Institute for Microbiology and Archaea Center, University of Regensburg, Regensburg, Germany.
ISME J. 2013 Mar;7(3):635-51. doi: 10.1038/ismej.2012.133. Epub 2012 Nov 22.
Archaea are usually minor components of a microbial community and dominated by a large and diverse bacterial population. In contrast, the SM1 Euryarchaeon dominates a sulfidic aquifer by forming subsurface biofilms that contain a very minor bacterial fraction (5%). These unique biofilms are delivered in high biomass to the spring outflow that provides an outstanding window to the subsurface. Despite previous attempts to understand its natural role, the metabolic capacities of the SM1 Euryarchaeon remain mysterious to date. In this study, we focused on the minor bacterial fraction in order to obtain insights into the ecological function of the biofilm. We link phylogenetic diversity information with the spatial distribution of chemical and metabolic compounds by combining three different state-of-the-art methods: PhyloChip G3 DNA microarray technology, fluorescence in situ hybridization (FISH) and synchrotron radiation-based Fourier transform infrared (SR-FTIR) spectromicroscopy. The results of PhyloChip and FISH technologies provide evidence for selective enrichment of sulfate-reducing bacteria, which was confirmed by the detection of bacterial dissimilatory sulfite reductase subunit B (dsrB) genes via quantitative PCR and sequence-based analyses. We further established a differentiation of archaeal and bacterial cells by SR-FTIR based on typical lipid and carbohydrate signatures, which demonstrated a co-localization of organic sulfate, carbonated mineral and bacterial signatures in the biofilm. All these results strongly indicate an involvement of the SM1 euryarchaeal biofilm in the global cycles of sulfur and carbon and support the hypothesis that sulfidic springs are important habitats for Earth's energy cycles. Moreover, these investigations of a bacterial minority in an Archaea-dominated environment are a remarkable example of the great power of combining highly sensitive microarrays with label-free infrared imaging.
古菌通常是微生物群落的次要组成部分，主要由大量多样的细菌种群所主导。相比之下，SM1 广古菌通过形成地下生物膜而主导硫化物含水层，该生物膜中仅含有非常少量的细菌部分（5%）。这些独特的生物膜以高生物量输送到泉水流出物中，为地下环境提供了一个绝佳的窗口。尽管之前曾尝试了解其自然作用，但迄今为止，SM1 广古菌的代谢能力仍然神秘莫测。在本研究中，我们专注于细菌的次要部分，以深入了解生物膜的生态功能。我们通过结合三种不同的最先进方法：PhyloChip G3 DNA 微阵列技术、荧光原位杂交（FISH）和基于同步辐射的傅里叶变换红外（SR-FTIR）光谱显微镜，将系统发育多样性信息与化学和代谢化合物的空间分布联系起来。PhyloChip 和 FISH 技术的结果提供了硫酸盐还原菌选择性富集的证据，通过定量 PCR 和基于序列的分析检测到细菌异化亚硫酸盐还原酶亚基 B（dsrB）基因，这一结果得到了证实。我们进一步通过基于同步辐射的傅里叶变换红外光谱显微镜基于典型的脂质和碳水化合物特征来区分古菌和细菌细胞，该方法表明在生物膜中有机硫酸盐、碳酸盐矿物和细菌特征的共定位。所有这些结果都强烈表明，SM1 广古菌生物膜参与了全球硫和碳循环，并支持了硫化泉水是地球能量循环的重要栖息地的假说。此外，对古菌主导环境中细菌少数群体的这些研究是将高度敏感的微阵列与无标记红外成像相结合的强大功能的一个显著例子。
