The Dirt That Refused To Die

What appear to be biochemical processes may instead be a natural feature of geology.

看似生化过程的东西可能实际上是地质学的自然特征。

Samuel Velasco/ Quanta Magazine

塞缪尔·贝拉斯科/广达杂志

For 15 years, Sébastien Fontaine has been trying to kill dirt.

15 年来，Sébastien Fontaine 一直致力于消除污垢。

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.

这位生物化学家在法国国家农业、食品和环境研究所经营一个实验室，他想知道土壤释放了多少碳——只是泥土，完全没有生命。

His team sealed dirt into jars and blasted them with sterilizing gamma radiation.

他的团队将泥土密封在罐子里，并用伽马射线进行消毒。

Then they waited for the carbon dioxide released by the soil — a sign of ongoing microbial respiration — to drop.

然后他们等待土壤释放的二氧化碳（微生物正在进行呼吸的迹象）下降。

They waited, and waited, and waited some more: weeks, then months.

他们等啊等，又等了几个星期，然后是几个月。

Under a microscope, the irradiated soil showed no signs of life, but it continued to emit carbon dioxide.

在显微镜下观察，受辐射的土壤没有任何生命迹象，但仍不断排放二氧化碳。

The soil wouldn’t stop breathing.

土壤不会停止呼吸。

Fontaine’s lab repeated the experiments and produced the same results.

方丹的实验室重复了这些实验并得出了相同的结果。

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.

最后，他们确信自己处理的不是实验装置的产物，于是开始在死土中寻找呼吸的来源。

Now, Fontaine and his colleagues have reported that their soil samples continued to consume oxygen and spew carbon dioxide for six years.

现在，方丹和他的同事报告说，他们的土壤样本六年来持续消耗氧气并喷出二氧化碳。

In a 2025 paper in Science Advances , they proposed that a metabolic process that powers much of life is also possible outside living cells.

在 2025 年《科学进展》杂志上的一篇论文中，他们提出，为大部分生命提供动力的代谢过程在活细胞外也是可能的。

Their experiments point to how it could work in dirt, absent the living proteins that would typically organize it.

他们的实验表明，在没有通常组织它的活蛋白质的情况下，它如何在污垢中发挥作用。

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.

如果他们是对的，那么一些生化反应，例如释放富含碳的糖分子能量的反应，可能并不是生物所独有的。

Such reactions — known as metabolism when performed by cells — could even predate life on Earth, Fontaine said.

方丹说，这种反应——由细胞进行时被称为新陈代谢——甚至可能早于地球上的生命。

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.

未参与这项研究的渥太华大学有机化学家约瑟夫·莫兰 (Joseph Moran) 表示，这些实验展示了“当生物分子自行处理时，它们会发生什么”。

They’re finding that the chemistry of life is not exclusive to life, he added.

他补充说，他们发现生命的化学反应并不是生命所独有的。

“It’s the chemistry of geology.”

“这是地质学的化学。”

When he made this accidental discovery, Fontaine was trying to establish a baseline for carbon in lifeless soil.

当他偶然发现这一点时，方丹正试图建立无生命土壤中碳的基线。

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.

研究人员使用无菌注射器定期对装有土壤的密封罐中的空气进行采样，并使用质谱仪测量其碳含量。

After radiation wiped out the soil microbes, the carbon emission rate declined quickly but didn’t disappear.

辐射消灭了土壤微生物后，碳排放率迅速下降，但并没有消失。

It remained stable for over 100 days.

100多天以来一直保持稳定。

The type of soil-filled vessel used for the lab’s experiments “represents the microcosms in which the whole story unfolded,” Bouquet said.

布凯说，用于实验室实验的装满土壤的容器类型“代表了整个故事展开的微观世界”。

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.

当他与其他研究人员分享结果时，他们建议他将其视为实验制品（不值得找出的错误来源）并继续前进。

But he couldn’t.

但他不能。

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.

他需要了解一种已知只发生在生物细胞中的代谢过程（精确协调的化学反应序列，需要多种分子和酶）是否正在无菌土壤中展开。

To see what was happening, his team added a dash of enzymes extracted from yeast cultures.

为了看看发生了什么，他的团队添加了少量从酵母培养物中提取的酶。

Immediately, the soil’s carbon emissions spiked.

土壤的碳排放量立即激增。

This, they speculated, was because the enzymes had ramped up a reaction that was already happening.

他们推测，这是因为酶增强了已经发生的反应。

Convincing the scientific community, however, was an uphill battle.

然而，说服科学界是一场艰苦的战斗。

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.

当方丹将手稿提交给期刊出版时，一些审稿人“非常积极，而其他人则非常怀疑，特别是关于土壤的贫瘠”，他回忆道。

In 2013 the results were published in the journal Biogeosciences .

2013年，研究结果发表在《生物地球科学》杂志上。

Still, Fontaine could not rest.

尽管如此，方丹仍无法休息。

Bruised by the harsh reviews, he decided to definitively prove that his irradiated soil samples remained free of life.

受到严厉评论的打击，他决定明确证明他的经过辐照的土壤样本仍然没有生命。

Over the following decade, his lab would, in fits and starts, chip away at their obsession.

在接下来的十年里，他的实验室断断续续地削弱了他们的痴迷。

They considered the possibility that the soil wasn’t really dead, and tried to kill it harder with more radiation, pressure, and heat.

他们考虑了土壤并没有真正死亡的可能性，并试图用更多的辐射、压力和热量来更有效地杀死它。

Still, the soil continued to emit carbon for months.

尽管如此，土壤仍持续排放碳数月。

Through an electron microscope, Benoit Kéraval, then a graduate student in Fontaine’s lab, found cells in the irradiated soil.

时任方丹实验室研究生的伯努瓦·克拉瓦尔 (Benoit Kéraval) 通过电子显微镜在受辐射的土壤中发现了细胞。

But staining showed no RNA or DNA molecules, indicating that the cells were definitely dead.

但染色显示没有 RNA 或 DNA 分子，表明细胞肯定已经死亡。

When they experimentally added microbes to simulate contamination, the cells rapidly recolonized the soil microcosm and released much more carbon dioxide.

当他们通过实验添加微生物来模拟污染时，细胞迅速在土壤微观世界中重新定居，并释放出更多的二氧化碳。

So what they were observing in the sterilized sample likely wasn’t a result of inadequate antiseptic measures.

因此，他们在灭菌样本中观察到的情况很可能不是防腐措施不充分的结果。

By 2018, when Clémentin Bouquet joined the lab, the team was confident in its findings and ready to dig into the underlying mechanisms.

2018 年，当 Clémentin Bouquet 加入实验室时，团队对其发现充满信心，并准备深入研究潜在机制。

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.

六年来，布凯和凯拉瓦尔研究了两组密封的、经过辐照的土壤样本——一组是普通土壤，一组是补充了葡萄糖的土壤。

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.

在 142 天的时间里，他们定期采集空气样本，发现每天的二氧化碳排放量有所下降，但并没有像以前一样消失。

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.

然后，这些样本在培养箱中放置了 1000 多天，研究人员则专注于微生物如何处理和储存土壤中的碳的其他实验。

When they measured the samples again, at days 1,606 and 2,442, the emissions had slowed further, but the soil was still breathing.

当他们在第 1,606 天和第 2,442 天再次测量样本时，排放量进一步减慢，但土壤仍在呼吸。

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.

葡萄糖增强的样品显示出更高的排放率，这加强了方丹的怀疑，即土壤中的非生物催化剂可以诱发类似于糖代谢分解的反应。

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.

在新陈代谢过程中，糖被分解成更小的碳分子，为克雷布斯循环提供能量，这是一系列反应，其中高能电子从富含碳的分子中被剥离。

Electrons liberated by the Krebs cycle then pass through another set of reactions that consume oxygen.

克雷布斯循环释放的电子然后通过另一组消耗氧气的反应。

For some researchers, it was a stretch to suggest that this process could unfold outside a cell.

对于一些研究人员来说，认为这一过程可以在细胞外展开有些牵强。

Fontaine would need to show that soil can play the same role.

方丹需要证明土壤也能发挥同样的作用。

He devised a fuel cell that could detect electrons zipping through soil in the form of a current.

他设计了一种燃料电池，可以检测以电流形式穿过土壤的电子。

His team added soil that had been irradiated almost five years earlier, and then closed the circuit.

他的团队添加了近五年前经过辐射的土壤，然后关闭了电路。

A current passed through the soil that was several times higher than in a control setup involving a saltwater solution.

通过土壤的电流比涉及盐水溶液的控制装置高几倍。

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.

方丹表示，实验证明，无菌土壤支持电子流，这表明类似于克雷布斯循环的氧依赖性代谢过程。

When Clémentin Bouquet joined the lab in 2018, he co-led a six-year experiment that suggests that lifelike biochemistry takes place even in sterile soil.

当 Clémentin Bouquet 于 2018 年加入该实验室时，他与他人共同领导了一项为期六年的实验，该实验表明即使在无菌土壤中也会发生逼真的生物化学反应。

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.

人们曾经认为克雷布斯循环不能在细胞的受控范围之外发生，细胞中充满了使一切保持运转并增加生物分子相互碰撞的机会的酶。

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.

在 biorxiv.org 上的 2025 年预印本中，Fontaine 及其同事报告称，在 6 个月大的无菌土壤样本中观察到了已知属于克雷布斯循环一部分的八种中间分子中的四种。

Many of these molecules formed after the irradiation.

许多这些分子是在辐射后形成的。

According to the authors, their results suggest that clods of earth can indeed catalyze these reactions without the presence of life.

这组作者说，他们的结果表明，土块确实可以在没有生命存在的情况下催化这些反应。

For Joshua Schimel, a soil ecologist at the University of California, Santa Barbara, Fontaine’s findings were not too surprising.

对于加州大学圣塔芭芭拉分校的土壤生态学家约书亚·希梅尔（Joshua Schimel）来说，方丹的发现并不令人意外。

“Glucose naturally, in the process of being oxidized, is going to form some of these Krebs-cycle intermediates,” he said.

“葡萄糖在被氧化的过程中自然会形成一些克雷布斯循环中间体，”他说。

Many soils are rich in iron oxides and aluminum oxides, which can catalyze this conversion, he added.

他补充说，许多土壤富含铁氧化物和铝氧化物，可以催化这种转化。

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.

金属可以催化生化反应的想法是过去十年出现的生命起源理论的核心。

Metals such as iron and zinc sit at the core of many of the most ancient enzymes found across life forms.

铁和锌等金属是生命形式中发现的许多最古老酶的核心。

Some researchers, including Moran, believe they might have catalyzed these reactions before life emerged.

包括莫兰在内的一些研究人员认为，他们可能在生命出现之前就催化​​了这些反应。

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.

包括他的研究在内的研究表明，分解和构建通常与生命相关的葡萄糖衍生物的化学反应可能早于在活细胞中启用它们的酶和基因就已经存在。

If [metabolism] would be very hard to do, then the planet would not be full of life now.

如果[新陈代谢]很难进行，那么地球现在就不会充满生命。

Markus Ralser, Charité University Hospital in Berlin

Markus Ralser，柏林夏里特大学医院

“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.

“有一些像我这样的研究人员认为，实际上，我们应该以不同的方式组织我们对生命的思考——我们实际上应该把新陈代谢作为生命活动的基础，然后基因是在更高水平上控制新陈代谢的一种方式，”莫兰说。

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 .

柏林夏里特大学医院的生物化学家马库斯·拉瑟 (Markus Ralser) 发现了一些第一个无酶代谢反应，他说，无细胞代谢反应可能比之前想象的更常见，并且不需要特殊条件即可开始。

“This fits a bit into my thinking about how metabolism started in evolution,” he said of the new work.

“这有点符合我对新陈代谢如何在进化中开始的思考，”他在谈到这项新工作时说道。

“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.

“如果这很难做到，那么这个星球现在就不会充满生命了。”然而，由于生命诞生的低氧条件，这个想法变得复杂。

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.

对观察到的结果的另一种解释可能是，从受辐射的细胞中释放出来的酶可能徘徊在土壤中并继续其生化工作。

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.

浦那印度科学教育与研究学院的天体生物学家苏达·拉贾马尼（Sudha Rajamani）表示，即使酶被降解，也具有稳定的骨架，可能能够催化反应。他没有参与这项研究。

Ralser agrees with her.

拉瑟同意她的观点。

“My gut feeling is they still have a lot of enzymes there [in Fontaine’s irradiated soil], even after six years,” he said.

“我的直觉是，即使六年过去了，[方丹受辐射的土壤]仍然含有大量酶，”他说。

To know whether metals and minerals in soil could spontaneously carry out these reactions, the researchers would have to eliminate enzymes from the mixture.

为了了解土壤中的金属和矿物质是否可以自发地进行这些反应，研究人员必须从混合物中消除酶。

But that’s really hard: They would have to get the soil so hot that it would damage the soil structure itself.

但这真的很难：他们必须使土壤变得非常热，以至于会损坏土壤结构本身。

However, the activity of such enzymes diminishes “exponentially” after they spill out of cells, Bouquet said.

然而，布凯说，这些酶的活性在溢出细胞后会“呈指数级”减弱。

Plus, no enzyme is known to last six years, Fontaine added.

此外，方丹补充说，目前还没有已知的酶可以持续六年。

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.

他并不怀疑活细胞和最近死亡的细胞释放的酶会导致现实世界土壤中的碳排放，但长期实验结果表明“我们观察到的呼吸作用不太可能是由酶引起的”，他说。

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.

对于 Bouquet 来说，对这种长达数年的痴迷的追求突显了“即使在我们像陆地土壤这样接近和熟悉的环境中，我们并不总是能够区分或识别表明生物体存在或不存在的过程。”现在，他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的益生元起源。

“I find it particularly interesting to imagine the survival of processes that may predate life itself,” Bouquet said, “right there under our feet.”

布凯说：“我发现想象可能早于生命本身的过程的生存特别有趣，就在我们脚下。”

Get highlights of the most important news delivered to your email inbox

获取发送到您的电子邮件收件箱的最重要新闻的摘要

Quanta Magazine moderates comments to facilitate an informed, substantive, civil conversation.

《Quanta》杂志对评论进行审核，以促进知情、实质性、文明的对话。

Abusive, profane, self-promotional, misleading, incoherent or off-topic comments will be rejected.

辱骂、亵渎、自我推销、误导、语无伦次或偏离主题的评论将被拒绝。

Moderators are staffed during regular business hours (New York time) and can only accept comments written in English.

版主在正常工作时间（纽约时间）有工作人员，并且只能接受英文评论。