内容来源：https://www.quantamagazine.org/the-dirt-that-refused-to-die-20260601/

内容总结：

《科学》新发现：无菌土壤持续“呼吸”六年，挑战生命定义边界

法国研究团队历时十五年证实，不含任何活体微生物的土壤样本仍能持续消耗氧气并释放二氧化碳，该现象或改写关于生命代谢过程的传统认知。

这项由法国国家农业、食品与环境研究所生物化学家塞巴斯蒂安·方丹领导的研究，发表于2025年的《科学进展》期刊。研究团队通过伽马射线彻底杀灭土壤中的所有微生物后，意外发现土壤依然在“呼吸”——其二氧化碳排放量虽随时间递减，但从未停止。在长达六年的观测中，经过灭菌处理的土壤样本持续释放碳，甚至补充葡萄糖的样本排放量更高。

为排除实验误差，团队采用更强烈的辐射、加压、加热等方式反复验证，并借助电子显微镜确认细胞内已不含RNA或DNA分子。他们还刻意添加微生物模拟污染，结果发现活菌会迅速繁殖并产生远高于无菌样本的二氧化碳，证明此前观察到的并非消毒不彻底所致。

更关键的突破在于，团队设计出一种燃料电池装置，检测到电流通过无菌土壤，暗示其中发生了类似细胞克雷布斯循环的电子传递过程。这种通常被认为只能在活细胞内完成的代谢反应，在无生命土壤中持续了超过2400天。研究人员还在土壤样本中发现了克雷布斯循环的四种中间分子——其中许多是辐射后才形成的。

“这意味着生物化学反应的某些环节并非生命的专利。”未参与该研究的渥太华大学有机化学家约瑟夫·莫兰评论道，“这是地质的化学。”

这一发现为生命起源理论提供了新视角。铁、锌等金属元素是许多古老酶的核心成分，有学者认为它们在生命出现之前就可能催化了类似的化学反应。柏林夏里特医院生物化学家马库斯·拉尔瑟指出，无细胞代谢反应可能比预想更普遍，“如果这些反应很难发生，地球现在就不会充满生命了”。

尽管有科学家质疑可能是死亡细胞释放的酶仍在起作用，但研究团队反驳称，目前已知没有酶能存活六年之久。该研究第一作者克莱芒坦·布凯表示：“即使在我们最熟悉的地球土壤中，我们有时也无法准确辨别生命存在与否的迹象。”他目前正在寻找其他生物化学级联反应的前生命起源证据。

“想象一下，可能比生命本身更古老的进程，就在我们脚下持续运转，这尤其令人着迷。”布凯说。

中文翻译：

《不肯死去的泥土》
引言
十五年来，塞巴斯蒂安·方丹一直试图杀死泥土。这位在法国国家农业、食品与环境研究所领导实验室的生物化学家，想要弄清楚土壤——仅仅是完全不含生命的泥土——会释放多少碳。他的团队将泥土密封在罐子里，用灭菌伽马射线进行照射，然后等待土壤释放的二氧化碳（微生物持续呼吸的标志）下降。

他们等啊等，等啊等，等了数周，又等了数月。在显微镜下，经过照射的土壤毫无生命迹象，但它仍在持续排放二氧化碳。这泥土竟不肯停止呼吸。

方丹的实验室重复了实验，得到了相同的结果。最终，他们确信这并非实验装置的误差所致，于是着手探寻这片"死土"中呼吸的来源。

如今，方丹及其同事报告称，他们的土壤样本连续六年都在消耗氧气并释放二氧化碳。在2025年发表于《科学进展》的一篇论文中，他们提出，一种为大部分生命提供能量的代谢过程，在活细胞之外也可能发生。他们的实验表明，在缺乏通常组织该过程的活性蛋白质的情况下，这一过程如何在泥土中运作。如果他们是对的，那么某些生化反应——例如那些释放富含碳的糖分子能量的反应——或许并非生命所独有。方丹表示，这类由细胞执行时被称为"代谢"的反应，甚至可能早于地球上的生命出现。

渥太华大学的有机化学家约瑟夫·莫兰（未参与此项研究）说，这些实验展示了"生物分子在自主运作时会发生什么"。他补充道，他们发现生命化学并非生命专属，"这是地质化学。"

活着的死土
在偶然发现这一现象时，方丹正试图为无生命土壤中的碳含量建立基准线。研究人员用无菌注射器定期从一个密封罐中采集空气样本（罐内装有土壤），并用质谱仪测量其碳含量。辐射消灭了土壤微生物后，碳排放率迅速下降，但并未消失。它在超过100天的时间里保持稳定。

当他与其他研究者分享这一结果时，他们建议将其视为实验误差——一个不值得深究的错误来源——然后继续前进。但他做不到。他需要弄清楚，一个通常只被认为在生物细胞中发生的代谢过程——一个需要多种分子和酶参与、精确协调的化学反应序列——是否也在无菌土壤中上演。为了观察发生了什么，他的团队添加了一点从酵母培养物中提取的酶。土壤的碳排放量立刻飙升。他们推测，这是因为酶加速了早已发生的反应。

然而，说服科学界是一场艰苦的战斗。方丹回忆起将论文手稿提交给期刊发表时，"一些审稿人非常积极，另一些则非常怀疑，尤其是关于土壤的无菌性问题。"2013年，这一结果发表在《生物地球科学》期刊上。即便如此，方丹仍无法安歇。被严苛的评审意见所伤，他决定最终证明其经辐射的土壤样本确实不含生命。在接下来的十年里，他的实验室断断续续地攻克着这个执念。

他们考虑了土壤可能并未真正死亡的可能性，并试图用更多的辐射、压力和热量来更彻底地"杀死"它。然而，土壤仍在数月内持续排放碳。

通过电子显微镜，当时在方丹实验室攻读研究生的伯努瓦·凯拉瓦尔在受辐射土壤中发现了细胞。但染色显示没有RNA或DNA分子，表明这些细胞确实已经死亡。当他们实验性地添加微生物以模拟污染时，这些细胞迅速在土壤微环境中重新定殖，并释放出更多的二氧化碳。因此，他们在灭菌样本中观察到的情况，很可能并非消毒措施不当所致。

到2018年克莱芒坦·布凯加入实验室时，团队已对其发现充满信心，并准备深入探究其背后的机制。

泥土中的电子
在六年时间里，布凯和凯拉瓦尔研究了两组密封且经过辐射的土壤样本——一组是普通土壤，另一组添加了葡萄糖。在142天里，他们定期采集空气样本，发现二氧化碳的日排放率在下降，但并未消失，与之前的情况一样。随后，样本在培养箱中放置了超过1000天，期间研究人员专注于其他关于微生物如何在土壤中处理和储存碳的实验。

当他们再次测量样本（分别在第1606天和第2442天）时，排放速率进一步减慢，但土壤仍在呼吸。添加了葡萄糖的样本显示出更高的排放率，这强化了方丹的猜测：土壤中的非生物催化剂能诱导类似于糖类代谢分解的反应。

在代谢过程中，糖被分解成较小的碳分子，这些分子进入克雷布斯循环——一系列从富含碳的分子中剥离高能电子的反应。克雷布斯循环释放出的电子随后通过另一组消耗氧气的反应。对一些研究者来说，认为这一过程能在细胞外进行有些牵强。方丹需要证明土壤能扮演同样的角色。

他设计了一个燃料电池，可以检测到以电流形式在土壤中穿梭的电子。他的团队加入了大约五年前经过辐射的土壤，然后闭合电路。流经土壤的电流比涉及盐水溶液的对照组高出数倍。据方丹称，该实验证明无菌土壤支持电子的流动，这指示着类似于克雷布斯循环中依赖氧气的代谢过程。

人们曾认为克雷布斯循环不可能在受到严密控制的细胞之外发生，因为细胞内充满了酶，确保一切有序运转，并增加生物分子相互碰撞的机会。在2025年一篇发表于biorxiv.org的预印本中，方丹及同事报告称，在放置了六个月的灭菌土壤样本中观察到了已知参与克雷布斯循环的八种中间分子中的四种。这些分子中有许多是在辐射之后形成的。

作者们认为，他们的结果表明，土壤团块确实可以在没有生命存在的情况下催化这些反应。

生命的起源？
对于加州大学圣塔芭芭拉分校的土壤生态学家约书亚·席梅尔来说，方丹的发现并不太令人惊讶。"葡萄糖在自然氧化过程中，会形成一些克雷布斯循环中间体。"他说。他补充道，许多土壤富含铁氧化物和铝氧化物，它们可以催化这种转化。

金属能催化生化反应这一观点，是过去十年间出现的一种关于生命起源理论的核心。铁和锌等金属位于许多最古老酶的核心，这些酶存在于各种生命形式中。包括莫兰在内的一些研究者认为，它们可能在生命出现之前就催化了这些反应。包括他的研究在内的多项研究表明，通常与生命相关的、分解和构建葡萄糖衍生物的化学反应，可能早于使它们在活细胞中得以实现的酶和基因而存在。

莫兰说："有一小部分像我这样的研究者认为，实际上，我们应该换一种方式来组织对生命的思考——我们应该把代谢作为生命活动的基础，而基因则是在更高层面上控制它的手段。"

柏林夏里特大学医院的生物化学家马库斯·拉尔瑟发现了一些最早的无酶代谢反应，他表示，无细胞代谢反应可能比以前认为的更常见，并且不需要特殊条件就能启动。

谈及这项新研究，他说："这有点符合我关于代谢如何在进化中起源的思考。如果它非常难以发生，那么地球现在就不会充满生命了。"然而，生命起源时的低氧条件使得这一观点变得复杂。

对观察到的结果的另一种解释是，从受辐射细胞中释放出来的酶可能仍留在土壤中，继续执行它们的生化任务。未参与此项研究的浦那印度科学教育与研究学院的太空生物学家苏达·拉贾马尼说，即使已经降解，酶也具有稳定的骨架，可能仍有能力催化反应。

拉尔瑟同意她的看法。他说："我的直觉是，即使过了六年，他们（在方丹的受辐射土壤中）仍然有很多酶。"要知道土壤中的金属和矿物质是否能自发地进行这些反应，研究人员必须从混合物中去除酶。但这非常困难：他们必须将土壤加热到会破坏土壤本身结构的程度。

不过，布凯表示，这些酶在从细胞中释放出来后，其活性会"指数级"下降。此外，方丹补充说，没有已知的酶能持续存在六年。他不怀疑来自活细胞和近期死亡细胞的酶在现实土壤的碳排放中有所贡献，但长期的实验结果使得"我们观察到的呼吸作用是由酶引起的可能性非常低"。

对布凯来说，追逐这个持续多年的执念凸显出，"即使是在像陆地土壤这样与我们如此贴近和熟悉的语境中，我们也并非总能区分或识别出指示生命体存在与否的过程。"他现在是法兰西学院和巴黎国家自然历史博物馆的研究员，正在寻找其他生化级联反应的"前生命"起源。

"我觉得特别有趣的是，想象那些可能早于生命本身的过程，"布凯说，"就在我们脚下继续存在。"

英文来源：

The Dirt That Refused To Die
Introduction
For 15 years, Sébastien Fontaine has been trying to kill dirt. The biochemist, who runs a lab at the French National Institute for Agriculture, Food, and Environment, wanted to know how much carbon is released by soil — just dirt alone, completely devoid of life. His team sealed dirt into jars and blasted them with sterilizing gamma radiation. Then they waited for the carbon dioxide released by the soil — a sign of ongoing microbial respiration — to drop.
They waited, and waited, and waited some more: weeks, then months. Under a microscope, the irradiated soil showed no signs of life, but it continued to emit carbon dioxide. The soil wouldn’t stop breathing.
Fontaine’s lab repeated the experiments and produced the same results. Finally, convinced that they weren’t dealing with an artifact of the experimental setup, they set out to find the source of breath in dead soil.
Now, Fontaine and his colleagues have reported that their soil samples continued to consume oxygen and spew carbon dioxide for six years. In a 2025 paper in Science Advances, they proposed that a metabolic process that powers much of life is also possible outside living cells. Their experiments point to how it could work in dirt, absent the living proteins that would typically organize it. If they’re right, some biochemical reactions, such as those that release the energy of carbon-rich sugar molecules, may not be unique to living things. Such reactions — known as metabolism when performed by cells — could even predate life on Earth, Fontaine said.
The experiments show “what happens to biomolecules when they’re left to their own devices,” said Joseph Moran, an organic chemist at the University of Ottawa who was not involved with the research. They’re finding that the chemistry of life is not exclusive to life, he added. “It’s the chemistry of geology.”
The Living Dead
When he made this accidental discovery, Fontaine was trying to establish a baseline for carbon in lifeless soil. Using a sterile syringe, the researchers periodically sampled the air in a hermetically sealed jar containing soil and measured its carbon content using a mass spectrometer. After radiation wiped out the soil microbes, the carbon emission rate declined quickly but didn’t disappear. It remained stable for over 100 days.
When he shared the results with other researchers, they advised him to treat it as an experimental artifact — a source of error not worth ferreting out — and move on. But he couldn’t. He needed to understand whether a metabolic process only known to occur in biological cells — a precisely orchestrated sequence of chemical reactions, requiring several molecules and enzymes — was unfolding in sterile soil. To see what was happening, his team added a dash of enzymes extracted from yeast cultures. Immediately, the soil’s carbon emissions spiked. This, they speculated, was because the enzymes had ramped up a reaction that was already happening.
Convincing the scientific community, however, was an uphill battle. When Fontaine submitted the manuscript to journals for publication, some reviewers “were highly positive, and others were really suspicious, especially concerning the sterility of the soil,” he recalled. In 2013 the results were published in the journal Biogeosciences. Still, Fontaine could not rest. Bruised by the harsh reviews, he decided to definitively prove that his irradiated soil samples remained free of life. Over the following decade, his lab would, in fits and starts, chip away at their obsession.
They considered the possibility that the soil wasn’t really dead, and tried to kill it harder with more radiation, pressure, and heat. Still, the soil continued to emit carbon for months.
Through an electron microscope, Benoit Kéraval, then a graduate student in Fontaine’s lab, found cells in the irradiated soil. But staining showed no RNA or DNA molecules, indicating that the cells were definitely dead. When they experimentally added microbes to simulate contamination, the cells rapidly recolonized the soil microcosm and released much more carbon dioxide. So what they were observing in the sterilized sample likely wasn’t a result of inadequate antiseptic measures.
By 2018, when Clémentin Bouquet joined the lab, the team was confident in its findings and ready to dig into the underlying mechanisms.
Dirty Electrons
For six years, Bouquet and Kéraval studied two sets of sealed, irradiated soil samples — one of normal soil, and one that was supplemented with glucose. For 142 days, they took regular air samples and saw the daily rate of carbon dioxide emissions decline but not disappear, just as they had before. Then the samples sat in an incubator for over 1,000 days, as the researchers focused on their other experiments into how microbes process and store carbon in soil.
When they measured the samples again, at days 1,606 and 2,442, the emissions had slowed further, but the soil was still breathing. The glucose-augmented samples showed higher emission rates, which strengthened Fontaine’s suspicion that nonbiological catalysts in soil can induce reactions that resemble the metabolic breakdown of sugar.
During metabolism, sugar is broken down into smaller carbon molecules, which feed the Krebs cycle — a series of reactions in which high-energy electrons are stripped from carbon-rich molecules. Electrons liberated by the Krebs cycle then pass through another set of reactions that consume oxygen. For some researchers, it was a stretch to suggest that this process could unfold outside a cell. Fontaine would need to show that soil can play the same role.
He devised a fuel cell that could detect electrons zipping through soil in the form of a current. His team added soil that had been irradiated almost five years earlier, and then closed the circuit. A current passed through the soil that was several times higher than in a control setup involving a saltwater solution. According to Fontaine, the experiment demonstrated that sterile soil supports a flow of electrons indicative of processes that resemble the oxygen-dependent metabolism of the Krebs cycle.
It was once thought that the Krebs cycle cannot occur outside the controlled confines of a cell, which teems with enzymes that keep everything ticking along and increases the chances that biomolecules will bump into each other. In a 2025 preprint on biorxiv.org, Fontaine and colleagues reported observing four of the eight intermediate molecules known to be part of the Krebs cycle in 6-month-old sterile soil samples. Many of these molecules formed after the irradiation.
According to the authors, their results suggest that clods of earth can indeed catalyze these reactions without the presence of life.
An Origin of Life?
For Joshua Schimel, a soil ecologist at the University of California, Santa Barbara, Fontaine’s findings were not too surprising. “Glucose naturally, in the process of being oxidized, is going to form some of these Krebs-cycle intermediates,” he said. Many soils are rich in iron oxides and aluminum oxides, which can catalyze this conversion, he added.
The idea that metals can catalyze biochemical reactions is central to a theory about the origins of life that has emerged over the last decade. Metals such as iron and zinc sit at the core of many of the most ancient enzymes found across life forms. Some researchers, including Moran, believe they might have catalyzed these reactions before life emerged. Studies, including his, suggest that the chemical reactions that break down and construct glucose derivatives, which are normally associated with life, might have existed before the enzymes and genes that enable them in living cells.
“There’s a handful of researchers like myself that think, actually, we should organize our thoughts about life in a different way — that we actually should put metabolism at the base of what life is doing, and then genes are a way of controlling that at a higher level,” Moran said.
Cell-free metabolic reactions could be more common than previously thought and don’t need special conditions to get started, said Markus Ralser, a biochemist at Charité University Hospital in Berlin, who found some of the first enzyme-free metabolic reactions.
“This fits a bit into my thinking about how metabolism started in evolution,” he said of the new work. “If it would be very hard to do, then the planet would not be full of life now.” This idea is complicated, however, by the low-oxygen conditions in which life arose.
Another explanation for the observed results could be that enzymes, loosed from the irradiated cells, might be hanging around in the soil and continuing their biochemical jobs. Even when degraded, enzymes have stable backbones that might be capable of catalyzing reactions, said Sudha Rajamani, an astrobiologist at the Indian Institute of Science Education and Research, Pune who wasn’t involved in the study.
Ralser agrees with her. “My gut feeling is they still have a lot of enzymes there [in Fontaine’s irradiated soil], even after six years,” he said. To know whether metals and minerals in soil could spontaneously carry out these reactions, the researchers would have to eliminate enzymes from the mixture. But that’s really hard: They would have to get the soil so hot that it would damage the soil structure itself.
However, the activity of such enzymes diminishes “exponentially” after they spill out of cells, Bouquet said. Plus, no enzyme is known to last six years, Fontaine added. He doesn’t doubt that enzymes released by living and recently dead cells contribute to carbon emissions in real-world soils, but the long-term experimental results make it “very unlikely that the respiration we observed is due to enzymes,” he said.
For Bouquet, chasing this years-long obsession has highlighted that “even in a context as close and familiar to us as terrestrial soil, we are not always able to distinguish or recognize processes that indicate the presence or absence of living organisms.” Now a researcher at the Collège de France and the National Museum of Natural History in Paris, he is looking for prebiotic origins of other biochemical cascades.
“I find it particularly interesting to imagine the survival of processes that may predate life itself,” Bouquet said, “right there under our feet.”