NRC Publications Archive (NPArC) Archives des publications du CNRC (NPArC) Publisher���s version / la version de l'��diteur: Applied and Environmental Microbiology, 75, 19, 2009 Microarray and real-time PCR analyses of the responses of high Arctic soil bacteria to hydrocarbon pollution and bioremediation treatments Yergeau, Etienne Arbour, M��lanie Brousseau, Roland Juck, David Lawrence, John Masson, Luke Whyte, Lyle Greer, Charles Contact us / Contactez nous: nparc.cisti@nrc-cnrc.gc.ca. http://nparc.cisti-icist.nrc-cnrc.gc.ca/npsi/jsp/nparc_cp.jsp?lang=fr L���acc��s �� ce site Web et l���utilisation de son contenu sont assujettis aux conditions pr��sent��es dans le site Web page / page Web http://dx.doi.org/10.1128/AEM.01029-09 http://nparc.cisti-icist.nrc-cnrc.gc.ca/npsi/ctrl?action=rtdoc&an=12726912&lang=en http://nparc.cisti-icist.nrc-cnrc.gc.ca/npsi/ctrl?action=rtdoc&an=12726912&lang=fr LISEZ CES CONDITIONS ATTENTIVEMENT AVANT D���UTILISER CE SITE WEB. READ THESE TERMS AND CONDITIONS CAREFULLY BEFORE USING THIS WEBSITE. Access and use of this website and the material on it are subject to the Terms and Conditions set forth at http://nparc.cisti-icist.nrc-cnrc.gc.ca/npsi/jsp/nparc_cp.jsp?lang=en

APPLIED AND ENVIRONMENTAL MICROBIOLOGY, Oct. 2009, p. 6258���6267 Vol. 75, No. 19 0099-2240/09/$08.00H110010 doi:10.1128/AEM.01029-09 Copyright �� 2009, American Society for Microbiology. All Rights Reserved. Microarray and Real-Time PCR Analyses of the Responses of High-Arctic Soil Bacteria to Hydrocarbon Pollution and Bioremediation TreatmentsH17188 Etienne Yergeau,1,2 Me ��lanie Arbour,1 Roland Brousseau,1 David Juck,1 John R. Lawrence,3 Luke Masson,1 Lyle G. Whyte,2 and Charles W. Greer1* Biotechnology Research Institute, National Research Council of Canada, Montre��al, QC, Canada1 Department of Natural Resource Sciences, McGill University, Montre��al, QC, Canada2 and Environment Canada, Saskatoon, SK, Canada3 Received 5 May 2009/Accepted 7 August 2009 High-Arctic soils have low nutrient availability, low moisture content, and very low temperatures and, as such, they pose a particular problem in terms of hydrocarbon bioremediation. An in-depth knowledge of the microbiology involved in this process is likely to be crucial to understand and optimize the factors most influencing bioremediation. Here, we compared two distinct large-scale field bioremediation experiments, located at the Canadian high-Arctic stations of Alert (ex situ approach) and Eureka (in situ approach). Bacterial community structure and function were assessed using microarrays targeting the 16S rRNA genes of bacteria found in cold environments and hydrocarbon degradation genes as well as quantitative reverse transcriptase PCR targeting key functional genes. The results indicated a large difference between sampling sites in terms of both soil microbiology and decontamination rates. A rapid reorganization of the bacterial community structure and functional potential as well as rapid increases in the expression of alkane monooxy- genases and polyaromatic hydrocarbon-ring-hydroxylating dioxygenases were observed 1 month after the bioremediation treatment commenced in the Alert soils. In contrast, no clear changes in community structure were observed in Eureka soils, while key gene expression increased after a relatively long lag period (1 year). Such discrepancies are likely caused by differences in bioremediation treatments (i.e., ex situ versus in situ), weathering of the hydrocarbons, indigenous microbial communities, and environmental factors such as soil humidity and temperature. In addition, this study demonstrates the value of molecular tools for the monitoring of polar bacteria and their associated functions during bioremediation. With ongoing climate warming and the possible opening of the Northwest Passage for commercial shipping in the near future, human activity will increase in the Canadian high Arc- tic, raising the potential for environmental contamination. The settlements in the high Arctic are using fuel for transportation and to produce electricity and heating, while spills from leaking tanks or pipelines are frequent (19, 34). Bioremediation is often the only feasible cleanup option because the remoteness and unique character of these sites preclude conventional physicochemical technologies for soil treatment. Arctic soils are characterized by extremely low temperatures and the lim- ited availability of water and nutrients, especially nitrogen (18, 26), which limit the degradation rates by indigenous soil mi- croorganisms. One of the possible bioremediation approaches is to stimulate indigenous cold-adapted microorganisms by the application of nutrients and water. This strategy was success- fully applied to diesel-contaminated soils in the Canadian high Arctic (9, 33, 34). However, these studies mostly focused on soil chemistry and general soil processes, with very few insights into the ecology and the functions of the microorganisms ac- tually involved in the bioremediation processes. Although this is not surprising since the common criterion for decommission- ing a polluted site is based on soil chemistry, the lack of knowledge of the dynamics of the microbial communities in- volved hampers the design of more efficient bioremediation approaches. Common diesel fuel is composed of H1101164% saturated ali- phatic hydrocarbons (alkanes), H110111 to 2% unsaturated aliphatic hydrocarbons, and H1101135% aromatic hydrocarbons (including polycyclic aromatic hydrocarbons [PAHs]) (23). Consequently, the complete degradation of diesel requires the presence of different microorganisms with complementary enzymatic ca- pacities. Alkanes form the part of diesel that is easier to de- grade, and the first step of their aerobic degradation is cata- lyzed by alkane monooxygenases, for which the alkB gene is particularly well characterized (38). Although Rhodococcus was hypothesized to be the predominant alkane-degrading ge- nus in polar soils, Pseudomonas is also thought to be enriched following hydrocarbon contamination (37). PAHs are more difficult to degrade and are therefore highly persistent in soils. The initial step of PAH degradation is carried out by multi- component aromatic-ring-hydroxylating dioxygenases (RHD) that contain regions conserved among all the different genes encoding PAH-degrading enzymes. The typical aromatic- degrading bacteria isolated from polar soils are Pseudomonas or Sphingomonas, with Sphingomonas having a wider range of substrates than Pseudomonas (1). It appears, therefore, that the relative responses of the different bacterial species to bioremediation treatments will have a strong effect on the efficiency of pollutant removal. * Corresponding author. Mailing address: Biotechnology Re- search Institute, 6100 Royalmount Ave., Montre ��al H4P 2R2, QC, Canada. Phone: (514) 496-6182. Fax: (514) 496-6265. E-mail: Charles.Greer@cnrc-nrc.gc.ca. H17188 Published ahead of print on 14 August 2009. 6258