A1 Refereed original research article in a scientific journal
Facultative predation expands the ecological repertoire of Streptomyces
Authors: Yamada, Keith; Koroleva, Arina; Tirkkonen, Heli; Siitonen, Vilja; Laughlin, Mitchell; Moglia, Amanda; Matroodi, Soheila; Akhgari, Amir; Mazurier, Guillaume; Niemi, Jarmo; Metsä-Ketelä, Mikko
Editors: Hoskisson Paul A.
Publication year: 2026
Journal: mBio
ISSN: 2161-2129
eISSN: 2150-7511
DOI: https://doi.org/10.1128/mbio.00563-26
Publication's open availability at the time of reporting: Open Access
Publication channel's open availability : Open Access publication channel
Web address : https://doi.org/10.1128/mbio.00563-26
Self-archived copy’s web address: https://research.utu.fi/converis/portal/detail/Publication/523084589
Self-archived copy's licence: CC BY
Self-archived copy's version: Publisher`s PDF
Microbial predators obtain energy from killing other living cells. Streptomyces are soil bacteria that are known to produce numerous catabolic enzymes and antimicrobial compounds to defend against competing organisms. Here, we demonstrate that Streptomyces are predatory bacteria that prey on Saccharomyces cerevisiae. Time-lapse fluorescence microscopy and scanning electron microscopy revealed that predation is initiated by physical contact between Streptomyces lavendulae YAKB-15 and yeast cells. Comparative transcriptomics indicated that the interaction triggered the production of numerous extracellular catabolic enzymes and natural products, while delaying morphological development. Proteomics and enzyme assays confirmed co-culture-dependent production of carbohydrate-active enzymes (CAZymes), including various glucanases, mannosidases, and chitinases, which degraded the yeast cell wall. Streptomyces lavendulae YAKB-15 destabilized yeast cell membranes through the production of two polyene antifungal agents, pentamycin and filipin III. We found that the bioactivity was enhanced by cell-associated cholesterol oxidase ChoD, putatively by modulating sterol extraction kinetics. Metabolomic analyses suggest Streptomyces assimilates yeast cell sterols as nutrients. Furthermore, we observed the depletion of yeast-derived phosphatidylcholine and phosphatidylethanolamine lipids, which points to their consumption. We show that yeast predation is a common phenomenon in Streptomyces, which changes the paradigm of how these bacteria should be considered in the soil microbiome ecosystem.IMPORTANCESoil is a rich environment for microbes, where they compete for space and resources. Streptomyces bacteria are well known for their ability to synthesize natural products, particularly antibiotics, that are used in chemical defense against competing microbes. Here, we show that Streptomyces are, in fact, predatory bacteria. Upon encountering yeast cells, Streptomyces initiate the production of numerous enzymes that digest the cell wall and cell membrane. In addition, the interaction triggers the production of natural products that destabilize the yeast cell membrane. Collectively, these actions lead to the death of yeast cells and release of cellular building blocks that Streptomyces can use as nutrients. The work fundamentally shifts the paradigm of how Streptomyces are perceived within the soil microbiome ecosystem.
Keywords: Streptomyces; catabolic enzymes; polyenes; predation; yeast.
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Funding information in the publication:
The authors wish to acknowledge CSC—IT Center for Science, Finland, for computational resources. Mass spectrometry analyses were performed at the Turku Proteomics Facility supported by Biocenter Finland. Fluorescence imaging was performed at the Cell Imaging and Cytometry Core, Turku Bioscience Centre, Turku, Finland, with the support of Biocenter Finland. Cultivations were performed using the shakers and bioreactors managed by Turku Protein Core.
The authors acknowledge the Electron Microscopy Laboratory, Institute of Biomedicine, University of Turku, for SEM sample preparation and the Materials Research Infrastructure (MARI) at the Department of Physics and Astronomy, University of Turku, for access and support with the SEM facilities.
We thank Associate Professor Anssi Malinen for providing Sacc. cerevisiae BY25610. We thank funding from the Novo Nordisk Foundation Grant NNF22OC0079557 (M.M.-K) and the Finnish Cultural Foundation (K.Y).
Keith Yamada: Conceptualization, Investigation, Formal analysis, Visualization, Funding acquisition, Writing—original draft, Writing—review & editing. Arina Koroleva: Conceptualization, Investigation, Formal analysis, Visualization, Writing—original draft, Writing—review & editing. Heli Tirkkonen: Investigation, Formal analysis, Visualization, Writing—review & editing. Vilja Siitonen: Investigation, Formal analysis. Mitchell Laughlin: Investigation, Formal analysis. Soheila Matroodi: Investigation, Formal analysis. Amir Akhgari: Investigation, Formal analysis. Guillaume Mazurier: Investigation, Formal analysis. Jarmo Niemi: Conceptualization, Supervision, Writing—review & editing. Mikko Metsä-Ketelä: Conceptualization, Project administration, Supervision, Funding acquisition, Writing—original draft, Writing—review & editing.
