title: Monitoring microbial community structure and dynamics during in situ U(VI) bioremediation with a field-portable microarray analysis system.
abstract: The objective of this study was to develop and validate a simple, field-portable, microarray system for monitoring microbial community structure and dynamics in groundwater and subsurface environments, using samples representing site status before acetate injection, during Fe-reduction, in the transition from Fe- to SO(4)(2-)-reduction, and into the SO(4)(2-)-reduction phase. Limits of detection for the array are approximately 10(2)-10(3) cell equivalents of DNA per reaction. Sample-to-answer results for the field deployment were obtained in 4 h. Retrospective analysis of 50 samples showed the expected progression of microbial signatures from Fe- to SO(4)(2-) -reducers with changes in acetate amendment and in situ field conditions. The microarray response for Geobacter was highly correlated with qPCR for the same target gene (R(2) = 0.84). Microarray results were in concordance with quantitative PCR data, aqueous chemistry, site lithology, and the expected microbial community response, indicating that the field-portable microarray is an accurate indicator of microbial presence and response to in situ remediation of a uranium-contaminated site.
authors.affiliation: Akonni Biosystems, Inc., Frederick, Maryland 21701, USA. dchandler@akonni.com
authors.forename: Darrell P
authors.initials: DP
authors.lastname: Chandler
authors.forename: Alexander
authors.initials: A
authors.lastname: Kukhtin
authors.forename: Rebecca
authors.initials: R
authors.lastname: Mokhiber
authors.forename: Christopher
authors.initials: C
authors.lastname: Knickerbocker
authors.forename: Dora
authors.initials: D
authors.lastname: Ogles
authors.forename: George
authors.initials: G
authors.lastname: Rudy
authors.forename: Julia
authors.initials: J
authors.lastname: Golova
authors.forename: Phil
authors.initials: P
authors.lastname: Long
authors.forename: Aaron
authors.initials: A
authors.lastname: Peacock
mesh_terms: D001419:Bacteria / Q000378:metabolism*; D001673:Biodegradation, Environmental; D004784:Environmental Monitoring / Q000295:instrumentation* / Q000379:methods; D004785:Environmental Pollutants; D046228:Microarray Analysis / Q000295:instrumentation*; D012987:Soil / Q000032:analysis; D012988:Soil Microbiology; D014501:Uranium / Q000737:chemistry / Q000378:metabolism*; D014871:Water Microbiology
chemical_list: D004785:Environmental Pollutants; D012987:Soil; D014501:Uranium