Scott Alexander Jarmusch

The Gram-negative bacterium Dickeya solani causes potato soft rot and blackleg, and effective control measures remain limited. We evaluated the agricultural potential of Aspergillus sulphureoviridis , a recently described and chemically unexplored fungus. Bioactivity-guided molecular networking of extracts that inhibited D. solani led to the isolation of six metabolites: cladobotrin IV ( 1 ), two new analogs cladobotrin VII and cladobotrin VIII ( 2 and 3 ), and the orsellinic acid-derived metabolites F9775A ( 4 ), F9775B ( 5 ), and violaceol I ( 6 ). Among these, the polyketide F9775B ( 5 ) inhibited both Bacillus subtilis and D. solani (IC ₅₀ 89.4 and 59.3 µg/mL, respectively), while cladobotrin VIII ( 3 ) was active against B. subtilis (IC ₅₀ 95 µg/mL). Furthermore, co-culture with the beneficial rhizobacterium B. subtilis revealed an additional interaction: A. sulphureoviridis induced a pronounced antifungal defense in B. subtilis . MALDI-MSI showed that this interaction spatially enriched canonical Bacillus lipopeptides (surfactins and fengycins) at the confrontation zone, whereas the shortened fengycins variants were detected only intracellularly within the Bacillus colony. This indicates that A. sulphureoviridis triggers B. subtilis to mobilize and secrete bioactive lipopeptides for defense while retaining the less active short-chain fengycin-like compounds intracellularly. Together, these results establish A. sulphureoviridis as both a source of antimicrobial compounds and an inducer of beneficial bacterial defenses, providing a rationale for further in-planta validation and development as a sustainable biocontrol agent. IMPORTANCE: Potato soft rot and blackleg caused by Dickeya solani are difficult to control, creating a need for sustainable biocontrol strategies. Here, we show that the recently described fungus Aspergillus sulphureoviridis has a dual function relevant to crop protection. Bioactivity-guided molecular networking enabled the targeted discovery of six antibacterial metabolites, including two new cladobotrin analogs and the first cladobotrins reported from Aspergillus , and identified F9775B as the main metabolite active against D. solani . Using MALDI mass spectrometry imaging, we further demonstrate that A. sulphureoviridis does not act only through its own metabolites but also triggers Bacillus subtilis to enrich and deploy surfactin and fengycins at the interaction zone. These findings expand the known chemical diversity of A. sulphureoviridis and support its potential as a dual-function contributor to sustainable microbe-based biocontrol.

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 nisin’s antimicrobial activity, the intrinsic resistance of both isolates suggests a role beyond detoxification. We further detected nisin biosynthetic genes in the source environment, supporting nisin’s 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. Importance: Natural 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.

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.

Vibrio anguillarum remains a major problem in marine aquaculture, motivating the search for ecologically grounded microbial strategies for pathogen control. We previously showed that a coculture of Vreelandella alkaliphila D2 and Sulfitobacter pontiacus D3, isolated from Isochrysis galbana, inhibited V. anguillarum more strongly than either strain alone. Here, we demonstrate that this suppression is driven by desferrioxamines (DFO) produced by V. alkaliphila, enabling synergistic iron sequestration through siderophore sharing with S. pontiacus. Mass spectrometry imaging revealed multiple DFO analogues spatially colocalized within inhibition zones and confirmed xenosiderophore uptake of DFO analogues by Sulfitobacter. Bioassays showed iron-chelation activity in V. alkaliphila, while iron supplementation and DFO-B standards validated siderophore-mediated bacteriostatic inhibition. Untargeted metabolomics found no increase in siderophore abundance in coculture, indicating that enhanced inhibition results from shared iron chelation rather than elevated production. Genome mining identified a complete DFO biosynthetic gene cluster in V. alkaliphila and a desferrioxamine receptor in Sulfitobacter. Finally, in axenic I. galbana, Sulfitobacter, alone or with Vreelandella, maintained V. anguillarum at the level of inoculation, highlighting that the substrate has a marked influence on inhibitory activity. Together, these findings show how DFOs act as shared public goods that enable both cooperation and pathogen antagonism.

Endogenous antimicrobial peptides (AMPs) derived from host proteins represent a largely underexplored class of natural products tied to innate immunity. Here, we investigated collagen proteins as a source of latent α-helical AMPs encoded within nonfibrous extracellular matrix domains. Using a targeted in silico approach, verified collagen sequences were mined and prioritized based on secondary structure and three essential physicochemical properties: net charge, Boman index, and hydrophobic moment, yielding 107 predicted α-helical AMP candidates. The highest ranked peptides were synthesized and experimentally evaluated alongside benchmark AMPs and peptides prioritized by machine learning-based prediction tools. Three collagen-derived peptides identified by the targeted physicochemical approach exhibited broad-spectrum bioactivity against bacterial and fungal pathogens with minimum inhibitory concentrations comparable to those of LL-37 and melittin. In contrast, peptides ranked highly by machine learning predictors showed reduced or no activity. Collagen-derived peptides disrupted bacterial mimicking lipid membranes yet displayed markedly reduced cytotoxicity toward human cells, maintaining high viability at concentrations well above their antimicrobial MICs. These findings demonstrate that nonfibrous domains of extracellular matrix collagens constitute a previously underexplored reservoir of endogenous antimicrobial peptides with favorable biocompatibility, expanding the natural product space of host defense peptides and identifying collagen-derived AMPs as promising scaffolds for future antimicrobial discovery.

Interkingdom interactions are crucial for community and ecosystem function; however, the secondary metabolites mediating interactions between plant beneficial bacteria and fungi remain understudied. Beneficial 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 lines in agar. Metabolomic analysis revealed that the presence of B. subtilis enhanced the production of fungal terrestric acid and its biosynthetic intermediates, which in turn induced lipopeptide precipitation, preventing P. hordei inhibition through 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 the 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.

Streptomyces are major players in soil microbiomes; however, their interactions with other actinobacteria remain largely unexplored. Given the complex developmental cycle of actinobacteria, a multi-omics approach is essential to unravel the interactions. This study originated 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, P9-2B2 triggered a wave-like sporulation pattern in strain P9-2B1. Mass s pectrometry imaging revealed that a suite of lydicamycins accumulated in the induced sporulation zone. Using CRISPR base editing, lydicamycin-deficient mutants were generated, and the inducible sporulation was ceased, confirming the role of lydicamycin in triggering morphological differentiation. In agar diffusion assays, pure lydicamycin was inhibitory when added concurrently with bacterial inoculation but induced sporulation when added later. The same inducible sporulation wave phenomenon was also observed in additional environmental isolates and Streptomyces coelicolor M145 and M1146. Transcriptomics analysis revealed differential gene expression linked to early aerial mycelium development at 4 days into co-culture, the transitional genes responsible for the development of spores at day 9, together with numerous genes for overall stress responses, particularly cell envelope stress responses. These findings highlight previously unrecognized actinobacteria interactions mediated by lydicamycins, suggesting a broader ecological role of bioactive metabolites in microbiomes. IMPORTANCE: Moving beyond an antibiotic discovery mindset, exploring the chemical ecology of secondary metabolites is key to maximizing their biotechnological potential. Dual cultures offer reduced complexity, enabling an in-depth analysis of these interactions via multi-omics, which provides complementary data for more robust conclusions. This study sheds light on the role of lydicamycins in dual cultures with other actinobacteria and establishes an integral roadmap for future chemical ecology work between microorganisms, particularly through mass spectrometry imaging.

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.

Despite being information rich, the vast majority of untargeted mass spectrometry data are underutilized; most analytes are not used for downstream interpretation or reanalysis after publication. The inability to dive into these rich raw mass spectrometry datasets is due to the limited flexibility and scalability of existing software tools. Here we introduce a new language, the Mass Spectrometry Query Language (MassQL), and an accompanying software ecosystem that addresses these issues by enabling the community to directly query mass spectrometry data with an expressive set of user-defined mass spectrometry patterns. Illustrated by real-world examples, MassQL provides a data-driven definition of chemical diversity by enabling the reanalysis of all public untargeted metabolomics data, empowering scientists across many disciplines to make new discoveries. MassQL has been widely implemented in multiple open-source and commercial mass spectrometry analysis tools, which enhances the ability, interoperability and reproducibility of mining of mass spectrometry data for the research community.