Geomicrobiology Group, Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Monobe B200, Nankoku, Kochi 783-8502, Japan.
Philos Trans R Soc Lond B Biol Sci. 2013 Mar 11;368(1616):20120249. doi: 10.1098/rstb.2012.0249. Print 2013 Apr 19.
Halogenated organic matter buried in marine subsurface sediment may serve as a source of electron acceptors for anaerobic respiration of subseafloor microbes. Detection of a diverse array of reductive dehalogenase-homologous (rdhA) genes suggests that subseafloor organohalide-respiring microbial communities may play significant ecological roles in the biogeochemical carbon and halogen cycle in the subseafloor biosphere. We report here the spatial distribution of dehalogenation activity in the Nankai Trough plate-subduction zone of the northwest Pacific off the Kii Peninsula of Japan. Incubation experiments with slurries of sediment collected at various depths and locations showed that degradation of several organohalides tested only occurred in the shallow sedimentary basin, down to 4.7 metres below the seafloor, despite detection of rdhA in the deeper sediments. We studied the phylogenetic diversity of the metabolically active microbes in positive enrichment cultures by extracting RNA, and found that Desulfuromonadales bacteria predominate. In addition, for the isolation of genes involved in the dehalogenation reaction, we performed a substrate-induced gene expression screening on DNA extracted from the enrichment cultures. Diverse DNA fragments were obtained and some of them showed best BLAST hit to known organohalide respirers such as Dehalococcoides, whereas no functionally known dehalogenation-related genes such as rdhA were found, indicating the need to improve the molecular approach to assess functional genes for organohalide respiration.
埋藏在海洋底层沉积物中的卤代有机物可能成为海底微生物无氧呼吸的电子受体来源。检测到大量还原脱卤酶同源（rdhA）基因表明，海底有机卤化物呼吸微生物群落可能在海底生物圈的碳和卤素生物地球化学循环中发挥重要的生态作用。我们在这里报告了日本纪伊半岛西北太平洋南海槽板块俯冲带中脱卤活性的空间分布。用从不同深度和位置采集的沉积物泥浆进行的培养实验表明，尽管在更深的沉积物中检测到了 rdhA，但只有在浅层沉积盆地中（海底以下 4.7 米），测试的几种有机卤化物才会发生降解。我们通过提取 RNA 研究了阳性富集培养物中代谢活跃微生物的系统发育多样性，并发现脱硫单胞菌目细菌占主导地位。此外，为了分离脱卤反应相关基因，我们对从富集培养物中提取的 DNA 进行了底物诱导基因表达筛选。获得了多种 DNA 片段，其中一些片段与已知的有机卤化物呼吸者（如 Dehalococcoides）的最佳 BLAST 命中，而没有发现功能上已知的脱卤相关基因，如 rdhA，这表明需要改进分子方法来评估有机卤化物呼吸的功能基因。
