In a groundbreaking study published in Nature Communications, researchers have unveiled the covert yet crucial role of microbial aerotrophy in sustaining primary production within cave ecosystems worldwide. This revelation profoundly alters our understanding of subterranean life, challenging the long-standing notion that these dark, isolated environments are strictly dependent on surface-derived organic matter for energy. Instead, it appears that a diverse array of microbes within caves are employing aerobic metabolism to continuously generate the organic carbon necessary to support complex biological communities, even in environments previously deemed inhospitable for sustained life.
Traditional ecological paradigms have long viewed caves as energy-poor refuges, where primary productivity is almost exclusively limited by organic material originating outside the underground systems. This concept has relegated caves to the status of ecological sinks, with life forms eking out survival on scarce imported nutrients. However, the novel findings emerging from this multi-institutional study reveal a fundamentally distinct energy acquisition strategy—microbial aerotrophy—that enables uninterrupted production of organic substrates through the oxidation of atmospheric or dissolved oxygen. This continuous primary production forms the foundation of cave food webs and biogeochemical cycling.
The research team embarked on an exhaustive survey of diverse cave systems, ranging from karstic limestone caverns to volcanic tubes scattered across varied geographic regions and climatic regimes. By integrating metagenomic sequencing, stable isotope probing, and advanced geochemical assays, the scientists could discern the intricate metabolic networks at play beneath the surface. The presence of a wide spectrum of aerobic microorganisms, including previously uncharacterized bacterial taxa, was ubiquitous and directly correlated with enhanced rates of inorganic carbon fixation, denoting active autotrophic processes.
Key to this discovery was the identification of previously underestimated microbial guilds capable of harnessing oxygen in subterranean settings, contrary to earlier assumptions that such environments were largely anoxic or microaerophilic. These microbes engage in chemolithoautotrophy, oxidizing reduced inorganic compounds such as sulfur, iron, and manganese, while utilizing molecular oxygen as the terminal electron acceptor. This metabolic versatility not only fuels their own growth but also generates organic carbon that subsequently sustains heterotrophic cave inhabitants including fungi, invertebrates, and even some vertebrates.
Furthermore, the continuous nature of this autotrophic activity suggests that cave ecosystems possess self-sustaining carbon cycles, decoupled from the ephemeral inputs of surface detritus. This has profound implications for the resilience and stability of subterranean biodiversity, enabling organisms to maintain stable populations amidst fluctuating external conditions such as seasonal changes or climatic perturbations. The ecological ramifications extend to deep biosphere studies and astrobiology, offering analogs for life-supporting processes on other planetary bodies where sunlight penetration is nonexistent.
The study also highlights the intricate interplay between geochemical conditions and microbial community structure within caves. Microbial aerotrophy prevalence strongly correlated with oxygen availability gradients shaped by cave morphology and airflow dynamics. In zones receiving minimal oxygen influx, aerobic microorganisms exhibited reduced abundance and metabolic activity, whereas well-ventilated chambers showcased thriving, metabolically active aerobic consortia. These findings underscore the pivotal role of cave ventilation in shaping subterranean ecosystems and suggest that anthropogenic disturbances affecting airflow could imperil endemic cave biota.
At the molecular level, metagenomic analyses unveiled gene clusters encoding key enzymes involved in oxygen-dependent respiration and carbon fixation pathways. Notably, enzymes associated with the Calvin-Benson-Bassham cycle and alternative carbon assimilation mechanisms were prominently expressed, signifying diverse strategies employed by different microbial taxa to exploit aerotrophic metabolisms. These insights provide genetic blueprints for understanding how life adapts to energy-limited subterranean conditions and may inform biotechnological applications leveraging such metabolic pathways.
Moreover, the discovery holds potential for refining global carbon cycle models. Caves occupy a significant terrestrial volume, and their microbial communities’ contribution to inorganic carbon conversion and organic matter generation has been largely overlooked. Incorporating microbial aerotrophy-driven primary production into carbon budget assessments could enhance the accuracy of climate change predictions and ecosystem services evaluations, recognizing caves as active biogeochemical reactors rather than inert geological formations.
Environmental microbiologists and cave ecologists alike are poised to further investigate how widespread and variable these aerotrophic processes are across different subterranean habitats. Questions remain regarding temporal dynamics, such as how microbial communities respond to episodic oxygen fluctuations or seasonal changes in cave microclimates. Long-term monitoring combined with experimental manipulations will be crucial for elucidating the stability and adaptability of these subterranean autotrophic systems.
In addition, the newfound understanding of continuous oxygen-utilizing primary productivity may motivate the search for novel bioactive compounds and enzymes with industrial relevance. Microbial taxa thriving on chemolithoautotrophic metabolisms in nutrient-limited, oxygen-variable cave environments possess unique biochemical adaptations, potentially yielding innovative catalysts or pharmaceuticals. Harnessing these adaptations could revolutionize sectors ranging from bioremediation to synthetic biology.
The discovery also adds a fascinating dimension to cave conservation efforts. Recognizing caves as dynamic ecosystems with internally sustained food webs challenges the perception of caves as mere geological curiosities. Conservation policies must now consider protecting the delicate ventilation patterns and geochemical balances that facilitate microbial aerotrophy. Disturbances such as tourism-induced airflow alteration, pollution, or climate-induced shifts in atmospheric composition may inadvertently disrupt these fundamental energy pathways.
Taken together, this comprehensive body of work heralds a paradigm shift in subterranean ecology. It paints caves not as biologically barren wastelands reliant solely on external resource influx but as vibrant microbial landscapes powered by continuous aerobic energy conversion. This urges a reevaluation of subterranean biodiversity’s ecological and evolutionary narratives, emphasizing microbial metabolic innovation as a cornerstone of underground life.
As we extend our exploration of Earth’s hidden biospheres, the importance of unseen microbial players and their metabolic ingenuity becomes increasingly apparent. With these insights, researchers are poised to unlock further secrets of life’s persistence in extreme, isolated environments and to apply these lessons to novel realms such as planetary exploration and synthetic ecosystem design. The implications of microbial aerotrophy extend far beyond cave walls, inviting a broader reconsideration of how life sustains itself where least expected.
In conclusion, this pioneering study not only illuminates a fundamental process sustaining subterranean ecosystems but also challenges conventional wisdom regarding energy flow in Earth’s dark realms. The recognition of microbial aerotrophy as a continuous primary production mechanism reshapes our understanding of cave ecology, from organismal survival to global biogeochemical cycles. As scientists delve deeper into these microbially driven subterranean worlds, who knows what other remarkable survival strategies await discovery?
Subject of Research: Microbial metabolic strategies sustaining primary production in cave ecosystems
Article Title: Microbial aerotrophy enables continuous primary production in diverse cave ecosystems
Article References:
Bay, S.K., Ni, G., Lappan, R. et al. Microbial aerotrophy enables continuous primary production in diverse cave ecosystems. Nat Commun 16, 10295 (2025). https://doi.org/10.1038/s41467-025-65209-w
Image Credits: AI Generated
DOI: https://doi.org/10.1038/s41467-025-65209-w
