This study demonstrates that Bacillus velezensis SPE2, a low-abundance isolate from the phycosphere of dinoflagellate, exhibits a wide degree of antagonistic activity against multiple marine Flavobacteriaceae strains, a dominant taxonomic group across the phycosphere of diverse phytoplankton species.
Abstract
Background
The phycosphere is a nutrient-rich microenvironment surrounding phytoplankton cells and serves as a hotspot for microbial interactions by releasing phytoplankton-derived organic molecules to dynamically attract and support the colonization of heterotrophic bacteria. Although the taxonomic composition, metabolic profiles, and host-microbe interactions of phycosphere bacterial communities have been extensively characterized, the underlying mechanisms driving competition among these co-existing bacterial taxa remain poorly understood.
Results
In this study, we demonstrate that Bacillus velezensis SPE2, a low-abundance isolate from the phycosphere of dinoflagellate, exhibits a wide degree of antagonistic activity against multiple marine Flavobacteriaceae strains, a dominant taxonomic group across the phycosphere of diverse phytoplankton species. Through an integrative approach combining genetics and metabolomics, we show that the antagonistic behavior of strain SPE2 is primarily mediated by the production of bioactive secondary metabolites. Activity-guided purification further leads to the identification of two antibacterial surfactin-like lipopeptides as key exometabolites responsible for these inhibitory effects. Mechanistically, these lipopeptides exert their antibacterial activity against Flavobacteriaceae species by disrupting the integrity of bacterial cell membranes.
Conclusions
Our findings reveal surfactin-like lipopeptides as key molecular mediators of bacterial interference competition, conferring a competitive strategy for Bacillus species to secure persistence in the phycosphere. Moreover, this work underscores phycosphere as a largely untapped ecological niche for discovering novel bioactive compounds with potential applications in pharmaceutical and biotechnological fields.
The treatment of invasive fungal infections remains challenging due to the limited availability of antifungal agents and the rapid emergence of drug resistance. Endophytic fungi, shaped by chemically mediated interactions within plant-associated niches, represent an important source of antifungal activity. Here, we investigated the contact-independent antagonistic potential of the endophytic fungus Diaporthe biconispora PBS24-3 against two opportunistic Penicillium species. In dual-culture assays, D. biconispora PBS24-3 consistently formed stable inhibition zones without direct hyphal contact, and antifungal activity was fully reproduced by cell-free culture filtrates, indicating a secretome-mediated mode of antagonism rather than physical competition. The inhibitory effect was target-dependent, with stronger mycelial growth inhibition observed for P. citrinum (65.97 ± 2.22%) than for P. sumatrense (45.10 ± 4.45%); notably, the inhibition against P. sumatrense was comparable to that of itraconazole under the same experimental conditions. Microscopic examination revealed hyphal distortion and reduced conidiation in treated Penicillium cultures. In parallel, untargeted UHPLC-Orbitrap-HRMS/MS metabolomic profiling combined with molecular network analysis revealed a chemically complex, multi-component secretome dominated by secondary-metabolite families consistent with antifungal activity. These findings demonstrate that D. biconispora PBS24-3 mediates antifungal antagonism through a contact-independent, secretome-driven mechanism.
Ling Yang, Y. Tan, C. Phan et al.· International Microbiology· 0 citations
This study provides novel and unexpected insights into the involvement of a LuxR homolog in regulating a QS system in Gram-positive bacteria and demonstrates that functional GBL-based QS systems are conserved and active in R. erythropolis.
Héloïse Bizière-Maco, Nathan Jordier, J. F. Barbosa-de-Bessa et al.· Frontiers in Microbiology· 0 citations
Cyanobacteria are key prokaryotic primary producers in diverse ecosystems, yet the role of cyanobacterial siderophores in shaping their associated microbiomes remains unexplored. Our study demonstrates the benefits provided to the heterotrophic co-habitants of filamentous cyanobacteria in terrestrial microbial biofilms, focusing on the recently discovered widespread siderophores cyanochelins. To address the acceptance of cyanochelin B (CychB) across multiple bacterial classes, we first investigated its role in providing iron to a model siderophore producer P. aeruginosa PAO1 and selected Pseudomonas natural isolates, which were found to utilize CychB under iron limiting conditions while downregulating endogenous siderophore production. In response to CychB, PAO1 expresses a siderophore internalization cluster, which is localized in multiple Pseudomonas natural isolates. Using metagenome analysis, we characterized the bacterial community recruited along with CychB producing Phormidesmis cyanobacteria under long-term iron starvation. Potential CychB acceptor bacteria associated with the CychB producer were predominantly lacking endogenous siderophore machineries. Using siderophore selective pressure, we isolated a genuine CychB acceptor, gram-negative bacterium Methyloversatilis sp. S146 and demonstrated that its genome hosts an iron processing cluster overexpressed after CychB feeding, recognizing Methyloversatilis as a candidate for further mechanistic investigation of iron acquisition–driven microbial interactions. Our results indicate that CychB supports a specific subset of co-habiting heterotrophic bacteria during iron starvation, further emphasizing the role of cyanobacteria as key drivers of nutrient flows within globally important microbial soil crust ecosystems, supporting microbial life in nutrient-limited environments. These findings provide a mechanistic foundation to elucidate the role of cyanochelins as a public good in these communities.
B. P. Falcao, Martinez Yerena Jose Alberto, T. Galica et al.· bioRxiv· 0 citations
BACKGROUND
Pelagic Sargassum has undergone significant range expansion and dramatic blooms in the Atlantic over the past 15 years. This alga's microbiome provides symbiotic functions that are believed to contribute to its ecological success. Recent research shows that Sargassum-associated bacteria are enriched in integrated prophages compared to the surrounding seawater and that these prophages are inducible by chemical and ultraviolet treatment.
RESULTS
Here, we investigated a Sargassum-derived in vitro multispecies biofilm encompassing the dominant heterotrophic microbial members associated with Sargassum to probe the impacts of prophage induction on the composition of Sargassum microbiomes. Induction was quantified by coverage-based virus-to-host ratios in chemically induced treatments with Mitomycin C and non-induced controls, and the community composition and metabolic profiles were analyzed after Mitomycin C treatment. Chemical induction led to a significant increase in abundance and virus-to-host ratio of viral genomes linked to Vibrio metagenome-assembled genomes. This was accompanied by altered biofilm community composition, with a reduction in Vibrio bacterial abundance that opened niche space for other biofilm members in the genera Pseudoalteromonas, Alteromonas, and Cobetia. The induced Vibrio-associated phages encoded genes involved in quorum sensing, biofilm formation, virulence, and host metabolism. Induction led to the depletion of 17 metabolic modules, including functions related to energy metabolism and nitrogen utilization.
CONCLUSION
Due to the high frequency of lysogeny in the Sargassum microbiome and the susceptibility of prophages to chemical and ultraviolet light induction, these results suggest that prophage integration and induction are mechanisms that contribute to structuring the Sargassum microbiome and its functional profiles, potentially aiding in microbiome flexibility in changing environmental contexts.
A. K. Stiffler, N. Varona, Bailey A. Wallace et al.· Environmental Microbiome· 0 citations
Cyanobacteria are among the oldest oxygenic photosynthetic organisms on Earth and occupy an extraordinarily broad range of ecological niches, from marine and freshwater systems to extreme terrestrial habitats. Their capacity to withstand intense ultraviolet radiation, desiccation, nutrient scarcity and microbial competition is underpinned by a rich biosynthetic repertoire of secondary metabolites, many of which display potent antibacterial, antifungal and antiviral activities. This review examines the chemical diversity, biosynthetic origin and mechanisms of action of cyanobacterial antimicrobial metabolites, situating the discussion within the contemporary crisis of antimicrobial resistance and the stagnation of conventional antibiotic discovery pipelines. Cyclic and linear peptides, alkaloids, polyketides, macrolides, lipids and lectins isolated predominantly from filamentous genera such as Nostoc, Lyngbya, Moorea, Fischerella, Calothrix and Anabaena are discussed with reference to their molecular targets, which include bacterial RNA polymerase, fungal ergosterol-rich membranes, viral envelope glycoproteins and components of the bacterial cell wall and electron transport chain. The contribution of non-ribosomal peptide synthetase and polyketide synthase gene clusters to this chemical diversity is examined alongside genome-mining approaches that have accelerated the discovery of cryptic biosynthetic pathways. Biotechnological obstacles to translating laboratory findings into clinically usable agents, including low and inconsistent yields, cultivation scale-up difficulties, structural complexity and the toxicological profile of certain cyanobacterial metabolites, are critically appraised, together with emerging nanoformulation strategies intended to overcome bioavailability constraints. The review concludes that cyanobacteria represent a comparatively underexploited reservoir of structurally novel antimicrobial chemotypes that merit sustained, mechanistically grounded investigation, while acknowledging that translational progress remains constrained by supply, safety and regulatory hurdles that have yet to be systematically resolved.
Kirtipal Singh, Akanksha Pal· Microbiology Research Journa...· 0 citations