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Researchers from the Cluster of Excellence »Balance of the Microverse« discover previously unknown viruses and their central role in ecosystems
Groundwater is considered the largest reservoir of liquid freshwater on Earth and a habitat for complex microbial communities that drive essential biogeochemical cycles. Until now, the role of viruses that infect microorganisms in this hidden ecosystem was largely unknown. An international research team, including Dr. Akbar Adjie Pratama and Prof. Dr. Kirsten Küsel from the »Balance of the Microverse« Cluster of Excellence at the University of Jena, as well as Prof. Dr. Matthew B. Sullivan from Ohio State University, has, for the first time, created a comprehensive picture of viral diversity and function in a groundwater system. The study was published in the journal Nature Communications.
More than 257,000 Viruses Discovered – Almost All New
The researchers analyzed large quantities of environmental genomic data (1.24 terabases) from seven groundwater wells at the Hainich Critical Zone Exploratory in Thuringia. The team identified over 257,000 viral operational taxonomic units, i.e. viruses at species level, 99 % of which were previously unknown.
Viruses Affect the Function of Their Microbial Hosts
The research team was particularly surprised to find that numerous viruses carrying so-called auxiliary metabolic genes (AMGs) were among the viruses detected. These AMGs allow viruses to reprogram host metabolism, directly influencing carbon, nitrogen, and sulfur cycling, processes central to ecosystem-level biogeochemical fluxes. Akbar Adjie Pratama (first author of the study) notes: »The occurrence and functional diversity of viral AMGs provide a baseline for investigating how viruses influence microbial community dynamics, metabolic reprogramming, and nutrient cycling in groundwater.«
Based on the widespread occurrence of AMGs, the researchers conclude that viruses play a role in modulating the metabolism of their microbial hosts. Although these conclusions are based on genomic data rather than experimental evidence, the results suggest that viruses have a significant impact on the groundwater microbiome.
New Perspectives on Complex Interactions
The data suggest that viruses do not only affect individual microbes, but also are integrated into complex microbial networks. Viruses could simultaneously control ultra-small organisms and their hosts—a mechanism previously only known from extreme habitats, such as acid mine drainage systems, hypersaline lakes, and hydrothermal ecosystems. By studying this groundwater system, while we often think of viruses infecting a single host, in groundwater it appears much more complicated than that. For example, viruses that infected the ultra-small microbes appear to be involved in a ménage à trois where three entities are infection impacted. The discovery of these multi-layer interactions expands the understanding of the groundwater microbiome and highlights the complex interconnectedness of these life communities. Furthermore, this study is hypothesis-generating, providing a foundation for future targeted experiments and studies.
Prof. Dr. Matthew B. Sullivan (co-corresponding author of the study) explains the significance of this finding: »Understanding viral roles in these systems is essential for predicting how groundwater ecosystems will react to environmental changes.«
»Our results show that viruses are not passive bystanders, but active players that influence key functions of the groundwater microbiome,« explains Prof. Dr. Kirsten Küsel, spokesperson for the Cluster.
Significance for the Environment and Water Management
The results also have practical relevance: understanding viral control over nutrient cycles provides the necessary indicators for modelling ecosystem responses. In future, changes in viral nutrient turnover can be used to predict how groundwater systems will respond to climate change, falling water levels or nutrient inputs. Furthermore, the knowledge about AMGs provides more precise models for global subsurface biogeochemical cycles and opens up potential for biotechnological applications.
Prof. Dr Kirsten Küsel
Institute for Biodiversity, Ecology and Evolution at the University of Jena
Dornburger Straße 159, 07743 Jena, Germany
Phone: +49 3641 9-49461
Email: kirsten.kuesel@uni-jena.de
Pratama, A.A., Pérez-Carrascal, O., Sullivan, M.B. et al. Diversity and ecological roles of hidden viral players in groundwater microbiomes. Nat Commun (2026). https://doi.org/10.1038/s41467-026-68914-2
Water sampling well in the Hainich.
Quelle: Akbar Adjie Pratama
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