Koo Hyunmin, Mojib Nazia, Huang Jonathan P, Donahoe Rona J, Bej Asim K
Department of Biology, University of Alabama at Birmingham, 1300 University Blvd., CH464, Birmingham, AL, 35294-1170, USA.
Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
3 Biotech. 2015 Aug;5(4):379-392. doi: 10.1007/s13205-014-0233-x. Epub 2014 Jul 10.
In this study, we examined the responses by the indigenous bacterial communities in salt-marsh sediment microcosms in vitro following treatment with Mississippi Canyon Block 252 oil (MC252). Microcosms were constructed of sediment and seawater collected from Bayou La Batre located in coastal Alabama on the Gulf of Mexico. We used an amplicon pyrosequencing approach on microcosm sediment metagenome targeting the V3-V5 region of the 16S rRNA gene. Overall, we identified a shift in the bacterial community in three distinct groups. The first group was the early responders (orders Pseudomonadales and Oceanospirillales within class Gammaproteobacteria), which increased their relative abundance within 2 weeks and were maintained 3 weeks after oil treatment. The second group was identified as early, but transient responders (order Rhodobacterales within class Alphaproteobacteria; class Epsilonproteobacteria), which increased their population by 2 weeks, but returned to the basal level 3 weeks after oil treatment. The third group was the late responders (order Clostridiales within phylum Firmicutes; order Methylococcales within class Gammaproteobacteria; and phylum Tenericutes), which only increased 3 weeks after oil treatment. Furthermore, we identified oil-sensitive bacterial taxa (order Chromatiales within class Gammaproteobacteria; order Syntrophobacterales within class Deltaproteobacteria), which decreased in their population after 2 weeks of oil treatment. Detection of alkane (alkB), catechol (C2,3DO) and biphenyl (bph) biodegradation genes by PCR, particularly in oil-treated sediment metacommunity DNA, delineates proliferation of the hydrocarbon degrading bacterial community. Overall, the indigenous bacterial communities in our salt-marsh sediment in vitro microcosm study responded rapidly and shifted towards members of the taxonomic groups that are capable of surviving in an MC252 oil-contaminated environment.
在本研究中，我们检测了用密西西比峡谷252号油（MC252）处理后，盐沼沉积物微观世界中本地细菌群落的反应。微观世界由从墨西哥湾阿拉巴马州沿海的拉巴特湾收集的沉积物和海水构建而成。我们对微观世界沉积物宏基因组采用扩增子焦磷酸测序方法，靶向16S rRNA基因的V3 - V5区域。总体而言，我们在三个不同的组中鉴定出细菌群落的转变。第一组是早期响应者（γ-变形菌纲中的假单胞菌目和海洋螺菌目），其相对丰度在油处理后2周内增加，并在3周后保持稳定。第二组被鉴定为早期但短暂的响应者（α-变形菌纲中的红杆菌目；ε-变形菌纲），其数量在2周时增加，但在油处理后3周恢复到基础水平。第三组是晚期响应者（厚壁菌门中的梭菌目；γ-变形菌纲中的甲基球菌目；以及柔膜菌门），其数量仅在油处理后3周增加。此外，我们鉴定出对油敏感的细菌分类群（γ-变形菌纲中的色菌目；δ-变形菌纲中的互营杆菌目），其数量在油处理2周后减少。通过PCR检测烷烃（alkB）、儿茶酚（C2,3DO）和联苯（bph）生物降解基因，特别是在油处理的沉积物元群落DNA中，描绘了烃降解细菌群落的增殖情况。总体而言，我们盐沼沉积物体外微观世界研究中的本地细菌群落反应迅速，并向能够在MC252油污染环境中存活的分类群成员转变。
