Department of Genetics in Ecology, University of Vienna, Vienna, Austria.
ISME J. 2013 Aug;7(8):1620-31. doi: 10.1038/ismej.2013.35. Epub 2013 Mar 7.
The functioning of Arctic soil ecosystems is crucially important for global climate, and basic knowledge regarding their biogeochemical processes is lacking. Nitrogen (N) is the major limiting nutrient in these environments, and its availability is strongly dependent on nitrification. However, microbial communities driving this process remain largely uncharacterized in Arctic soils, namely those catalyzing the rate-limiting step of ammonia (NH3) oxidation. Eleven Arctic soils were analyzed through a polyphasic approach, integrating determination of gross nitrification rates, qualitative and quantitative marker gene analyses of ammonia-oxidizing archaea (AOA) and bacteria (AOB) and enrichment of AOA in laboratory cultures. AOA were the only NH3 oxidizers detected in five out of 11 soils and outnumbered AOB in four of the remaining six soils. The AOA identified showed great phylogenetic diversity and a multifactorial association with the soil properties, reflecting an overall distribution associated with tundra type and with several physico-chemical parameters combined. Remarkably, the different gross nitrification rates between soils were associated with five distinct AOA clades, representing the great majority of known AOA diversity in soils, which suggests differences in their nitrifying potential. This was supported by selective enrichment of two of these clades in cultures with different NH3 oxidation rates. In addition, the enrichments provided the first direct evidence for NH3 oxidation by an AOA from an uncharacterized Thaumarchaeota-AOA lineage. Our results indicate that AOA are functionally heterogeneous and that the selection of distinct AOA populations by the environment can be a determinant for nitrification activity and N availability in soils.
北极土壤生态系统的功能对全球气候至关重要，但我们对其生物地球化学过程的基本知识还很缺乏。氮 (N) 是这些环境中的主要限制营养物质，其可用性强烈依赖于硝化作用。然而，在北极土壤中，驱动这一过程的微生物群落，尤其是那些催化氨 (NH3) 氧化限速步骤的微生物群落，仍在很大程度上未被描述。通过多相方法分析了 11 种北极土壤，包括测定总硝化速率、氨氧化古菌 (AOA) 和细菌 (AOB) 的定性和定量标记基因分析以及 AOA 在实验室培养物中的富集。在 11 种土壤中的 5 种中，只检测到 AOA 是 NH3 的氧化菌，在其余 6 种土壤中的 4 种中，AOA 的数量超过了 AOB。鉴定出的 AOA 具有很大的系统发育多样性，并与土壤特性呈多因素关联，反映了与苔原类型和几个物理化学参数相结合的整体分布。值得注意的是，土壤之间不同的总硝化速率与 5 个不同的 AOA 分支有关，这代表了土壤中大多数已知的 AOA 多样性，这表明它们的硝化潜力存在差异。这一结果得到了两个分支在不同 NH3 氧化速率的培养物中选择性富集的支持。此外，这些富集物提供了第一个直接证据，证明了一个未被描述的泉古菌- AOA 谱系中的 AOA 能够进行 NH3 氧化。我们的研究结果表明，AOA 具有功能异质性，环境对不同 AOA 种群的选择可能是土壤硝化活性和 N 可利用性的决定因素。
