Groundwater, the hidden reservoir beneath soils, rocks and sediments, supports drinking-water supplies and agricultural irrigation for billions of people. Yet far below the surface, where sunlight is absent and nutrients can be scarce, an immense biological world is active. A new review by Wu, Ning, Fields and colleagues synthesizes current knowledge of groundwater microbiomes, revealing how bacteria, archaea, microeukaryotes and viruses shape the chemistry, safety and resilience of subsurface ecosystems.
The review emphasizes that groundwater is not a biologically empty medium. Subsurface environments are estimated to contain more than 30% of Earth’s microorganisms, although many of these organisms remain difficult to cultivate and characterize. Advances in metagenomic sequencing, single-cell analysis and other culture-independent techniques have exposed a remarkable diversity of microbial lineages, including organisms with unusual metabolisms adapted to darkness, high pressure, low energy availability, salinity, acidity and contamination.
Among the most important discoveries is the extent to which groundwater communities include previously unknown bacteria and archaea. These prokaryotes can use a wide range of electron donors and acceptors to obtain energy, driving transformations of carbon, nitrogen, sulfur, iron and other elements. Some organisms oxidize hydrogen or reduced sulfur compounds, while others perform anaerobic respiration using nitrate, sulfate, metals or carbon dioxide. Through these reactions, groundwater microbes influence the movement and chemical form of elements throughout aquifers and connected surface ecosystems.
Viruses add another layer of complexity to this hidden biosphere. Groundwater viral communities include bacteriophages that infect bacteria and archaea, as well as viruses associated with microeukaryotes and potentially with animals or humans. By destroying host cells, viruses release organic matter and nutrients back into the surrounding water, a process that can redirect carbon and energy through microbial food webs. Viral infections can also alter the genetic potential of their hosts when viruses transfer genes between organisms, potentially spreading traits linked to metabolism, stress tolerance, virulence or antimicrobial resistance.
The review describes groundwater microbiomes as interconnected communities rather than isolated collections of species. Microeukaryotes, including protists and fungi, may consume bacteria and influence the abundance of particular lineages, while bacteria and archaea provide food and chemical substrates for other organisms. Viruses can suppress dominant populations and promote coexistence among competing microbes. These interactions create a dynamic network in which predation, infection, competition, cooperation and genetic exchange collectively influence ecosystem function.
Groundwater microbiomes also show distinct biogeographic patterns. Communities differ among shallow and deep aquifers, fractured bedrock systems, porous sediments, karst environments, geothermal waters and contaminated sites. Some groundwater habitats share microbial groups with soils, rivers or marine environments, while others contain lineages that appear highly specialized to the subsurface. Water chemistry, geological structure, residence time, temperature, oxygen availability and the movement of organic carbon all help determine which organisms can persist.
According to the review, stochastic processes are often the dominant force assembling groundwater communities. Random dispersal, ecological drift and the chance arrival of microorganisms can strongly influence local diversity, particularly in environments where energy and nutrients are limited. However, deterministic processes also become important when environmental stress intensifies. Toxic metals, hydrocarbons, salinity, acidity, oxygen depletion and other pressures can select for organisms with specific physiological traits, narrowing community composition while favoring microbes capable of surviving or transforming hazardous compounds.
These ecological patterns have direct consequences for water quality and public health. Groundwater microorganisms can degrade petroleum compounds, chlorinated solvents, pesticides and other contaminants, making them potential partners in natural attenuation and engineered remediation. At the same time, aquifers may harbor pathogens, opportunistic microorganisms and genes associated with antimicrobial resistance. Microbial activity can either reduce or increase risk depending on local conditions, because processes such as biofilm formation, gene exchange and viral infection may alter the persistence and transmission of harmful traits.
The authors frame groundwater microbiomes within the broader concept of One Health, which recognizes the links among environmental, animal and human health. Changes in groundwater use, pollution, land management, climate and recharge patterns may reshape microbial communities and their functions. Warmer temperatures, altered precipitation and seawater intrusion can modify redox conditions, salinity and nutrient availability, potentially changing both contaminant degradation and pathogen behavior. Understanding these shifts will require monitoring not only which organisms are present, but also which genes, metabolic pathways and viral interactions are active.
The review concludes that groundwater microbiomes could become a source of eco-sustainable solutions for protecting and restoring aquifers. Future research may combine high-resolution sequencing with geochemical measurements, laboratory experiments, field-scale monitoring and predictive ecological models. Such approaches could help identify microbial consortia that remove pollutants, stabilize water chemistry or suppress harmful organisms without relying exclusively on energy-intensive treatment technologies. As scientists continue to explore the planet’s largest accessible freshwater resource, the subterranean microbial world is emerging as both a critical driver of Earth-system processes and a potential ally in safeguarding water for a changing world.
Subject of Research: Groundwater microbiome diversity, biogeography, community assembly, microbial interactions, elemental cycling, contaminant degradation, water quality and One Health.
Article Title: Diversity, biogeography and assembly mechanisms of groundwater microbiomes
Article References: Wu, Z., Ning, D., Fields, M.W. et al. “Diversity, biogeography and assembly mechanisms of groundwater microbiomes.” Nature Reviews Earth & Environment (2026). https://doi.org/10.1038/s43017-026-00813-y
Image Credits: AI Generated
DOI: 10.1038/s43017-026-00813-y
Keywords: groundwater microbiomes, viruses, bacteriophages, archaea, bacteria, microeukaryotes, biogeography, microbial ecology, elemental cycling, contaminant degradation, antimicrobial resistance, One Health
