Swiss Federal Institute for Technology (ETH-Zürich), Institute of Terrestrial Ecology, Soil Biology, 8952 Schlieren, Switzerland.
FEMS Microbiol Ecol. 2002 Oct 1;42(1):89-98. doi: 10.1111/j.1574-6941.2002.tb00998.x.
Abstract Archaea have been shown to be ubiquitous among soil microbial communities. However, our knowledge on their diversity and spatial distribution in soil ecosystems is still limited. This study was conducted to investigate archaeal community changes along a forest soil depth profile in Unterehrendingen, Switzerland. From four consecutive soil depth layers, bulk soil DNA was extracted. Archaea-specific PCR amplification of small subunit ribosomal RNA genes (rDNA) was performed and combined with restriction fragment length polymorphism (RFLP) analysis with restriction endonuclease HaeIII [Bundt et al., Soil Biol. Biochem. 33 (2001) 729-738]. Significant changes of the RFLP fingerprints were reproducibly observed from the soil surface to 1 m depth. From the surface soil layer (0-9 cm) and the bottom soil layer (50-100 cm), libraries of PCR-amplified archaeal rDNA fragments were constructed. Screening of the libraries yielded various clones of different HaeIII RFLP types from the surface and the bottom soil layers, revealing shifts in major archaeal components along the soil depth profile. Clones of all RFLP types were sequenced and phylogenetically affiliated. These analyses revealed even more pronounced Archaea community shifts along the depth gradient. Several novel soil archaeal clusters were identified and some appeared predominantly associated to either the surface or the bottom soil layer. Euryarchaeal rDNA sequences, not yet reported from aerated soils, were found in the surface soil layer and were affiliated to the order Thermoplasmales and relatives. Novel crenarchaeal soil clusters were identified that included sequences only retrieved from the bottom soil layer. In this study, a this far unreported variety of archaeal groups was found in a forest soil ecosystem. The distinct depth-related community shift suggested the occurrence of different archaeal types that depend on environmental parameters that change along the soil depth profile.
摘要 古菌在土壤微生物群落中普遍存在。然而，我们对土壤生态系统中古菌多样性和空间分布的了解仍然有限。本研究旨在调查瑞士 Unterehrendingen 森林土壤深度剖面中古菌群落的变化。从四个连续的土壤深度层中提取了土壤总 DNA。对小亚基核糖体 RNA 基因（rDNA）进行古菌特异性 PCR 扩增，并与限制性内切酶 HaeIII 的限制性片段长度多态性（RFLP）分析相结合[Bundt 等人，土壤生物化学 33（2001）729-738]。从土壤表面到 1 米深度，可重复性地观察到 RFLP 指纹图谱的显著变化。从表层土壤（0-9 厘米）和底层土壤（50-100 厘米）构建了 PCR 扩增古菌 rDNA 片段的文库。从表层和底层土壤文库中筛选出各种不同 HaeIII RFLP 类型的克隆，揭示了主要古菌成分沿土壤深度剖面的变化。对所有 RFLP 类型的克隆进行测序并进行系统发育分析。这些分析显示，古菌群落沿深度梯度的变化更为显著。鉴定出了几个新的土壤古菌类群，其中一些主要与表层或底层土壤有关。在表层土壤中发现了尚未报道的有氧土壤中存在的广古菌 rDNA 序列，它们与 Thermoplasmales 目及其亲缘关系密切。鉴定出了新的泉古菌土壤类群，其中仅包含从底层土壤中获得的序列。在本研究中，在森林土壤生态系统中发现了迄今为止尚未报道的各种古菌群体。明显的与深度相关的群落变化表明，存在不同的古菌类型，它们依赖于沿土壤深度剖面变化的环境参数。
