Fungi are phylogenetically and functionally diverse ubiquitous components of almost all ecosystems on Earth, including aquatic environments stretching from high montane lakes down to the deep ocean. Aquatic ecosystems, however, remain frequently overlooked as fungal habitats, although fungi potentially hold important roles for organic matter cycling and food web dynamics. Recent methodological improvements have facilitated a greater appreciation of the importance of fungi in many aquatic systems, yet a conceptual framework is still missing. In this Review, we conceptualize the spatiotemporal dimensions, diversity, functions and organismic interactions of fungi in structuring aquatic food webs. We focus on currently unexplored fungal diversity, highlighting poorly understood ecosystems, including emerging artificial aquatic habitats.

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The authors thank J. Salazar for help designing the draft figures. H.P.G. was supported by Deutsche Forschungsgemeinschaft (DFG) grants GR1540/23-1 and GR1540/ 30–1, S.V.d.W. by DFG grant WY175/1-1 and M.C. by European Research Council (ERC) grant MYCO-CARB 772584. They thank the reviewers for their valuable comments and suggestions.

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Nature Reviews Microbiology thanks L. Tedersoo and the other anonymous reviewer(s) for their contribution to the peer review of this work.

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  1. Department of Experimental Limnology, Leibniz Institute of Freshwater Ecology and Inland Fisheries, Stechlin, Germany

    • Hans-Peter Grossart
    •  & Silke Van den Wyngaert
  2. Institute of Biochemistry and Biology, Potsdam University, Potsdam, Germany

    • Hans-Peter Grossart
  3. Yokohama National University, Graduate School of Environment and Information Sciences, Hodogaya-ku, Yokohama, Kanagawa, Japan

    • Maiko Kagami
  4. Chair of Urban Water Systems Engineering, Technical University of Munich, Garching, Germany

    • Christian Wurzbacher
  5. Marine Biological Association of the United Kingdom, The Laboratory, Citadel Hill, Plymouth, Devon, UK

    • Michael Cunliffe
  6. School of Biological and Marine Sciences, University of Plymouth, Drake Circus, Plymouth, Devon, UK

    • Michael Cunliffe
  7. Escuela de Biologia, Universidad de Costa Rica, San Pedro, San Jose, Costa Rica

    • Keilor Rojas-Jimenez


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H.P.G. researched data for the article. H.P.G., S.V.d.W., M.K., C.W., M.C. and K.R-J. wrote the article, contributed substantially to discussion of the content and reviewed and edited the manuscript before submission.

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The authors declare no competing interests.

Corresponding author

Correspondence to Hans-Peter Grossart.

Supplementary information



Fungi that are well adapted and constantly active in aquatic habitats.

Periodic immigrants

Fungi that are less adapted to and only periodically active in aquatic habitats.

Versatile immigrants

Fungi that are little adapted to and only sporadically active in aquatic habitats.

Carbon pump

A mechanism whereby atmospheric carbon is sequestered by vertical transfer to deep waters and sediments.

Short-term disturbances

Pulsed event-based disturbances referring to strong single events such as storms and droughts.

Long-term anthropogenic disturbances

Gradually increasing press disturbances such as global climate change or urbanization, both leading to species loss and shifts in community composition.


A fungus in symbiosis with a vascular plant via the root in the rhizosphere.


Fungi parasitizing on other fungi.


Parasites of a host that is also a parasite.

Precursor rRNA

The precursor ribosomal RNA (rRNA) is a prespliced, full-length transcribed ribosomal operon including all functional and spacer regions.

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