被遗忘的生物大类——古生菌

NEW RESEARCH SHOWS THE IMPORTANCE OF ARCHAEA, ONE OF THREE DOMAINS INTO WHICH ALL LIVING THINGS ARE CLASSIFIED, FOR UNDERSTANDING ALL OF BIOLOGY.

一项最新研究显示了古生菌的重要性。为了了解所有的生物，可以将生物划分为三大类，古生菌便是这三大类中的一类生物。

All of life can be divided into three domains: Eukarya (including plants, animals, fungi, and other organisms) Bacteria, and Archaea. But take a look at a typical US high-school biology text (in this case, my daughter’s), and you’d hardly notice it. Her book devotes a single page (out of 848) to Archaea. Sure, the concept of Archaea as a domain on the level of bacteria and eukaryotes is relatively recent, but the science behind the distinction is quite solid.

所有的生命形式可以划分为三大类：真核生物（包括植物，动物，真菌，以及其他生物）、细菌以及古生菌。但是如果你翻看美国高中标准生物学课本的话，你无法完整看到这三类生物。一本848页厚的生物学课本，仅有一页是讲解古生菌的。的确，古生菌是与细菌、真核生物同等水平的生物类别，这一概念是新近才有的，但是这种划分背后的科学基础却是相当坚实的。

Archaea had previously been lumped in with bacteria as kingdom Monera—the so-called prokaryotes, which lack a cellular nucleus—in the five-kingdom classification system many of us (including myself) learned in high school. But as the biologist who blogs as “Lab Rat” pointed out last June, this doesn’t make much sense: “‘prokaryotes,’” she tells us, “is not much more than a scientific word for ‘blobs I don’t care about.’”

在之前的五大类分类系统中，古生菌一直作为没有细胞核的原核生物，被归在细菌这个类别下面。但是正如一位生物学家今年六月份指出的那样，这不太讲得通：“原核生物这个词，根本就不是一个科学的词汇。”

Perhaps Archaea has been relegated to its seemingly second-class status because it is a relatively recent discovery—the separate domain was first proposed in 1977. Perhaps they just seem “more unusual” than organisms like bacteria that most of us are more familiar with—after all, they’re often found in extreme environments like undersea thermal vents, high-salinity ponds, and toxic mine tailings.

古生菌被归为不太重要的二等类别，或许是因为它是新近才被发现的——首次提议将古生菌作为单独的类别是在1977年。也许古生菌只是比细菌这种我们较为熟悉的生物体“更加不寻常”而已——毕竟它们往往是在极端环境中被发现，比如海底暖气流的出口处，高含盐度的池塘里以及有毒的矿渣里。

But lumping Archaea in with Bacteria simply doesn’t make biological sense. While, like bacteria, archaeans don’t have a cell nucleus, they share other traits with eukaryotes like you and me. An archaean converts DNA into proteins very differently from, say, Streptococcus—in fact, protein synthesis in Archaea is more similar to the human process than to bacteria. Archaeans have cell membranes that are completely different from both bacteria and eukaryotes.

但是将古生菌归在细菌这个类别下面，在生物学上便讲不通。虽然，像细菌一样，古生菌也没有细胞核，但是它们与你我这样的真核生物具有其他共同的特性。古生菌，比如链球菌，将DNA转录成蛋白质会非常困难——实际上与细菌相比，古生菌的蛋白质合成过程与人类的蛋白质合成过程更相似。古生菌还具有完全与细菌和真核生物不同的细胞膜。

Microbiologist and computer scientist Iddo Friedberg blogged last week that archaeans don’t just live in extreme environments. They may constitute as much as 20 percent of the free-drifting microbes in the earth’s oceans. A study published this month in Environmental Microbiology describes a “giant” archaean that grows to 3 centimeters long and is nearly visible without magnification (it’s just 0.1 mm thick). The species lives in mangrove swamps in the West Indies, with each individual wearing a coat of hundreds of much-smaller bacteria, living in a mutualistic relationship—neither organism could survive without the other.

微生物学家以及计算机科学家易多·弗里德伯格（Iddo Friedberg）上周在博客中写道，古生菌并不仅仅只是生活在极端环境中。它们在地球海洋自由漂流的微生物中，构成比例可能高达20%。这个月发表在《环境微生物学杂志》（Environmental Microbiology）上的一篇研究，描述了一个长到3厘米长的“巨型”古生菌，而且几乎不需要放大就能看见（厚度仅有0.1毫米）。这一物种生活在西印度群岛上的红树林沼泽里，每个古生菌表面都覆盖着成百上千个更小的细菌组成的“外衣”，古生菌与这些细菌处于一种互惠共生的关系——没有彼此，其中任何一种生物都无法存活。

But many of the most fascinating archaeans do manage to survive in extreme environments. Microbiologist Moselio Schaechter described one such habitat in August. The abandoned Richmond Mine in California has the most acidic waters in the world, courtesy of underground microbes that consume sulfides and excrete sulfuric acid. In water acidic enough to dissolve metal, archaeans form biofilms that researchers call “blanket strips” because they look like pink fiberglass insulation. The individual archaeans are some of the smallest organisms ever found. Even their genomes are about 10 percent smaller than in other, similar organisms. Like other archaeans, their genomes share some similarities with both eukaryotes and bacteria. The researchers who first identified them, led by Jill Banfield, have found other enigmatic features such as mysterious tubular structures whose function is not yet known. The research was published in PNAS.

但是许多最吸引人的古生菌都在极端环境中设法生存。微生物学家莫塞利奥（Moselio Schaechter）在今年8月份描述了一个这样环境极端的栖息地。美国加州被废弃的里士满矿，拥有世界上酸性最强的水，这种强酸性是地下的微生物消耗硫化物并排出硫酸造成的。在足够溶化金属的酸水中，古生菌形成了一层生物膜，研究人员将这层生物膜称为“红毯带”，因为它们看起来就像粉红色的玻璃纤维隔离层。这种古生菌是迄今为止发现的最小的生物体中的一种。它们的基因组甚至也比其他相似的生物体基因组要少10%左右。像其他古生菌一样，这种古生菌的基因组同时与真核生物和细菌的基因组具有一些相似性。最早识别出这种古生菌的研究者吉尔·班菲尔德（Jill Banfield）还发现了其他神秘的特征，比如神秘的管状结构，这种结构的功能目前还不清楚。这项研究发表在《美国科学院院刊》（PNAS）上。

Since archaeans have unique cell membranes, they are typically not susceptible to viruses that infect eukaryotes and bacteria (most viruses replicate by budding off a cell’s membrane). But this doesn’t mean there are no viruses that affect the Archaea. As Columbia University virologist Vincent Racaniello writes, Archaea have their own viruses. Some of these even survive in the highly acidic environment of the Richmond Mine, or as a team led by Maija K. Pietil found, in high-salinity ponds used to manufacture gourmet sea-salt. This virus may have a unique structure not found in viruses affecting bacteria and eukaryotes—it has to be able to survive in the same extreme environment as the organism it infects. The research was published in Journal of Virology.

由于古生菌具有独特的细胞膜，所以它们的一大特色就是不易受病毒影响，而真核生物与细菌则容易被病毒感染（大多数病毒通过穿透细胞膜出芽而进行再生）。但是这也并不意味着没有病毒可以影响到古生菌。正如美国哥伦比亚大学（Columbia University）病毒学家文森特（Vincent Racaniello）所述，古生菌拥有它们自己的病毒。这些病毒中的一些病毒甚至能够在里士满矿的强酸环境中存活下来，或者如麦加（Maija K. Pietil）领导的研究小组所发现的那样，这些病毒能够在用于制作美味海盐的高含盐度池塘中存活。这种病毒可能具有某种独特的结构，这种结构是能够影响细菌与真核生物的病毒所不具有的——它不得不像其感染的生物体一样，能够在同样极端的环境中生存。这项研究发表在《病毒学杂志》（Journal of Virology）上。

Although based on its protein-synthesis apparatus Archaea is in many ways most similar to the Eukarya domain, archeans can also share and exchange DNA with the denizens of the Bacteria domain. So it seems that Archaea, straddling between the more familiar eukaryotes and higher-profile bacteria, can probably tell us something substantial about the origins of both. For much more on Archaea, try a search on ResearchBlogging.org.

虽然从蛋白质合成器官上来看，古生菌在许多方式上与真核生物最为相似；但是古生菌还会与自己身上寄居的细菌共享并交换DNA物质。所以看起来情况是，古生菌跨在较为熟悉的真核生物与知名度较高的细菌之间，或许能够告诉我们一些关于真核生物与细菌起源的本质。

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