Community structure of sulfate reducing bacteria in the sediment of the arctic Smeerenburgfjorden

The community structure of sulfate-reducing bacteria (SRB) of a marine Arctic sediment (Smeerenburgfjorden, Svalbard) was characterized by both fluorescence in situ hybridization (FISH) by using group- and genus-specific 16S rRNA-targeted oligonucleotide probes. Samples stored in PBS-ethanol were diluted and treated by mild sonication. A 10-ml aliquot of a 1:40 dilution was filtered onto a 0.2-mm-pore-size type GTTP polycarbonate filter (Millipore, Eschborn, Germany). Hybridization and microscopic counting of hybridized and 49,69-diamidino-2-phenylindole (DAPI)-stained cells were performed as described previously from Snaidr et al. (1997, http://aem.asm.org/content/63/7/2884.full.pdf). Details of probes and formamide concentrations which were used are listed in futher details.. Means were calculated by using 10 to 20 randomly chosen fields for each filter section, which corresponded to 800 to 1,000 DAPI-stained cells. Counting results were always corrected by subtracting signals observed with probe NON338. The SRB community was dominated by members of the Desulfosarcina-Desulfococcus group. This group accounted for up to 73% of the SRB detected. The predominance was shown to be a common feature for different stations along the coast of Svalbard. In a top-to-bottom approach we aimed to further resolve the composition of this large group of SRB by using probes for cultivated genera. While this approach failed, directed cloning of probe-targeted genes encoding 16S rRNA was successful and resulted in sequences which were all affiliated with the Desulfosarcina-Desulfococcus group. A group of clone sequences (group SVAL1) most closely related to Desulfosarcina variabilis (91.2% sequence similarity) was dominant and was shown to be most abundant in situ, accounting for up to 54.8% of the total SRB detected.

北极海洋沉积物（斯瓦尔巴德群岛斯梅伦堡峡湾）中硫酸盐还原菌（SRB）的群落结构通过荧光原位杂交（FISH）技术进行表征，该技术使用群特异性和属特异性的靶向16S rRNA的寡核苷酸探针。PBS-乙醇中保存的样本经稀释后，采用温和超声处理。取1:40稀释液的10ml等分试样，过滤到孔径为0.2mm的GTTP型聚碳酸酯滤膜（Millipore公司，德国埃施博恩）上。杂交及杂交细胞与4',6-二脒基-2-苯基吲哚（DAPI）染色细胞的显微镜计数均按照Snaidr等人（1997，http://aem.asm.org/content/63/7/2884.full.pdf）先前描述的方法进行。所用探针及甲酰胺浓度的详细信息见后续内容。每个滤膜片段随机选取10至20个视野计算平均值，对应800至1000个DAPI染色细胞。计数结果始终通过减去NON338探针观察到的信号进行校正。SRB群落以Desulfosarcina-Desulfococcus组的成员为主，该组占检测到的SRB的比例高达73%。这种优势地位在斯瓦尔巴德海岸的不同站点中是常见特征。我们采用自上而下的方法，试图通过使用培养属特异性探针进一步解析这一大组SRB的组成，但未成功；转而通过靶向16S rRNA编码基因的定向克隆取得成功，获得的序列均隶属于Desulfosarcina-Desulfococcus组。一组克隆序列（SVAL1组）与可变脱硫球菌（Desulfosarcina variabilis）的亲缘关系最近（序列相似性为91.2%），且在原位环境中最为丰富，占检测到的总SRB的比例高达54.8%。