A New Way That a Cow’s Inner World Shapes Earth’s Atmosphere

An organelle discovered inside a microbe inside a cow’s gut helps explain how livestock burps contribute to warming our planet. Within every cow is a thriving ecosystem. Churning deep in its intestines, a massive fermentation chamber known as the rumen hosts a robust microbiome that can consume up to 100 pounds of feed daily. Inside this gut pouch, tens of millions of bacteria scavenge for scraps of fiber, starch, and other nutrients, and break down cellulose and proteins. They get a hand from microbial fungi, whose enzymes demolish stiff cell walls, and all are ruled by ciliates: large, predatory microbes that gorge themselves on bacteria. This complex food web transforms a bounty of compounds to fuel the cow’s metabolism. Little goes to waste: Even hydrogen gas and carbon dioxide, the byproducts of fermentation, are scavenged by opportunists in this dark, warm, oxygen-free world. Those opportunists are rumen microbes called methanogens, and their waste product is methane, a notoriously powerful heat-trapping greenhouse gas. In this way, the inner world of a cow has global significance. Ruminant livestock, including cows, goats, and sheep, have burped out about a third of all methane gas in the atmosphere. All told, when combined with more methane from landfills and fossil fuels, the gas is responsible for around 30% of the rise in global temperatures over the past 150 years. But it has a weak spot: It decays more quickly than carbon dioxide. That’s why cow gas has attracted interest from researchers across the globe. They are looking into livestock’s specialized stomachs to identify the biological mechanisms that produce methane, which could be targeted to slow global warming within our lifetimes. A recent study published in Science has revealed a clue wrapped in a membrane. Amid new genome sequences for 450 ciliates — the rumen’s apex predators — researchers followed a trail that led them to an organelle, new to science, that is essential to the biochemical process of rebuilding atoms into compounds that are heating the planet. They named it the “hydrogenobody” because it produces hydrogen gas, which methanogens then turn into methane. The findings offer new ideas for managing this pervasive source of warming, said Juan Tricarico, who researches enteric, or intestinal, methane at Dairy Management Inc., a nonprofit trade association for dairy farmers, and was not involved in the recent study. “Just targeting the methanogens is probably not enough.” Understanding how microscopic organisms lead to changes at a planetary scale will require further disentangling of the rumen’s microbial food web and the specific mechanisms by which they produce methane, he added. “We want to understand the environment under which these microbes thrive.” How the Methane Gets Made Even though ciliates have been studied for over a century, their role in the cow-gut ecosystem has been neglected compared to the far more numerous bacteria. Microbiologists know they are the largest single-celled organisms in the rumen. Under a microscope, their hairlike cilia sweep the area outside the cell like wispy brooms, pulling bacteria into their mouths and pushing them around. Powering all those cilia takes a lot of energy, and making that energy releases hydrogen gas, which is then consumed by bacteria and archaea, including methanogens. “The whole rumen system is highly evolved, it’s highly synergistic, it’s highly symbiotic, and it’s evolved to consume all of that hydrogen,” said Rod Mackie, a rumen microbiologist at University of Illinois, Urbana-Champaign, who was not involved in the new study. “And they [methanogenic archaea] do it by shunting that into mainly methanogenesis.” To better understand the specific roles of rumen ciliates in methane emissions, microbiologists have turned to genomics. In 2021, Zhongtang Yu, a rumen microbiologist at Ohio State University, sequenced the very first rumen ciliate genome from a species called Entodinium caudatum; its genus includes roughly 90% of all ciliates in livestock rumens. A few years later, Yu assisted another team in sequencing the genomes of 52 additional rumen ciliates — a good start, but far from representative of the cow microbiome’s ciliate diversity. So when the 2026 study in Science reported 450 new ciliate genome sequences, jaws dropped across the rumen microbiome community. (The study’s authors, most of whom are based at the Chinese Academy of Sciences or Nanjing Agricultural University, did not respond to interview requests from Quanta Magazine.) The genomes have been added to a database where any researcher can access and study the ciliate sequences. The paper’s authors got a head start by searching the genomes for gene sequences of methane-making enzymes — including hydrogenases, the enzymes that catalyze the formation of hydrogen gas. They found that some of the ciliates’ hydrogenases were different from all known versions of the enzymes found across life. Experiments to locate these unusual enzymes found them in an unusual place, too: right at the edge of the cell membrane. Electron microscope images of several prominent ciliate species revealed why. Lining the outer cell membrane, at the base of the cilia, were simple structures, each encircled by a single membrane. Inside was hydrogenase. The ciliates seemed to have organelles, the newly described hydrogenobodies, specially placed to provide energy to cilia. Mark Belan/Quanta Magazine At its most basic, an organelle is a membrane-bound structure with a specialized function that is “recognized as having a different molecular signature than anything else in the cell,” said Aaron Turkewitz, a cell biologist and emeritus professor at the University of Chicago who was not involved in the research. The hydrogenobody, like the nucleus and mitochondria, fits this description. “Finding a new organelle is pretty exciting,” he said. When the study’s authors looked closer, they noticed that some ciliates had more hydrogenobodies than others. Isotrichs, one prominent type, are “huge,” Tricarico said, at least by microbial standards. They are covered in cilia that resemble fur and have far more hydrogenobodies on their cell membrane to fuel those cilia. Entodinomorphs, on the other hand, are smaller, with cilia and hydrogenobodies only in certain areas. Each type of ciliate occupies a different niche in the rumen, the same way that lions and cheetahs have different roles as predators on the savanna, Tricarico said. Within the organelle, the hydrogenase enzyme isn’t just interesting for its role in hydrogen production; it also uses up oxygen. This action supports methanogens, too, since they are inhibited by oxygen. The hydrogenobodies therefore help keep the dark cave of the rumen oxygen-free enough for methanogens to thrive, in addition to providing them with a raw material. It seemed plausible that these hydrogen-producing organelles were part of the methane puzzle, but to be certain, the researchers needed to know whether they noticeably affected methane production. To test this, they measured methane emissions from 100 dairy cows using a gas-measuring device called a head box, which is exactly what it sounds like: a box that surrounds a cow’s head to measure its methane burps. Then they analyzed the composition of isotrich and entodinomorph ciliates within the cows’ rumens. They found that cows with more isotrichs — and therefore more hydrogenobodies — had much higher methane readings than those whose microbiomes were dominated by entodinomorphs. Scientists have long suspected that ciliates are associated with methane emissions, Yu said. The new study confirms the suspicion at a mechanistic level, presenting new ideas for how to tackle livestock’s methane emissions from the inside out. From Organelle to Atmosphere In the rumen microbiome, bacteria are essential to cow digestion, but ciliates may not be. If scientists and farmers could remove or reduce ciliates from the rumen without disrupting digestion too much, they can curb the burp, and with it, methane. The basic idea goes back decades, Tricarico said, to when rumen microbiologists proposed removing all protozoans — the group of single-celled protists that includes ciliates — from livestock rumens as a potential methane mitigation strategy. But just like on a coral reef or savanna, eliminating predators threw the entire ecosystem out of whack. In experiments, wiping out protozoans allowed bacteria to grow exponentially, which generated more hydrogen and more methane, Mackie said. The new study helps identify which specific protozoans, such as isotrichs, are more problematic — producing more hydrogen — than others, he said, offering a more precise target. Another possibility is to redirect the excess hydrogen away from methanogens. Indeed, other microbes in the rumen consume hydrogen without making methane, but methanogens put up stiff competition. By congregating on the ciliates’ surface, right next to the hydrogenobodies, they position themselves to get first dibs on any hydrogen that comes out of the organelles. Now that the new study has clarified the process, “scientists could actually start looking at these hydrogenobodies” themselves as additional targets, Tricarico said. Take Bovaer, a popular feed additive that reduces cows’ methane emissions — or, in other words, minimizes the methane in their burps. The synthetic compound, 3-Nitrooxypropanol, interferes with enzymes that produce methane, but it doesn’t work consistently for all cows, diets, and environments. “This study could actually tell us why it’s not so effective in those other circumstances,” Tricarico said. By detailing the methane-making mechanisms, “you could create circumstances that allow probiotics [or feed additives such as Bovaer] to be more successful.” While the study has been a leap forward for rumen microbiology, there are a few caveats. “This paper, important as it is, still has huge gaps connecting it to methane production,” Mackie said. While the head-box experiment is helpful, it doesn’t close the case on how different ciliate species, or the hydrogenobodies themselves, contribute to methane emissions. Importantly, he noted, the authors did not specify the cows’ diet — a primary factor in microbial methane-making, since different feed types result in different amounts of hydrogen gas. Already, the study has inspired Mackie to explore new research questions. Instead of looking at hydrogen transfer between different species of bacteria and methanogens, “I think that now I should be looking at interkingdom hydrogen transfer,” he said, between bacteria, archaea, fungi, and protozoans. By looking at the basic biochemistry that underpins these processes, scientists can refine the ways we wrangle methane, from a microscopic organelle, through a teeming ecosystem, and up into the atmosphere.