activator of the subtilosin A encoding BGC, while removal or Rok and AbrB repressors increased expression of the BGC that was further enhanced by additional deletion of surfactin, suggesting that a so far unidentified regulator might mediate the influence of surfactin on production of subtilosin A. Our study reveals a regulatory influence of one secondary metabolite on another, highlighting that the function of secondary metabolites could be more complex than its influence on other organisms and interactions among secondary metabolites could also contribute to their ecological significance. ImportanceSecondary metabolites play an important role in the life of microorganisms facilitating their fitness in the environment, including competing against other microorganisms, interacting with their host or environment, and allowing expansion in their environment. However, secondary metabolites also function as cue molecules influencing gene expression between and within species. Here, we describe that the non-ribosomally synthesized peptide surfactin repress the production of ribosomally synthesized and post translationally modified peptide, subtilosin A in Bacillus subtilis, revealing an ecological interaction between two secondary metabolites that could potentially influence the biocontrol efficiency of B. subtilis strain that depends on the production of these secondary metabolites against plant pathogen microorganisms.

microbiology↗

bioRxiv2024

Surfactin facilitates the establishment of Bacillus subtilis in synthetic communities

Soil bacteria are prolific producers of a myriad of biologically active secondary metabolites. These natural products play key roles in modern society, finding use as anti-cancer agents, as food additives, and as alternatives to chemical pesticides. As for their original role in interbacterial communication, secondary metabolites have been extensively studied under in vitro conditions, revealing a multitude of roles including antagonism, effects on motility, niche colonization, signaling, and cellular differentiation. Despite the growing body of knowledge on their mode of action, biosynthesis, and regulation, we still do not fully understand the role of secondary metabolites on the ecology of the producers and resident communities in situ. Here, we specifically examine the influence of Bacillus subtilis-produced cyclic lipopeptides (LPs) during the assembly of a bacterial synthetic community (SynCom), and simultaneously, explore the impact of LPs on B. subtilis establishment success in a SynCom propagated in an artificial soil microcosm. We found that surfactin production facilitates B. subtilis establishment success within multiple SynComs. Surprisingly, while neither a wild type nor a LP non-producer mutant had major impact on the SynCom composition over time, the B. subtilis and the SynCom metabolomes are both altered during co-cultivation. Overall, our work demonstrates the importance of surfactin production in microbial communities, suggesting a broad spectrum of action of this natural product.

microbiology↗

bioRxiv2024

Secondary metabolites shape Streptomyces-Streptomyces interaction: Mass Spectrometry Imaging reveals lydicamycins broadly induce sporulation

Streptomyces are major players in soil microbiomes, however, interactions involving Streptomyces and other actinobacteria are rarely described. The complex developmental cycle of actinobacteria necessitates a multi-omics approach to unravel the web of information. This study resulted from the observation of induced morphogenesis between two environmental isolates from the same site, Kitasatospora sp. P9-2B1 and Streptomyces sp. P9-2B2. When co-cultivated on potato dextrose agar (PDA), P9-2B2 induced a wave-like sporulation in strain P9-2B1. Using mass spectrometry imaging, we revealed that a suite of lydicamycins were present in this induced sporulation zone. Lydicamycin deficient mutants were generated using CRISPR Base-Editing and the inducible sporulation ceased, confirming their role in triggering morphological differentiation. In agar diffusion assays, pure lydicamycin was inhibitory when added concurrently with bacterial inoculation and induced sporulation with delayed addition. Subsequent testing of additional environmental isolates resulted in the same inducible sporulation wave phenomenon, including Streptomyces coelicolor M145 and M1146. Using transcriptomics, we observed the differential expression of genes related to early aerial mycelium development four days into cocultivation and the transitional genes responsible for development of spores on day 9. Along with these differentially expressed genes, we also observed numerous overall stress responses, specifically cell envelope stress responses. These findings uncovered actinobacteria interactions mediated by lydicamycins, pointing to a potential role of certain groups of bioactive metabolites in nature. ImportanceShifting away from an antibiotic discovery mindset, uncovering the chemical ecology of secondary metabolites is key to maximizing their biotechnological application. The reduced complexity of dual cultures allows for in depth analysis and investigation of these interactions via multi-omics provides orthogonal data leading to more robust conclusions. This study provides insight into the role of lydicamycins in dual cultures with other actinobacteria and provides an integral roadmap for future chemical ecology work between microorganisms, especially through the use of mass spectrometry imaging.

ecology↗

bioRxiv2023

Biosynthesis of the azoxy compound azodyrecin from Streptomyces mirabilis P8-A2

Azoxy compounds are a distinctive group of bioactive secondary metabolites, characterized by a unique RN=N+(O-)R moiety. The azoxy moiety is present in various classes of metabolites that exhibit various biological activities. The enzymatic mechanisms underlying azoxy bond formation remain enigmatic. Azodyrecins are cytotoxic azoxy metabolites produced by Streptomyces mirabilis P8-A2. Here we cloned and confirmed the putative azd biosynthetic gene cluster through CATCH cloning followed by expression and production of azodyrecins in two heterologous hosts, S. albidoflavus J1074 and S. coelicolor M1146, respectively. We explored the function of 14 enzymes in azodyrecin biosynthesis through gene knock-out using CRISPR-Cas9 base editing in the native producer, S. mirabilis P8-A2. The key intermediates were analyzed in the mutants through MS/MS fragmentation studies, revealing azoxy bond formation via the conversion of hydrazine to azo compound; followed by further oxygenation. Additionally, N-oxygenase and dehydrogenase activities were confirmed among 8 core biosynthetic genes and five helper genes. Moreover, the distribution of the azoxy biosynthetic gene clusters across Streptomyces spp. genomes is explored, highlighting the presence of these clusters in over 20% of the Streptomyces spp. genomes and revealing that azoxymycin and valanimycin are scarce, while azodyrecin and KA57A like clusters are widely distributed across the phylogenetic tree.

microbiology↗

bioRxiv2023

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

The role of antagonistic secondary metabolites produced by Pseudomonas protegens in suppression of soil-borne phytopathogens has been clearly documented. However, their contribution to the ability of P. protegens to establish in soil and rhizosphere microbiomes remains ambiguous. Here, we use a four-species synthetic community to determine how antibiotic production contributes to P. protegens community invasion and identify community traits that alter the abundance of key P. protegens antimicrobial metabolites (DAPG, pyoluteorin and orfamide A). Surprisingly, mutants deficient in antimicrobial production caused similar perturbations in community composition compared to invasion by wildtype P. protegens. Intriguingly, while pyoluteorin and orfamide A are secreted at levels toxic to individual bacterial strains, community-level resistance circumvents toxicity. Here, we identify the underlying mechanism by which the cyclic lipopeptide, orfamide A, is inactivated and degraded by Rhodococcus globerulus D757 and Stenotrophomonas indicatrix D763. Altogether, the demonstration that the synthetic community constrains P. protegens invasion by detoxifying its antibiotics may provide a mechanistic explanation to inconsistencies in biocontrol effectiveness in situ.

microbiology↗

bioRxiv2023

Competition for iron shapes metabolic antagonism between Bacillus subtilis and Pseudomonas

Siderophores have long been implicated in sociomicrobiology as determinants of bacterial interrelations. For plant-associated genera like Bacillus and Pseudomonas, siderophores are well known for their biocontrol functions. Here, we explored the functional role of the Bacillus subtilis siderophore bacillibactin in an antagonistic interaction with Pseudomonas marginalis. The presence of bacillibactin strongly influenced the outcome of the interaction in an iron-dependent manner. The bacillibactin producer B. subtilis restricts colony spreading of P. marginalis by repressing the transcription of histidine kinase-encoding gene gacS, thereby abolishing production of secondary metabolites such as pyoverdine and viscosin. By contrast, lack of bacillibactin restricted B. subtilis colony growth in a mechanism reminiscent of a siderophore tug-of-war for iron. Our analysis revealed that the Bacillus-Pseudomonas interaction is conserved across fluorescent Pseudomonas spp., expanding our understanding of the interplay between two genera of the most well-studied soil microbes.

microbiology↗

bioRxiv2023

Enhanced niche colonisation and competition during bacterial adaptation to a fungus

Bacterial-fungal interactions (BFIs) influence microbial community performance of most ecosystems and elicit specific microbial behaviours, including stimulating specialised metabolite production. Using a simple BFI system encompassing the Gram-positive bacterium Bacillus subtilis and the black mould fungus Aspergillus niger, we established a co-culture experimental evolution method to investigate bacterial adaptation to the presence of a fungus. In the evolving populations, B. subtilis was rapidly selected for enhanced production of the lipopeptide surfactin and accelerated surface spreading ability, leading to inhibition of fungal expansion and acidification of the environment. These phenotypes were explained by specific mutations in the DegS-DegU two-component system. In the presence of surfactin, fungal hyphae exhibited bulging cells with delocalised secretory vesicles and RlmA-dependent cell wall stress induction. Increased surfactin production typically enhances the competitive success of bacteria against fungi, which likely explains the primary adaption path in the presence of A. niger. Significance statementExperimental evolution and co-cultivation of different microbes are important and useful techniques for discovering new traits and unravelling cryptic regulatory connections. We combined these methods by evolving the Gram-positive bacterium Bacillus subtilis in the presence of the black mould fungus Aspergillus niger that were previously shown to engage in an intricate and physical interaction. Both are ubiquitous, environmentally and industrially relevant model microbes in the colonisation of rhizo- and endosphere and in the production of enzymes. Our results demonstrate how laboratory adaptation can be exploited to improve biocontrol properties of bacteria.

microbiology↗

bioRxiv2022

A Universal Language for Finding Mass Spectrometry Data Patterns

Even though raw mass spectrometry data is information rich, the vast majority of the data is underutilized. The ability to interrogate these rich datasets is handicapped by the limited capability and flexibility of existing software. We introduce the Mass Spec Query Language (MassQL) that addresses these issues by enabling an expressive set of mass spectrometry patterns to be queried directly from raw data. MassQL is an open-source mass spectrometry query language for flexible and mass spectrometer manufacturer-independent mining of MS data. We envision the flexibility, scalability, and ease of use of MassQL will empower the mass spectrometry community to take fuller advantage of their mass spectrometry data and accelerate discoveries.

bioinformatics↗

bioRxiv2021

GNPS Dashboard: Collaborative Analysis of Mass Spectrometry Data in the Web Browser

Access to web-based platforms has enabled scientists to perform research remotely. A critical aspect of mass spectrometry data analysis is the inspection, analysis, and visualization of the raw data to validate data quality and confirm statistical observations. We developed the GNPS Dashboard, a web-based data visualization tool, to facilitate synchronous collaborative inspection, visualization, and analysis of private and public mass spectrometry data remotely.

bioinformatics↗

bioRxiv2020

Iron-meditated fungal starvation by Lupine rhizosphere-associated and extremotolerant Streptomyces sp. S29 desferrioxamine production

Siderophores are iron-chelating compounds that aid iron uptake, one of the key strategies for microorganisms to carve out ecological niches in microbially diverse environments. Desferrioxamines are the principal siderophores produced by Streptomyces spp. Their biosynthesis has been well studied and as a consequence, the chemical potential of the pathway continues to expand. With all of this in mind, our study aimed to explore extremotolerant and Lupine rhizosphere-derived Streptomyces sp. S29 for its potential antifungal capabilities. Cocultivation of isolate S29 was carried out with Aspergillus niger and Botrytis cinerea, both costly fungal phytopathogens in the wine industry, to simulate their interaction within the rhizosphere. The results indicate that not only is Streptomyces sp. S29 extraordinary at producing hydroxamate siderophores but uses siderophore production as a means to starve the fungi of iron. High resolution LC-MS/MS followed by GNPS molecular networking was used to observe the datasets for desferrioxamines and guided structure elucidation of new desferrioxamine analogues. Comparing the new chemistry, using tools like molecular networking and MS2LDA, with the known biosynthesis, we show that the chemical potential of the desferrioxamine pathway has further room for exploration.

microbiology↗

bioRxiv2019

Repository-scale Co- and Re-analysis of Tandem Mass Spectrometry Data

Metabolomics data are difficult to find and reuse, even in public repositories. We, therefore, developed the Reanalysis of Data User (ReDU) interface (https://redu.ucsd.edu/), a community- and data-driven approach that solves this problem at the repository scale. ReDU enables public data discovery and co- or re-analysis via uniformly formatted, publicly available MS/MS data and metadata in the Global Natural Product Social Molecular Networking Platform (GNPS), consistent with findable, accessible, interoperable, and reusable (FAIR) principles.1

bioinformatics↗