Abstract
Fungi that live in deep-sea sediments experience extreme environmental conditions, yet little is known about how they adapt their growth and metabolism to these stresses. This study explores the morphogenetic and metabolomic responses of three black yeasts—Salinomyces thailandicus, Neophaeotheca triangularis, and N. salicorniae—isolated from deep-sea sediments of the Gulf of Mexico under varying salinities and exposure to the melanin inhibitor pthalide. Each species displays distinct growth adaptations: S. thailandicus shifts from filamentous to yeast-like forms as salinity increases, N. triangularis exhibits the opposite trend, and N. salicorniae remains dimorphic but grows more slowly at high salinities. Phthalide inhibits hyphal development in all three species. An exploratory metabolic analysis, conducted on pooled samples, indicates that metabolomic profiles change with salinity, with fatty acids dominating across species, suggesting membrane remodeling as an adaptation to osmotic stress. N. triangularis uniquely accumulates amino acids and peptides, a response previously reported mainly in plants. Additional metabolites, including aminocyclitols and compounds associated with extracellular polymeric substances, suggest the involvement of uncharacterized adaptive mechanisms contributing to stress protection. These findings advance our understanding of how black yeasts adapt to osmotic stress and provide a foundation for future studies.
Similar content being viewed by others
Data availability
Data sets of eukaryotic nuclear rRNA/ITS gene amplicon sequences were deposited in GenBank (database accession numbers shown in Table 1). LC-MS/MS data can be accessed at MassIVE (accession no. MSV000098170; accessed June 12, 2025), https://massive.ucsd.edu/ProteoSAFe/dataset.jsp?task=e9bb27d863a44851af057b411b5bd4e5. The parameters for feature-based molecular networking and spectral matching using all data sets, MolDiscovery, and DEREPLICATOR+ results are available in the links found in the Supplementary material.
References
Bik, H. M., Halanych, K. M., Sharma, J. & Thomas, W. K. Dramatic shifts in benthic microbial eukaryote communities following the Deepwater Horizon oil spill. PloS One 7, e38550 (2012).
Herzka, S. Z., Zaragoza Álvarez, R. A., Peters, E. M. & Hernández Cárdenas G. In Atlas de línea base ambiental del golfo de México (tomo III, Segunda Parte), México: Consorcio de Investigación del Golfo de México (ed. Herzka, S. Z.) (México, 2021).
Yáñez-Arancibia, A. & Day, J. W. The Gulf of Mexico: towards an integration of coastal management with large marine ecosystem management. Ocean Coast. Manag. 47, 537–563 (2004).
Vargas-Gastélum, L. et al. Targeted ITS1 sequencing unravels the mycodiversity of deep-sea sediments from the Gulf of Mexico. Environ. Microbiol. 21, 4046–4061 (2019).
Romero-Hernández, L. et al. Extra-heavy crude oil degradation by Alternaria sp. isolated from deep-sea sediments of the Gulf of Mexico. Appl. Sci. 11, 6090 (2021).
Vélez, P., Gasca-Pineda, J. & Riquelme, M. Cultivable fungi from deep-sea oil reserves in the Gulf of Mexico: Genetic signatures in response to hydrocarbons. Mar. Environ. Res. 153, 104816 (2020).
Mitchison-Field, L. M. et al. Unconventional cell division cycles from marine-derived yeasts. Curr. Biol. 29, 3439–3456.e3435 (2019).
Gunde-Cimerman, N., Zalar, P., de Hoog, S. & Plemenitaš, A. Hypersaline waters in salterns–natural ecological niches for halophilic black yeasts. FEMS Microbiol. Ecol. 32, 235–240 (2000).
Crous, P. W. et al. Fungal Planet description sheets: 400-468. Persoonia 36, 316–458 (2016).
Selbmann, L. et al. Shed light in the dark lineages of the fungal tree of Life-STRES. Life 10, 362 (2020).
Sterflinger, K. In Biodiversity and Ecophysiology of Yeasts (eds. Péter, G., Rosa, C.) 501–514 (Springer, 2006).
Goshima, G. Growth and division mode plasticity is dependent on cell density in marine-derived black yeasts. Genes Cells 27, 124–137 (2022).
Gunde-Cimerman, N. & Plemenitaš. A. Ecology and molecular adaptations of the halophilic black yeast Hortaea werneckii. In Reviews in Environmental Science and Biotechnology. Life in Extreme Environments. (eds Amils, R., Ellis-Evans, C. & Hinghofer-Szalkay, H.) 177–185 (Springer, Dordrecht, 2006).
Gunde-Cimerman, N., Plemenitas, A. & Oren, A. Strategies of adaptation of microorganisms of the three domains of life to high salt concentrations. FEMS Microbiol. Rev. 42, 353–375 (2018).
Kogej, T., Wheeler, M. H., Lanisnik Rizner, T. & Gunde-Cimerman, N. Evidence for 1,8-dihydroxynaphthalene melanin in three halophilic black yeasts grown under saline and non-saline conditions. FEMS Microbiol. Lett. 232, 203–209 (2004).
Kogej, T. et al. Osmotic adaptation of the halophilic fungus Hortaea werneckii: role of osmolytes and melanization. Microbiology 153, 4261–4273 (2007).
Camacho, E. et al. The structural unit of melanin in the cell wall of the fungal pathogen Cryptococcus neoformans. J. Biol. Chem. 294, 10471–10489 (2019).
Pralea, I. E. et al. From extraction to advanced analytical methods: the challenges of melanin analysis. Int. J. Mol. Sci. 20, 3943 (2019).
Cao, W. et al. Unraveling the structure and function of melanin through synthesis. J. Am. Chem. Soc. 143, 2622–2637 (2021).
Pal, A. K., Gajjar, D. U. & Vasavada, A. R. DOPA and DHN pathway orchestrate melanin synthesis in Aspergillus species. Med. Mycol. 52, 10–18 (2014).
Jiménez-Gómez, I. et al. Surviving in the brine: a multi-omics approach for understanding the physiology of the halophile fungus Aspergillus sydowii at saturated NaCl concentration. Front. Microbiol. 13, 840408 (2022).
Agrawal, S., Chavan, P. & Dufosse, L. Hidden treasure: Halophilic fungi as a repository of bioactive lead compounds. J. Fungi 10, https://doi.org/10.3390/jof10040290 (2024).
Gadanho, M., Almeida, J. M. & Sampaio, J. P. Assessment of yeast diversity in a marine environment in the south of Portugal by microsatellite-primed PCR. Antonie Van. Leeuwenhoek 84, 217–227 (2003).
Gardes, M. & Bruns, T. D. ITS primers with enhanced specificity for basidiomycetes-application to the identification of mycorrhizae and rusts. Mol. Ecol. 2, 113–118 (1993).
White, T. J., Bruns, T., Lee, S. & Taylor, J. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In PCR Protocols: A Guide to Methods and Applications, 18, 315–322 (Academic Press, 1990).
Kurtzman, C. P. & Robnett, C. J. Identification and phylogeny of ascomycetous yeasts from analysis of nuclear large subunit (26S) ribosomal DNA partial sequences. Antonie Van. Leeuwenhoek 73, 331–371 (1998).
Kumar, S. et al. MEGA12: Molecular Evolutionary Genetic Analysis version 12 for adaptive and green computing. Mol. Biol. Evol. 41, msae263 (2024).
Benson, D. A. et al. GenBank. Nucleic Acids Res. 41, D36–D42 (2012).
Tamura, K. & Nei, M. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol. Biol. Evol. 10, 512–526 (1993).
Atlas, R. M. The Handbook of Microbiological Media for the Examination of Food (CRC press, 2006).
Kejzar, A., Gobec, S., Plemenitas, A. & Lenassi, M. Melanin is crucial for growth of the black yeast Hortaea werneckii in its natural hypersaline environment. Fungal Biol. 117, 368–379 (2013).
Hickey, P. C., Swift, S. R., Roca, M. G. & Read, N. D. Live-cell imaging of filamentous fungi using vital fluorescent dyes and confocal microscopy. In Methods in Microbiology. Microbial Imaging. (eds Savidge, T. & Charalabos, P.) 34, 63–87 (Academic Press, 2004).
Schindelin, J. et al. Fiji: an open-source platform for biological-image analysis. Nat. Methods 9, 676–682 (2012).
Gniewosz, M. & Duszkiewicz-Reinhard, W. Comparative studies on pullulan synthesis, melanin synthesis and morphology of white mutant Aureobasidium pullulans B-1 and parent strain A.p.-3. Carbohydr. Polym. 72, 431–438 (2008).
Schmid, R. et al. Integrative analysis of multimodal mass spectrometry data in MZmine 3. Nat. Biotechnol. 41, 447–449 (2023).
Nothias, L. F. et al. Feature-based molecular networking in the GNPS analysis environment. Nat. Methods 17, 905–908 (2020).
Dührkop, K. et al. SIRIUS 4: a rapid tool for turning tandem mass spectra into metabolite structure information. Nat. Methods 16, 299–302 (2019).
Hernández-Melgar, A. G., Guerrero, A. & Moreno-Ulloa, A. Chronic exposure to petroleum-derived hydrocarbons alters human skin microbiome and metabolome profiles: a pilot study. J. Proteome Res. 23, 4273–4285 (2024).
Aron, A. T. et al. Reproducible molecular networking of untargeted mass spectrometry data using GNPS. Nat. Protoc. 15, 1954–1991 (2020).
Sumner, L. W. et al. Proposed minimum reporting standards for chemical analysis: chemical analysis working group (CAWG) metabolomics standards initiative (MSI). Metabolomics 3, 211–221 (2007).
Cao, L. et al. MolDiscovery: learning mass spectrometry fragmentation of small molecules. Nat. Commun. 12, 3718 (2021).
Dührkop, K., Shen, H., Meusel, M., Rousu, J. & Böcker, S. Searching molecular structure databases with tandem mass spectra using CSI: FingerID. Proc. Natl. Acad. Sci. 112, 12580–12585 (2015).
Mohimani, H. et al. Dereplication of microbial metabolites through database search of mass spectra. Nat. Commun. 9, 4035 (2018).
Dührkop, K. et al. Systematic classification of unknown metabolites using high-resolution fragmentation mass spectra. Nat. Biotechnol. 39, 462–471 (2021).
Chung, D., Kim, H. & Choi, H. S. Fungi in salterns. J. Microbiol. 57, 717–724 (2019).
Carr, E. C. et al. Characterization of a novel polyextremotolerant fungus, Exophiala viscosa, with insights into its melanin regulation and ecological niche. G3 Genes Genomes Genet. 13, 1–37 (2023).
Czachura, P., Owczarek-Kościelniak, M. & Piątek, M. Salinomyces polonicus: a moderately halophilic kind of the most extremely halotolerant fungus Hortaea werneckii. Fungal Biol. 125, 459–468 (2021).
Abdollahzadeh, J., Groenewald, J. Z., Coetzee, M. P. A., Wingfield, M. J. & Crous, P. W. Evolution of lifestyles in Capnodiales. Stud. Mycol. 95, 381–414 (2020).
Kogej, T., Gorbushina, A. A. & Gunde-Cimerman, N. Hypersaline conditions induce changes in cell-wall melanization and colony structure in a halophilic and a xerophilic black yeast species of the genus Trimmatostroma. Mycological Res. 110, 713–724 (2006).
Zalar, P. et al. The extremely halotolerant black yeast Hortaea werneckii - a model for intraspecific hybridization in clonal fungi. IMA Fungus 10, 1–27 (2019).
Coleine, C. et al. Peculiar genomic traits in the stress-adapted cryptoendolithic Antarctic fungus Friedmanniomyces endolithicus. Fungal Biol. 124, 458–467 (2020).
Kralj Kuncic, M., Kogej, T., Drobne, D. & Gunde-Cimerman, N. Morphological response of the halophilic fungal genus Wallemia to high salinity. Appl. Environ. Microbiol. 76, 329–337 (2010).
de Souza Pereira, R. & Geibel, J. Direct observation of oxidative stress on the cell wall of Saccharomyces cerevisiae strains with atomic force microscopy. Mol. Cell. Biochem. 201, 17–24 (1999).
Jacobson, E. S. & Ikeda, R. Effect of melanization upon porosity of the cryptococcal cell wall. Med. Mycol. 43, 327–333 (2005).
Turk, M. et al. Salt-induced changes in lipid composition and membrane fluidity of halophilic yeast-like melanized fungi. Extremophiles 8, 53–61 (2004).
Heidarzadeh, A. Role of amino acids in plant growth, development, and stress responses: A comprehensive review. Discov. Plants 2, 1–31 (2025).
Derkaczew, M., Martyniuk, P., Osowski, A. & Wojtkiewicz, J. Cyclitols: From basic understanding to their association with neurodegeneration. Nutrients 15, 2029 (2023).
Mahmud, T. Progress in aminocyclitol biosynthesis. Curr. Opin. Chem. Biol. 13, 161–170 (2009).
Chrissian, C. et al. Solid-state NMR spectroscopy identifies three classes of lipids in Cryptococcus neoformans melanized cell walls and whole fungal cells. J. Biol. Chem. 295, 15083–15096 (2020).
Koroleva, E. et al. Exploring polyamine metabolism of the yeast-like fungus, Emergomyces africanus. FEMS Yeast Res. 24, foae038 (2024).
Niu, M. et al. Fungal oxylipins direct programmed developmental switches in filamentous fungi. Nat. Commun. 11, 5158 (2020).
Naruzawa, E. S., Malagnac, F. & Bernier, L. Effect of linoleic acid on reproduction and yeast–mycelium dimorphism in the Dutch elm disease pathogens. Botany 94, 31–39 (2016).
Kupfahl, C., Tsikas, D., Niemann, J., Geginat, G. & Hof, H. Production of prostaglandins, isoprostanes and thromboxane by Aspergillus fumigatus: Identification by gas chromatography–tandem mass spectrometry and quantification by enzyme immunoassay. Mol. Immunol. 49, 621–627 (2012).
Noverr, M. C. & Huffnagle, G. B. Regulation of Candida albicans morphogenesis by fatty acid metabolites. Infect. Immun. 72, 6206–6210 (2004).
Yurchenko, A. N., Girich, E. V. & Yurchenko, E. A. Metabolites of marine sediment-derived fungi: actual trends of biological activity studies. Mar. Drugs 19, 88 (2021).
Goncalves, M. F. M., Hilario, S., Van de Peer, Y., Esteves, A. C. & Alves, A. Genomic and metabolomic analyses of the marine fungus Emericellopsis cladophorae: Insights into saltwater adaptability mechanisms and its biosynthetic potential. J. Fungi 8, https://doi.org/10.3390/jof8010031 (2021).
Zheng, W., Han, L., He, Z. J. & Kang, J. C. New spirostane from a fungus Neohelicomyces hyalosporus and its bioactivity. Chem. Biodivers. 20, e202300313 (2023).
Chen, M., Fu, X.-M., Kong, C.-J. & Wang, C.-Y. Nucleoside derivatives from the marine-derived fungus Aspergillus versicolor. Nat. Prod. Res. 28, 895–900 (2014).
Huang, R.-M. et al. Marine nucleosides: Structure, bioactivity, synthesis and biosynthesis. Mar. Drugs 12, 5817–5838 (2014).
Liu, F. -a. et al. Xanthones and quinolones derivatives produced by the deep-sea-derived fungus Penicillium sp. SCSIO Ind16F01. Molecules 22, 1999 (2017).
Amin, M., Liang, X., Ma, X., Dong, J.-D. & Qi, S.-H. New pyrone and cyclopentenone derivatives from marine-derived fungus Aspergillus sydowii SCSIO 00305. Nat. Prod. Res. 35, 318–326 (2021).
Zhou, X.-M. et al. Antibacterial α-pyrone derivatives from a mangrove-derived fungus Stemphylium sp. 33231 from the South China Sea. J. Antibiot. 67, 401–403 (2014).
Chen, S. et al. Tersaphilones AE, cytotoxic chlorinated azaphilones from the deep-sea-derived fungus Phomopsis tersa FS441. Tetrahedron 78, 131806 (2021).
Shi, Q. et al. Diterpenoids of marine organisms: isolation, structures, and bioactivities. Mar. Drugs 23, 131 (2025).
Hu, Y. et al. Cytotoxic pyridine alkaloids from a marine-derived fungus Arthrinium arundinis exhibiting apoptosis-inducing activities against small cell lung cancer. Phytochemistry 213, 113765 (2023).
Hao, M.-J. et al. β-Carboline alkaloids from the deep-sea fungus Trichoderma sp. MCCC 3A01244 as a new type of anti-pulmonary fibrosis agent that inhibits TGF-β/smad signaling pathway. Front. Microbiol. 13, 947226 (2022).
Ryan, W. B. et al. Global multi-resolution topography synthesis. Geochem. Geophys. Geosyst. 10, Q03014 (2009).
Acknowledgements
Research was funded by the National Council of Science and Technology of Mexico—Mexican Ministry of Energy—Hydrocarbon Trust, project 201441. This is a contribution of the Gulf of Mexico Research Consortium (CIGoM). We thank the National Laboratory of Advanced Microscopy (LNMA) at the Centro de Investigación Científica y de Educación Superior de Ensenada (CICESE) for the use of the facilities. The authors thank Lluvia Vargas-Gastélum for her support in isolating the fungi and for creating the map in Fig. 1, Ivonne Martínez-Mendoza for collecting the sediment samples during the XIXIM-7 campaign, Rodrigo Villanueva-Silva for his support with the initial metabolomic analysis, and Samantha V. González-Téllez for contributing to the graphical abstract figures. This work was partially supported by grants from UNAM-DGAPA PAPIIT IN203923 and FQ-PAIP 5000-9145 awarded to M.F. M.D.C.-L. was supported by a fellowship from the National Council of Humanities, Sciences, and Technologies (CONAHCyT, grant no. 315758). We declare the use of ChatGPT only to improve the readability and proofreading of the manuscript.
Author information
Authors and Affiliations
Contributions
M.D.C.L. contributed to conceptualization, investigation, writing the original draft, methodology, formal analysis, data curation, and editing; M.F. contributed with funding acquisition, writing, review and editing, data curation, and supervision; A.H.M. contributed with data curation, formal analysis, and writing, review and editing; M.R.: contributed to conceptualization, funding acquisition, writing, review and editing, formal analysis, supervision, project administration, and investigation.
Corresponding author
Ethics declarations
Competing interests
The authors declare no competing interests.
Peer review
Peer review information
Communications Biology thanks Louisi Souza de Oliveira, Federico Laich and the other, anonymous, reviewer(s) for their contribution to the peer review of this work. Primary Handling Editors: Linn Hoffmann and Tobias Goris.
Additional information
Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Rights and permissions
Open Access This article is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License, which permits any non-commercial use, sharing, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if you modified the licensed material. You do not have permission under this licence to share adapted material derived from this article or parts of it. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by-nc-nd/4.0/.
About this article
Cite this article
Camacho-López, M.D., Figueroa, M., Hernández-Melgar, A. et al. Salinity stress response of black yeasts isolated from deep-sea sediments of the Gulf of Mexico. Commun Biol (2026). https://doi.org/10.1038/s42003-026-09673-0
Received:
Accepted:
Published:
DOI: https://doi.org/10.1038/s42003-026-09673-0
