Holmes Dawn E, O'Neil Regina A, Vrionis Helen A, N'guessan Lucie A, Ortiz-Bernad Irene, Larrahondo Maria J, Adams Lorrie A, Ward Joy A, Nicoll Julie S, Nevin Kelly P, Chavan Milind A, Johnson Jessica P, Long Philip E, Lovley Derek R
Department of Microbiology, Morrill IV North Science Center, University of Massachusetts, Amherst, MA, USA.
ISME J. 2007 Dec;1(8):663-77. doi: 10.1038/ismej.2007.85. Epub 2007 Oct 18.
There are distinct differences in the physiology of Geobacter species available in pure culture. Therefore, to understand the ecology of Geobacter species in subsurface environments, it is important to know which species predominate. Clone libraries were assembled with 16S rRNA genes and transcripts amplified from three subsurface environments in which Geobacter species are known to be important members of the microbial community: (1) a uranium-contaminated aquifer located in Rifle, CO, USA undergoing in situ bioremediation; (2) an acetate-impacted aquifer that serves as an analog for the long-term acetate amendments proposed for in situ uranium bioremediation and (3) a petroleum-contaminated aquifer in which Geobacter species play a role in the oxidation of aromatic hydrocarbons coupled with the reduction of Fe(III). The majority of Geobacteraceae 16S rRNA sequences found in these environments clustered in a phylogenetically coherent subsurface clade, which also contains a number of Geobacter species isolated from subsurface environments. Concatamers constructed with 43 Geobacter genes amplified from these sites also clustered within this subsurface clade. 16S rRNA transcript and gene sequences in the sediments and groundwater at the Rifle site were highly similar, suggesting that sampling groundwater via monitoring wells can recover the most active Geobacter species. These results suggest that further study of Geobacter species in the subsurface clade is necessary to accurately model the behavior of Geobacter species during subsurface bioremediation of metal and organic contaminants.
纯培养的地杆菌属物种在生理方面存在明显差异。因此，为了解地下环境中地杆菌属物种的生态，了解哪些物种占主导地位很重要。利用从三个地下环境中扩增的16S rRNA基因和转录本构建了克隆文库，在地杆菌属物种被认为是微生物群落重要成员的这三个地下环境中：（1）位于美国科罗拉多州赖夫尔的一个正在进行原位生物修复的受铀污染含水层；（2）一个受醋酸盐影响的含水层，可作为原位铀生物修复提议的长期醋酸盐改良的模拟环境；（3）一个受石油污染的含水层，其中地杆菌属物种在芳香烃氧化与Fe(III)还原耦合过程中发挥作用。在这些环境中发现的大多数地杆菌科16S rRNA序列聚集在一个系统发育连贯的地下分支中，该分支还包含一些从地下环境中分离出的地杆菌属物种。用从这些位点扩增出的43个地杆菌基因构建的串联体也聚集在这个地下分支内。赖夫尔站点沉积物和地下水中的16S rRNA转录本和基因序列高度相似，这表明通过监测井采集地下水能够获取最活跃的地杆菌属物种。这些结果表明，有必要进一步研究地下分支中的地杆菌属物种，以便准确模拟地杆菌属物种在金属和有机污染物地下生物修复过程中的行为。
