Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen AB24 3UU, United Kingdom.
Proc Natl Acad Sci U S A. 2010 Oct 5;107(40):17240-5. doi: 10.1073/pnas.1004947107. Epub 2010 Sep 20.
Nitrification plays a central role in the global nitrogen cycle and is responsible for significant losses of nitrogen fertilizer, atmospheric pollution by the greenhouse gas nitrous oxide, and nitrate pollution of groundwaters. Ammonia oxidation, the first step in nitrification, was thought to be performed by autotrophic bacteria until the recent discovery of archaeal ammonia oxidizers. Autotrophic archaeal ammonia oxidizers have been cultivated from marine and thermal spring environments, but the relative importance of bacteria and archaea in soil nitrification is unclear and it is believed that soil archaeal ammonia oxidizers may use organic carbon, rather than growing autotrophically. In this soil microcosm study, stable isotope probing was used to demonstrate incorporation of (13)C-enriched carbon dioxide into the genomes of thaumarchaea possessing two functional genes: amoA, encoding a subunit of ammonia monooxygenase that catalyses the first step in ammonia oxidation; and hcd, a key gene in the autotrophic 3-hydroxypropionate/4-hydroxybutyrate cycle, which has been found so far only in archaea. Nitrification was accompanied by increases in archaeal amoA gene abundance and changes in amoA gene diversity, but no change was observed in bacterial amoA genes. Archaeal, but not bacterial, amoA genes were also detected in (13)C-labeled DNA, demonstrating inorganic CO(2) fixation by archaeal, but not bacterial, ammonia oxidizers. Autotrophic archaeal ammonia oxidation was further supported by coordinate increases in amoA and hcd gene abundance in (13)C-labeled DNA. The results therefore provide direct evidence for a role for archaea in soil ammonia oxidation and demonstrate autotrophic growth of ammonia oxidizing archaea in soil.
硝化作用在全球氮循环中起着核心作用，它导致了大量氮肥的损失、温室气体氧化亚氮对大气的污染以及地下水的硝酸盐污染。氨氧化作用，硝化作用的第一步，曾被认为是由自养细菌完成的，直到最近才发现古菌氨氧化菌。自养古菌氨氧化菌已经从海洋和温泉环境中培养出来，但细菌和古菌在土壤硝化作用中的相对重要性尚不清楚，人们认为土壤古菌氨氧化菌可能使用有机碳，而不是自养生长。在这项土壤微生物群研究中，稳定同位素示踪法被用来证明含有（13）C 丰富的二氧化碳被具有两个功能基因的泉古菌基因组所吸收：amoA，编码氨单加氧酶的亚基，该酶催化氨氧化的第一步；hcd，是自养 3-羟基丙酸/4-羟基丁酸循环中的关键基因，迄今为止只在古菌中发现过。硝化作用伴随着古菌 amoA 基因丰度的增加和 amoA 基因多样性的变化，但细菌 amoA 基因没有变化。在（13）C 标记的 DNA 中也检测到了古菌和细菌 amoA 基因，但在（13）C 标记的 DNA 中没有检测到细菌 amoA 基因，这表明只有古菌的无机 CO（2）固定。amoA 和 hcd 基因丰度在（13）C 标记的 DNA 中协同增加，进一步支持了古菌的自养氨氧化作用。因此，这些结果为古菌在土壤氨氧化中的作用提供了直接证据，并证明了氨氧化古菌在土壤中的自养生长。
