Microarray and real-time PCR analyses of the responses of high-arctic soil bacteria to hydrocarbon pollution and bioremediation treatments.
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 monooxygenases 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.
Yergeau
Etienne
E
Biotechnology Research Institute, National Research Council of Canada, Montréal, QC, Canada.
Arbour
Mélanie
M
Brousseau
Roland
R
Juck
David
D
Lawrence
John R
JR
Masson
Luke
L
Whyte
Lyle G
LG
Greer
Charles W
CW
D001110:Arctic Regions; D001419:Bacteria / Q000235:genetics* / Q000378:metabolism*; D001673:Biodegradation, Environmental; D044822:Biodiversity; D002170:Canada; D004269:DNA, Bacterial / Q000235:genetics; D004275:DNA, Ribosomal / Q000235:genetics; D006838:Hydrocarbons / Q000378:metabolism*; D046228:Microarray Analysis; D012329:RNA, Bacterial / Q000235:genetics; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D020133:Reverse Transcriptase Polymerase Chain Reaction; D012988:Soil Microbiology; D012989:Soil Pollutants / Q000378:metabolism*
D004269:DNA, Bacterial; D004275:DNA, Ribosomal; D006838:Hydrocarbons; D012329:RNA, Bacterial; D012336:RNA, Ribosomal, 16S; D012989:Soil Pollutants
FEMS Microbiol Ecol. 2004 Sep 1;49(3):401-17
19712290
FEMS Microbiol Ecol. 2005 Jun 1;53(1):141-55
16329936
Appl Environ Microbiol. 2005 Apr;71(4):2036-45
15812036
Appl Microbiol Biotechnol. 2002 Aug;59(4-5):551-6
12172625
FEMS Microbiol Ecol. 2005 Feb 1;51(3):375-88
16329885
Environ Sci Technol. 2002 Sep 15;36(18):3977-84
12269751
Environ Sci Technol. 2006 Mar 15;40(6):2011-7
16570629
FEMS Microbiol Ecol. 2002 Aug 1;41(2):141-50
19709248
FEMS Microbiol Ecol. 2007 Feb;59(2):466-75
17313586
Can J Microbiol. 1996 Mar;42(3):252-8
8868232
Bioinformatics. 2003 May 1;19(7):796-802
12724288
Can J Microbiol. 1996 Feb;42(2):99-106
8742353
J Microbiol Methods. 2008 May;73(2):148-59
18329116
ISME J. 2007 May;1(1):67-77
18043615
Nucleic Acids Res. 2002 Jan 1;30(1):207-10
11752295
Appl Environ Microbiol. 1998 Jul;64(7):2578-84
9647833
FEMS Microbiol Ecol. 2000 Sep 1;33(3):241-249
11098075
Microbiol Mol Biol Rev. 1997 Dec;61(4):533-616
9409151
J Ind Microbiol. 1996 Jan;16(1):36-41
8820018
Appl Environ Microbiol. 2007 Mar;73(5):1532-43
17220254
Microb Ecol. 1995 Nov;30(3):297-307
24185566
FEMS Microbiol Ecol. 2000 Apr 1;32(1):17-23
10779615
Microb Ecol. 2007 Apr;53(3):371-83
17334858
ISME J. 2007 Jun;1(2):163-79
18043626
Extremophiles. 2006 Jun;10(3):171-9
16514512
Appl Environ Microbiol. 2005 Jul;71(7):4117-20
16000830
Microb Ecol. 2009 May;57(4):598-610
18685886
ISME J. 2009 Mar;3(3):340-51
19020556
Microb Ecol. 2006 Oct;52(3):523-32
16944337
Appl Environ Microbiol. 2002 Dec;68(12):5933-42
12450813
Arch Microbiol. 1990;154(4):317-22
2244784