The argument rests on a striking gap in environmental surveillance. Water quality monitoring around the world routinely tracks bacterial indicators such as Escherichia coli and Legionella, along with enteric viruses, because these signal faecal contamination or acute failures in water treatment. Pathogenic free-living amoebae, however, are rarely included in any surveillance programme, despite living in exactly the environments that are already being sampled. The authors point out that conventional indicators primarily reflect contamination events, whereas amoebae integrate something far richer: the broader dynamics of microbial communities through their grazing behaviour and their remarkable ability to encyst. In other words, amoebae capture ecological information that bacteria and viruses alone cannot reveal, making them potential sentinels of ecosystem instability that public health systems have never learned to read.

The technical case for concern is grounded in amoebal biology. Free-living amoebae alternate between an active feeding stage called the trophozoite and a dormant, extraordinarily resistant cyst, with some genera such as Naegleria adding a temporary flagellate stage to the life cycle. The cyst stage allows both the amoeba and any bacteria it harbours internally to withstand desiccation, temperature fluctuations, ultraviolet radiation, chemical exposure, and standard disinfection procedures for prolonged periods. This persistence exceeds that of many free-living bacteria, and it creates a plausible pathway by which pathogens could survive harsh conditions and subsequently enter human-related environments. Climate-driven changes in temperature, precipitation, salinity, soil moisture, and ultraviolet radiation are likely to affect amoebic survival, encystment, and virulence, potentially increasing human exposure through soil disturbance, aerosols, recreational waters, and urban water systems, particularly in coastal zones and regions hit by extreme weather.

Perhaps the most provocative element of the argument concerns what amoebae do to the bacteria they encounter. Bacterial species have evolved mechanisms to survive digestion and persist within both trophozoite and cyst stages of their predators. By sheltering microorganisms from hostile conditions, amoebae facilitate horizontal gene transfer, promote microbial persistence, and contribute to the evolution of traits that enhance survival and virulence. Many microorganisms that resist amoebal digestion carry traits that also serve them well under stress, including antimicrobial resistance, increased biofilm formation, and improved tolerance to desiccation and temperature swings. The authors suggest that climate change may preferentially favour microorganisms that are pre-adapted to amoebal predation, and that the same adaptations that help bacteria survive inside a predator can also help them infect human hosts. This is the proposed mechanistic bridge between environmental change and emerging health risk.

The ecological stakes extend well beyond human disease. In soil ecosystems, Acanthamoeba species act as dominant bacterial grazers, consuming primary decomposers and releasing mineral nutrients sequestered within bacterial biomass, functioning as secondary decomposers in the soil food web. Amoebal grazing reshapes bacterial community composition and accelerates nutrient mineralisation, linking microbial turnover directly to soil fertility and carbon cycling. Recent work in soil microbial ecology has shown that protist-driven grazing enhances litter decomposition and increases microbial carbon flux, with the magnitude of these effects varying according to temperature. Because these processes are climate-sensitive, shifts in amoebal activity under warming conditions could influence soil function and microbial succession, with consequences for how carbon moves through ecosystems on a planetary scale.

The authors frame their argument within the One Health perspective, which recognises the health of humans, animals, plants, and the environment as interconnected, and within the emerging concept of the planetary microbiome: the interconnected microbial systems spanning soil, water, air, and host organisms that both shape and respond to planetary-scale ecological processes. Within this framework, amoebae occupy a peculiar position. They are ubiquitous, inhabiting soil, dust, air, and water, and they respond rapidly to changes in moisture, temperature, and nutrient availability, which makes them sensitive bioindicators of environmental instability. Shifts in their abundance, in the ratio of cysts to active trophozoites, and in their intracellular microbiota can be detected at the species or genus level, typically over seasonal timescales, offering a resolution that coarser microbial indicators cannot match.

Several pathogenic genera sharpen the urgency of the argument. Acanthamoeba species, Naegleria fowleri, Balamuthia mandrillaris, Sappinia pedata, Vahlkampfia species, Paravahlkampfia species, and Vermamoeba species can cause infections ranging from keratitis, a sight-threatening corneal disease, to fatal encephalitis. Rising temperatures may expand the geographic range of Naegleria fowleri, the so-called brain-eating amoeba, while changing moisture conditions may alter the behaviour of Acanthamoeba and Balamuthia in soil and dust. Salinity fluctuations impose osmotic stress on amoebae, and experimental evidence demonstrates differential growth responses among pathogenic genera under elevated salt conditions, suggesting that climate-driven hydrological change could restructure which amoebae thrive where. The authors are careful to note that these are plausible ecological links rather than direct causal relationships, and that environmental mediators likely modulate the outcomes, but the direction of the evidence is consistent enough to warrant systematic study.

What would it take to close the knowledge gap? The authors lay out a concrete research agenda. Experimental studies should link amoebal abundance, cyst prevalence, and intracellular microbiota to temperature, moisture, and land use, while climate-simulation systems could assess how warming and drying shift encystment and grazing behaviour. Multi-omic approaches, combining genomics, transcriptomics, and proteomics, should be applied to characterise the intracellular microorganisms carried by amoebae across different climates, with priority given to representative taxa such as Acanthamoeba, Naegleria, and Balamuthia and their internal microbiota. Useful metrics include the relative abundance of amoebae within total microbial or eukaryotic community reads, cyst prevalence, and detectable intracellular bacteria. Feasible detection methods range from microscopy with molecular confirmation to targeted quantitative PCR for key taxa and metagenomic screening, and seasonal sampling in coastal zones, urban water systems, and agricultural soils would capture climate-linked fluctuations over time.

The authors also propose that amoebae be incorporated into routine soil and water surveillance, particularly in regions experiencing sustained warming of more than 0.2 to 0.3 degrees Celsius per decade or marked precipitation variability exceeding 20 percent between years. Biosensor-based early warning tools for climate-sensitive hazards could provide a practical route to this goal, and the authors acknowledge that such approaches face limitations, including non-climatic drivers of amoebal ecology and technical constraints in detection, underscoring the need for simplified, comparable monitoring tools that can be deployed at scale. Systems that simulate future climate scenarios would additionally allow researchers to explore how amoebae influence microbial succession, biogeochemical cycling, and the persistence of opportunistic pathogens under conditions that have not yet arrived in the field.

The broader message is one of humility about what we know. To the authors’ knowledge, no global regulations currently address the presence of amoebae in environmental or built water systems, and no standardised prevention or disinfection protocols exist for them, even as their cysts shrug off the disinfectants that water utilities rely upon. As global temperatures rise and ecosystems transform, the microbial communities that underpin planetary health are changing in ways we are only beginning to measure, and the organisms that connect those changes to human exposure may be ones we have never thought to count. Incorporating free-living amoebae into planetary microbiome and One Health models, the authors argue, would provide a practical indicator system for tracking microbial responses to climate change, one that links the fate of soil carbon, the safety of drinking water, and the emergence of drug-resistant pathogens through a single, overlooked predator.

Subject of Research: The role of free-living amoebae in climate-driven microbiome dynamics and One Health

Article Title: Climate change and planetary microbiome: Are we overlooking free-living amoebae in climate-microbiome dynamics?

Article References: Siddiqui, R., Lloyd, D., & Khan, N. A. (2026). Climate change and planetary microbiome: Are we overlooking free-living amoebae in climate-microbiome dynamics?. PLOS Ecosystems, 1(1), e0000016. https://doi.org/10.1371/journal.pesy.0000016

Image Credits: AI Generated

DOI: 10.1371/journal.pesy.0000016

Keywords: free-living amoebae, climate change, planetary microbiome, One Health, Acanthamoeba, Naegleria fowleri, Balamuthia mandrillaris, soil ecology, water surveillance, encystment, horizontal gene transfer, antimicrobial resistance

These sacs are called expelled food vacuoles, or EFVs. When a protozoan such as the ciliate Tetrahymena feeds, it engulfs bacteria into food vacuoles, compartments that normally mature into digestive vacuoles filled with the acidic enzymes and molecular machinery needed to dismantle their cargo. In many cases, that is exactly what happens, and the bacterium is destroyed. But a growing list of bacterial species has evolved the ability to resist this digestive programme. Rather than being killed, the survivors remain inside the vacuole, which the protozoan then expels intact. Earlier studies referred to these expelled structures by a variety of names, including expelled vesicles, faecal pellets and multilamellar bodies, and often regarded them as little more than the discarded refuse of protozoan digestion. The new review contends that this interpretation has understated their importance.

The central claim of the review is that EFVs should be understood as biologically generated reservoirs: protective containers that package viable pathogenic bacteria and release them into the environment already primed for persistence, dissemination and host colonisation. Far from being waste, these structures behave like miniature transport capsules, each one shielding its bacterial passengers from a hostile outside world. The authors describe this as a distinct environmental transmission state, a phase of a pathogen’s life in which it is neither free-swimming in water nor established inside a host, but travelling in a self-contained vehicle manufactured by another organism.

The evidence for this concept comes from a strikingly diverse set of pathogens. The review gathers findings from studies of Vibrio cholerae, the agent of cholera; Salmonella enterica, a leading cause of food poisoning; Legionella pneumophila, the cause of Legionnaires’ disease; Campylobacter jejuni, a common cause of gastroenteritis; Listeria monocytogenes, which can cause severe disease in pregnant people and the immunocompromised; Escherichia coli; the opportunistic pathogen Burkholderia cenocepacia; and the soil bacterium Mycobacterium smegmatis, a widely used model for tuberculosis research. Across these very different organisms, a common pattern emerges: bacteria that have passed through protozoa and emerged inside EFVs display measurable increases in resistance to stresses that would normally kill them.

The protective effects documented in the literature are broad. EFV-associated bacteria withstand acid exposure better than their free-living counterparts, an advantage that matters enormously when a waterborne pathogen confronts the acidic environment of the human stomach. They also survive starvation for longer periods, tolerate disinfectants and biocides, resist oxidative stress, and endure desiccation. In practical terms, a cholera bacterium packaged inside an expelled vacuole can persist in a drying pond, in treated drinking water, or on a contaminated surface for far longer than one floating alone, and it arrives at the next host in a hardier condition. The review also highlights reports of enhanced infectivity among EFV-associated pathogens, suggesting that the vacuolar packaging does not merely prolong survival but may actively prime the bacteria for subsequent colonisation of new hosts.

One of the most consequential findings relates to horizontal gene transfer, the process by which bacteria exchange genetic material. Because multiple bacteria can be concentrated inside a single small vesicle, EFVs create crowded micro-environments in which cells sit close together in fluid enclosed by a membrane. This physical intimacy facilitates the exchange of plasmids and other genetic elements, potentially accelerating the spread of antibiotic resistance genes through environmental microbial communities. In an era when antimicrobial resistance is recognised as one of the greatest threats to global public health, the possibility that protozoan predators inadvertently act as genetic mixing vessels for pathogens is a finding with far-reaching implications.

The review’s authors frame their synthesis around a conceptual shift. If EFVs are merely waste, then monitoring programmes that count free bacteria in water may be missing a hidden reservoir of infectious agents entirely. But if EFVs are vehicles of transmission, as the accumulated evidence suggests, then they represent a measurable and potentially targetable stage in the life cycle of environmental pathogens. The authors propose that EFV-associated pathogens could serve as useful targets for water surveillance and outbreak prediction. Detecting these vesicles in reservoirs, drinking water systems, or recreational waters could provide an early warning that a pathogen population has entered a particularly durable and transmissible state, before cases begin to appear in clinics.

This perspective also reframes the ecological relationship between protozoa and bacteria. The traditional view holds that protozoan grazing suppresses bacterial populations, acting as a check on microbial growth. The EFV concept reveals a paradox at the heart of that relationship: the predator that kills most bacteria may simultaneously serve as an incubator and distributor for the few that can resist digestion. In effect, protozoa may function as accidental selective agents, culling susceptible cells while packaging the resistant ones for wider dispersal. Over evolutionary time, this could help explain why so many environmental pathogens, including Legionella and various non-tuberculous mycobacteria, show an inherent ability to survive inside protozoa and, later, inside human cells. The machinery that lets a bacterium resist digestion in a Tetrahymena vacuole may be the same machinery that lets it resist killing by macrophages, the immune cells that patrol human tissue.

The authors are careful to present their synthesis as a framework rather than a settled conclusion, and they call for the field to move past the fragmented terminology of earlier decades and treat expelled food vacuoles as a unified object of study. Doing so, they argue, will allow researchers to connect environmental persistence with infection biology in a single mechanistic story: a pathogen that survives protozoan digestion exits the predator inside a protective vesicle, persists longer in the environment, resists treatment more effectively, exchanges genes more readily, and colonises new hosts more successfully. For public health authorities, the message is that the journey of a waterborne pathogen between hosts may be far more sophisticated than previously appreciated, and that the humble vacuole, long dismissed as refuse, may hold keys to predicting and preventing outbreaks. For microbiologists, the review opens a research agenda in which the ecology of single-celled predators and the epidemiology of human disease are inseparable parts of the same system.

Subject of Research: Expelled food vacuoles produced by protozoa as protective vehicles that promote bacterial persistence, stress resistance, gene transfer and transmission of pathogens

Article Title: Expelled Food Vacuoles as Protozoan-Derived Vehicles for Bacterial Persistence and Transmission

Article References: Faruque, S. N., Ponton, I. A., Moon, J. M., & Espinoza-Vergara, G. (2026). Expelled Food Vacuoles as Protozoan-Derived Vehicles for Bacterial Persistence and Transmission. Microbial Ecology. https://doi.org/10.1007/s00248-026-02880-6

Image Credits: AI Generated

DOI: 10.1007/s00248-026-02880-6

Keywords: protozoa, expelled food vacuoles, bacteria, Vibrio cholerae, Legionella pneumophila, Tetrahymena, water surveillance, antibiotic resistance, horizontal gene transfer, pathogen transmission, microbial ecology, environmental persistence