Dar Shabir A, Yao Li, van Dongen Udo, Kuenen J Gijs, Muyzer Gerard
Environmental Biotechnology, Department of Biotechnology, Delft University of Technology, NL-2628 BC Delft, The Netherlands.
Appl Environ Microbiol. 2007 Jan;73(2):594-604. doi: 10.1128/AEM.01875-06. Epub 2006 Nov 10.
Here we describe the diversity and activity of sulfate-reducing bacteria (SRB) in sulfidogenic bioreactors by using the simultaneous analysis of PCR products obtained from DNA and RNA of the 16S rRNA and dissimilatory sulfite reductase (dsrAB) genes. We subsequently analyzed the amplified gene fragments by using denaturing gradient gel electrophoresis (DGGE). We observed fewer bands in the RNA-based DGGE profiles than in the DNA-based profiles, indicating marked differences in the populations present and in those that were metabolically active at the time of sampling. Comparative sequence analyses of the bands obtained from rRNA and dsrB DGGE profiles were congruent, revealing the same SRB populations. Bioreactors that received either ethanol or isopropanol as an energy source showed the presence of SRB affiliated with Desulfobulbus rhabdoformis and/or Desulfovibrio sulfodismutans, as well as SRB related to the acetate-oxidizing Desulfobacca acetoxidans. The reactor that received wastewater containing a diverse mixture of organic compounds showed the presence of nutritionally versatile SRB affiliated with Desulfosarcina variabilis and another acetate-oxidizing SRB, affiliated with Desulfoarculus baarsii. In addition to DGGE analysis, we performed whole-cell hybridization with fluorescently labeled oligonucleotide probes to estimate the relative abundances of the dominant sulfate-reducing bacterial populations. Desulfobacca acetoxidans-like populations were most dominant (50 to 60%) relative to the total SRB communities, followed by Desulfovibrio-like populations (30 to 40%), and Desulfobulbus-like populations (15 to 20%). This study is the first to identify metabolically active SRB in sulfidogenic bioreactors by using the functional gene dsrAB as a molecular marker. The same approach can also be used to infer the ecological role of coexisting SRB in other habitats.
在此，我们通过对从16S rRNA以及异化亚硫酸盐还原酶（dsrAB）基因的DNA和RNA中获得的PCR产物进行同步分析，来描述产硫化物生物反应器中硫酸盐还原菌（SRB）的多样性和活性。随后，我们使用变性梯度凝胶电泳（DGGE）对扩增的基因片段进行分析。我们观察到，基于RNA的DGGE图谱中的条带比基于DNA的图谱中的条带少，这表明在采样时存在的菌群以及代谢活跃的菌群存在显著差异。对从rRNA和dsrB DGGE图谱中获得的条带进行的比较序列分析结果一致，揭示了相同的SRB菌群。以乙醇或异丙醇作为能源的生物反应器中，存在与横纹脱硫球菌和/或脱硫弧菌相关的SRB，以及与乙酸氧化脱硫杆菌相关的SRB。接收含有多种有机化合物混合物废水的反应器中，存在与可变脱硫球菌相关的营养用途广泛的SRB以及与巴氏脱硫微菌相关的另一种乙酸氧化SRB。除了DGGE分析外，我们还使用荧光标记的寡核苷酸探针进行全细胞杂交，以估计主要硫酸盐还原细菌菌群的相对丰度。相对于总的SRB群落，类乙酸氧化脱硫杆菌菌群最为占主导（50%至60%），其次是类脱硫弧菌菌群（30%至40%）和类脱硫球菌菌群（15%至20%）。本研究首次使用功能基因dsrAB作为分子标记，鉴定产硫化物生物反应器中代谢活跃的SRB。同样的方法也可用于推断其他生境中共存的SRB的生态作用。
