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Mapping the metagenomic diversity of the multi-kingdom glacier-fed stream microbiome

Nature Microbiology volume 10, pages 217–230 (2025)Cite this article

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Abstract

Glacier-fed streams (GFS) feature among Earth’s most extreme aquatic ecosystems marked by pronounced oligotrophy and environmental fluctuations. Microorganisms mainly organize in biofilms within them, but how they cope with such conditions is unknown. Here, leveraging 156 metagenomes from the Vanishing Glaciers project obtained from sediment samples in GFS from 9 mountains ranges, we report thousands of metagenome-assembled genomes (MAGs) encompassing prokaryotes, algae, fungi and viruses, that shed light on biotic interactions within glacier-fed stream biofilms. A total of 2,855 bacterial MAGs were characterized by diverse strategies to exploit inorganic and organic energy sources, in part via functional redundancy and mixotrophy. We show that biofilms probably become more complex and switch from chemoautotrophy to heterotrophy as algal biomass increases in GFS owing to glacier shrinkage. Our MAG compendium sheds light on the success of microbial life in GFS and provides a resource for future research on a microbiome potentially impacted by climate change.

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Fig. 1: Prokaryotic MAGs sourced from glacier-fed streams sampled by the Vanishing Glaciers project.
Fig. 2: Regional distribution and environmental drivers of the glacier-fed stream microbiome.
Fig. 3: Functional metabolism of the prokaryotic community.
Fig. 4: Viral MAGs and their hosts.
Fig. 5: Presence of genes linked to algal–bacterial interactions.
Fig. 6: Relationships between glacier-fed stream chlorophyll a and prokaryotic community functions.

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Data availability

All sequencing raw data and MAGs are deposited in NCBI under bioproject PRJNA781406. The MAGs annotations are deposited in Zenodo at https://doi.org/10.5281/zenodo.13890040 (ref. 97). Source data are provided with this paper.

Code availability

The code and data used in this study to create the figures are available in GitHub at https://github.com/michoug/VanishingGlaciersRcode (ref. 98). The code for binning is also available in GitHub at https://github.com/michoug/VanishingGlacierMAGs (ref. 99).

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Acknowledgements

The Vanishing Glaciers project is supported by The NOMIS Foundation (to T.J.B.) We thank A. McIntosh and L. Morris of New Zealand; J. Abermann and T. Juul-Pedersen of Greenland; O. Solomina and T. Kuderina Maratovna of Russia; V. Crespo-Pérez and P. Andino Guarderas of Ecuador; J. Yde and S. Leth Jørgensen of Norway; S. Sharma and P. Joshi of Nepal; N. Shaidyldaeva-Myktybekovna and R. Kenzhebaev of Kyrgyzstan; J. Nattabi Kigongo, R. Nalwanga and C. Masembe of Uganda; and M. Gonzlaléz and J. Luis Rodriguez of Chile for logistical support (see https://www.glacierstreams.ch for all institutions involved in the logistics of the expeditions). We particularly acknowledge the help of porters and guides in Nepal, Uganda and Kyrgyzstan; E. Oppliger for general laboratory support; and the Functional Genomics Centre Zurich for DNA sequencing. T.J.K. was also supported by the Charles University project PRIMUS/22/SCI/001. S.B.B. was supported by the Swiss National Science Foundation grant CRSII5_180241 to T.J.B.

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Authors and Affiliations

  1. River Ecosystems Laboratory, Alpine and Polar Environmental Research Center, ENAC, Ecole Polytechnique Fédérale de Lausanne, Sion, Switzerland

    Grégoire Michoud, Hannes Peter, Massimo Bourquin, Aileen Geers, Michael Styllas, Martina Schön, Matteo Tolosano, Vincent de Staercke & Tom J. Battin

  2. UK Centre for Ecology and Hydrology, Wallingford, UK

    Susheel Bhanu Busi

  3. Department of Ecology, Faculty of Science, Charles University, Prague, Czechia

    Tyler J. Kohler & Tyler Kohler

  4. MARBEC, University of Montpellier, CNRS, Ifremer, IRD, Montpellier, France

    Leila Ezzat

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  1. Grégoire Michoud
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The Vanishing Glaciers Field Team

  • Michael Styllas
  • , Martina Schön
  • , Matteo Tolosano
  • , Vincent de Staercke
  • , Hannes Peter
  • , Tyler Kohler
  •  & Tom J. Battin

Contributions

G.M. was responsible for conceptualization, methodology, software, data curation, investigation, formal analysis, visualization and writing of the original draft. H.P. was responsible for conceptualization, methodology, data curation, investigation, formal analysis, visualization and writing of the original draft. S.B.B. and M.B. were responsible for the methodology, software, data curation, investigation and formal analysis. T.J.K. performed conceptualization and writing of the original draft. A.G., L.E. and the V.G.F.T. developed methodology and conducted investigations. T.J.B. was responsible for conceptualization, methodology, investigation, writing of the original draft, supervision, project administration and funding acquisition.

Corresponding authors

Correspondence to Grégoire Michoud or Tom J. Battin.

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Extended data

Extended Data Fig. 1

World map depicting the mountain ranges where the Vanishing Glaciers Project sampled glacier-fed streams studied in the present paper.

Source data

Extended Data Fig. 2 Maximum likelihood phylogenetic tree of the archaeal MAGs.

The colors of the branches correspond to the taxonomical affiliation of the MAGs at the class level. Then, the presence of similar MAGs (ANI% > 95%) in another dataset (GFS rocks from New Zealand and Caucasus8). The gradient colors from blue to yellow show the normalized abundance of the different MAGs.

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Extended Data Fig. 3 Comparative genomic organization of the mcrABDG cluster across the GFS_11005 (a) and GFS_3223 MAGs (b) and their closest relatives.

For each MAGs, only one contig is shown possessing the specified cluster. Similarities across genomes were calculated using minimap293. Representations were generated using gggenomes96.

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Extended Data Fig. 4 Eukaryotic MAGs sourced from glacier-fed streams sampled by the Vanishing Glaciers project.

Maximum likelihood phylogenetic tree of the eukaryotic MAGs and reference genomes. The colors of the branches correspond to the taxonomic affiliation of MAGs at phylum level. The black color represents other branches of the eukaryotic tree of life. MAGs are indicated by the red dots. The gradient colors from blue to yellow show the normalized abundance of the different MAGs.

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Extended Data Fig. 5

Differences in numbers (a,b) and relative abundance (c,d) of MAGs classified as specialists or generalists based on the levins index.

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Extended Data Fig. 6

Barplot indicative of the predicted trophic state of the MAGs present in the different functional clusters either characterized as specialists (blue) or generalists (red).

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Extended Data Fig. 7 Differences in estimated genome length between the pMAGs classified as specialists or generalists.

Mann-Whitney U Test showed a statistical difference between generalist and specialist genome length (U = 3.26 × 105, p = 1.42 × 10−9). Red circles show the medians while the box limits denote the 25th and 75th percentiles. The solid lines extend 1.5 times the interquartile range from these percentiles. The polygons represent density estimates of the data. The plot was made with ggstatsplot95.

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Extended Data Fig. 8 Differences in genome length between the pMAGs present in the different functional clusters.

Red circles show the medians while the box limits denote the 25th and 75th percentiles. The solid lines extend 1.5 times the interquartile range from these percentiles. The polygons represent density estimates of the data. The plot was made with ggstatsplot95.

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Extended Data Fig. 9

Presence of genes linked to photrophy per functional cluster.

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Supplementary information

Reporting Summary

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Supplementary Tables 1–6

Supplementary Table 1 General physicochemical characteristics of the different samples selected in this study. Table 2 General features and statistics of the metagenomes in glacier-fed streams. Table 3 General features and characteristics of the prokaryotic MAGs in glacier-fed streams. Table 4 General features and characteristics of the eukaryotic MAGs in glacier-fed streams. Table 5 Carotenoid genes coverage and originating MAG phylogeny. Table 6 List of genes potentially involved in the relationship between bacteria and algae in glacier-fed streams.

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Michoud, G., Peter, H., Busi, S.B. et al. Mapping the metagenomic diversity of the multi-kingdom glacier-fed stream microbiome. Nat Microbiol 10, 217–230 (2025). https://doi.org/10.1038/s41564-024-01874-9

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