A global mitochondrial genomic atlas illuminates freshwater microeukaryote diversity
10 affiliations
- 1Limnological Station, Department of Plant and Microbial Biology, University of Zurich, Kilchberg, Switzerland
- 2Institute of Microbiology, Department of Biology, ETH Zurich, Zurich, Switzerland
- 3Swiss Institute of Bioinformatics, Lausanne, Switzerland
- 4Department of Experimental Limnology, Leibniz Institute for Freshwater Ecology and Inland Fisheries, Stechlin, Germany
- 5Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre of the Czech Academy of Sciences, Ceské Budejovice, Czech Republic
- 6Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Japan
- 7GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
- 8Chair of Microbial Physiology, Technical University of Munich, Freising, Germany
- 9Institute of Biochemistry and Biology, Potsdam University, Potsdam, Germany
- 10Berlin-Brandenburg Institute of Advanced Biodiversity Research, Free University, Berlin, Germany
Abstract
Environmental genomics has transformed our view of the microbial world, yet progress remains largely prokaryote-centric. Among microbial eukaryotes, inconsistent marker choice and limited species-level resolution blunt diversity estimates and hinder cross-study synthesis. Consequently, regional‑to‑global gradients in richness, turnover, and phylogenetic structure remain poorly resolved. Here we establish a global mitogenome-based framework that converts shotgun metagenomes into species‑resolved, phylogeny‑anchored inventories. From 3,400 metagenomes spanning 362 lakes on seven continents, we reconstruct ~20,000 mitochondrial metagenome-assembled genomes (mitoMAGs), densely populating previously sparse branches of the eukaryotic tree—notably SAR (Stramenopiles–Alveolata–Rhizaria), Cryptophyceae, and Haptista. An empirically calibrated 98.1% mitoMAG‑identity threshold delineates species and tethers community profiles to an evolutionary backbone. On this backbone, coverage‑standardized inventories recover canonical ecological patterns: mesotrophic richness peaks, surface-layer expansion of phylogenetic breadth, and spring maxima with the strongest surface–deep coupling at vernal mixing; supporting the framework. Treating mitoMAGs as primer‑free barcodes yields a single, species‑level, phylogeny‑aware currency that renders richness, evenness, and phylogenetic breadth directly comparable across datasets, depths, seasons, and regions. By placing microbial eukaryotes on an analytical footing comparable to prokaryotes, the resulting atlas brings their diversity into reach and lays the groundwork for future high-throughput, species-aware monitoring and ecological forecasting.
Related
- Genomic Variation and Phenotypic Diversity of Coffee-Derived Lactiplantibacillus plantarum Isolates
- Extensive genomic diversity in Desulfovibrio reveals species-specific functional traits associated with disease
- Comparative mitogenomics of Roscoea alpina and R. purpurea from contrasting elevations reveals mitochondrial genomic differentiation
- Genomic Landscape Underlying Biofilm Formation Diversity in Nakaseomyces glabratus Clinical Isolates.
- New Genomic Resources for an Invasive Mite Pest Expand the Known Diversity of Pesticide Resistance Mechanisms and Guide Development of KASP Diagnostic Markers
BibTeX
@article{moncadas2026global,
title = {{A global mitochondrial genomic atlas illuminates freshwater microeukaryote diversity}},
author = {Lucas Serra Moncadas and Hans-Joachim Ruscheweyh and Jason Woodhouse and Michaela M. Salcher and Yusuke Okazaki and David Kamanda Ngugi and Michael Pester and Thomas Posch and Rohit Ghai and Hans-Peter Grossart and Shinichi Sunagawa and Jakob Pernthaler and Adrian-Stefan Andrei},
journal = {Nature Communications},
year = {2026},
month = sep,
doi = {10.1038/s41467-026-78160-1},
url = {https://doi.org/10.1038/s41467-026-78160-1},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - A global mitochondrial genomic atlas illuminates freshwater microeukaryote diversity
AU - Lucas Serra Moncadas
AU - Hans-Joachim Ruscheweyh
AU - Jason Woodhouse
AU - Michaela M. Salcher
AU - Yusuke Okazaki
AU - David Kamanda Ngugi
AU - Michael Pester
AU - Thomas Posch
AU - Rohit Ghai
AU - Hans-Peter Grossart
AU - Shinichi Sunagawa
AU - Jakob Pernthaler
AU - Adrian-Stefan Andrei
PY - 2026
DA - 2026/09/25
JO - Nature Communications
DO - 10.1038/s41467-026-78160-1
UR - https://doi.org/10.1038/s41467-026-78160-1
AB - Environmental genomics has transformed our view of the microbial world, yet progress remains largely prokaryote-centric. Among microbial eukaryotes, inconsistent marker choice and limited species-level resolution blunt diversity estimates and hinder cross-study synthesis. Consequently, regional‑to‑global gradients in richness, turnover, and phylogenetic structure remain poorly resolved. Here we establish a global mitogenome-based framework that converts shotgun metagenomes into species‑resolved, phylogeny‑anchored inventories. From 3,400 metagenomes spanning 362 lakes on seven continents, we reconstruct ~20,000 mitochondrial metagenome-assembled genomes (mitoMAGs), densely populating previously sparse branches of the eukaryotic tree—notably SAR (Stramenopiles–Alveolata–Rhizaria), Cryptophyceae, and Haptista. An empirically calibrated 98.1% mitoMAG‑identity threshold delineates species and tethers community profiles to an evolutionary backbone. On this backbone, coverage‑standardized inventories recover canonical ecological patterns: mesotrophic richness peaks, surface-layer expansion of phylogenetic breadth, and spring maxima with the strongest surface–deep coupling at vernal mixing; supporting the framework. Treating mitoMAGs as primer‑free barcodes yields a single, species‑level, phylogeny‑aware currency that renders richness, evenness, and phylogenetic breadth directly comparable across datasets, depths, seasons, and regions. By placing microbial eukaryotes on an analytical footing comparable to prokaryotes, the resulting atlas brings their diversity into reach and lays the groundwork for future high-throughput, species-aware monitoring and ecological forecasting.
SN - 2041-1723
ER -