全球大约10-25%的甲烷来自于水稻田。甲烷这种温室气体由多种微生物群（产烷生物）产生，而位于水稻作物根部的主要产烷者是“水稻簇I（RC-I）Archaea”。对这些微生物而言，氧是一种有毒物。
这些Archaea保持其竞争优势的机制尚不清楚，因为不能得到它们的纯培养物。如今，来自德国马尔堡的马克斯·普朗克学会的陆地微生物研究所和分子遗传研究所的科学家们已经完成了对产烷微生物混合培养体中的RC-I Archaea的基因测序。从基因序列来看，研究人员能够推断出其中存在大量的酶结构，而这些Archaea中酶之前是不为人所知的。这些酶帮助RC-I Archaea在有氧条件下生存。它们使RC-I Archaea适应了水稻根部周围特殊的富氧环境。该研究结果解释了为何RC-I Archaea保持了其生存优势（结果发表在2006年7月21日出版的《科学》杂志上）。
最近的研究中，马普学会的研究人员研究了一种RC-I Archaeon的全部基因序列，这种微生物经常出现在MRE50混合培养物中。通常，彻底分析一种微生物的基因需要纯培养物，这些纯培养物具有相类似的遗传信息。但对RC-I Archaea这种情况来说，无法得到纯培养物，因此，MRE50混合培养体的所有遗传信息被当作是给整个RC-I 基因排序的基础。这种来自混合培养物中多种不同微生物体的不同种类的遗传信息被称着Meta基因（Metagenome）。分析中最主要的困难是要从Meta基因中筛选出RC-I Archaeon完整的同类基因。研究人员使用了一种特殊的生物信息学分析技术来实现这个目标。
RC-I Archaeon的染色体由320万个碱基对组成，3103个蛋白质编码。其中的蛋白质能够根据产烷微生物新陈代谢的需要进行合成，这是为何它们只需简单地减少二氧化碳与氢的结合就能够生成甲烷的原因。作为产烷微生物营养物质的酶并非由RC-I基因编码。因此，RC-I Archaeon可以分为氢产烷微生物Archaea，只能产生甲烷，当在完全缺氧的条件下，能量就从这里产生。
通常氧的存在对它们是非常不利的。然而，对RC-I Archaea来说并非如此，产烷微生物Archaea的RC-I的酶的基因代码是独特的，这使其能够在富氧环境下生存。整组酶都属于这种机制。这些酶迅速分解氧活性粒子的毒性，如过氧化物阴离子，过氧化氢物等。这些氧活性粒子对活细胞来说毒性很重。当存在氧的时候，RC-I Archaea迅速切换到zymoma发酵模式。
RC-I基因系列为研发利用分子生物学来监测自然环境中RC-I Archaea的活动的方法打下了基础。然而，离我们最终降低RC-I Archaea及水稻田产生甲烷的能力还需要多少时间还有待确定。这个项目受到了马普学会和德国联邦教育研究部的联合资助。
英文原文：
Sequencing The Genome Of A New Kind Of Methane Producer
About 10 to 25 percent of the world's methane emissions come from flooded rice paddies. Methane is a greenhouse gas produced by various groups of microorganisms (methanogenic Archaea). Oxygen is usually highly toxic for these microorganisms. The major producer of methane in the roots of rice plants is what is known as "Rice Cluster I" (RC-I) Archaea.
The mechanisms that give these Archaea a competitive advantage remained unexplained, because it was impossible to get a pure culture of them. Now, scientists from the Max Planck Institute for Terrestrial Microbiology in Marburg, Germany and the Max Planck Institute for Molecular Genetics in Berlin have fully sequenced the genome of an RC-I archaeon from a methane-producing microbial mixed culture. From the genome sequence, the researchers were able to deduce the existence of a number of enzymatic mechanisms, unknown in methanogenic Archaea until now. The mechanisms help the RC-I Archaea to survive when oxygen is present. They allow the RC-I Archaea to adapt specifically to the oxygen-rich area around the roots of the rice plant. The results explain why RC-I Archaea have a selective survival advantage (Science, July 21, 2006).
In the current study, Max Planck researchers from Marburg and Berlin investigated the complete genome sequence of an RC-I archaeon that appears frequently in the mixed culture MRE50. As a rule, the starting point for analysis of a complete microbial genome is a pure culture - and its corresponding homogeneous component of genetic information. But in the case of RC-I Archaea, no pure culture was available. So all the genetic information of the mixed culture MRE 50 served as the starting point for sequencing the complete RC-I genome. Such heterogeneous genetic information, stemming from various microorganisms in the mixed culture, is called a metagenome. One particular analytical challenge was filtering out the complete, homogeneous genome of a defined RC-I archaeon from the metagenome. The researchers were able to do this using a specific bio-informatics analytical methodology.
The genome of the RC-I archaeon is made from 3.2 million base pairs, and codes for 3,103 proteins. The proteins can, among other things, be organized according to their methanogenic metabolism - that is, how they create methane simply by reducing carbon dioxide with hydrogen. Enzymes for the analysis of alternative methanogenic nutrients are not encoded by the RC-I genome. The RC-I archaeon can thus be categorised as hydrogenotroph Methanogenic Archaea can only produce methane, and the energy that comes from it, when oxygen is completely absent. The presence of oxygen is normally very hostile to them. However, this is not the case for RC-I Archaea - the RC-I genome codes for enzymatic mechanisms which are unique for methanogenic Archaea and make it possible for them to survive in an oxygenated environment. A whole group of enzymes belongs to this mechanism. These enzymes quickly detoxify highly reactive oxygen species, such as superoxide anion or hydrogen peroxide. These oxygen species are extremely toxic for living cells. When oxygen is present, RC-I Archaea quickly switch to a zymoma fermentative.
Sequencing the RC-I genome offers the groundwork for developing a means of monitoring the activity of RC-I Archaea in their natural environments, using molecular biological methods. It is uncertain, however, how long it will take before we can actually reduce the methane production of RC-I Archaea - and methane emissions from places like rice paddies.
