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.

Profiling In Situ Microbial Community Structure with an Amplification Microarray

“…In order to translate the power of microarrays into user-friendly environmental diagnostic tools, we have been developing a low-density, field-portable microarray system for monitoring in situ microbial community structure and dynamics. We recently deployed a system at a U(VI)-contaminated U.S. Department of Energy (DOE) site and readily processed up to 24 samples in 6 h within the confines of a field trailer (8). The premise of the microarray-based monitoring tool is to use gene sequences as indicators of taxonomic or functionally relevant microorganisms or activity for which the taxonomy-function link has been established in laboratory and field experiments.…”

“…The field-portable methods described elsewhere (8) are still based on an open-amplicon work flow, which can be problematic in the field or laboratory environments that are not specifically configured for routine molecular biology work (and PCR technology, in particular). Furthermore, while traditional sample preparation, amplification, and microarray hybridization chemistries can be incorporated into a consumable via microfluidic transfer steps (9)(10)(11)(12)(13)(14)(15), the engineering, manufacturing, and quality control challenges of such consumables (and control instruments) scale with the complexity of the microfluidic architecture.…”

“…Hybridization microarrays were manufactured with 6% 2-(hydroxyethyl)-methacrylamide and 0.125 mM immobilized probes as described elsewhere (8), except that we excluded 46 probes for the denitrifiers and dechlorinators. Amplification microarrays were manufactured with 4% 2-(hydroxyethyl)-methacrylamide essentially as described in reference 21 and included all microarray probes described elsewhere (8), except that probes were immobilized in duplicate rather than quadruplicate (see Table S1 in the supplemental material).…”

“…Amplification microarrays were manufactured with 4% 2-(hydroxyethyl)-methacrylamide essentially as described in reference 21 and included all microarray probes described elsewhere (8), except that probes were immobilized in duplicate rather than quadruplicate (see Table S1 in the supplemental material). Cy3-labeled 8-mer oligonucleotides served as positional reference beacons.…”

Evaluation of a Field-Portable DNA Microarray Platform and Nucleic Acid Amplification Strategies for the Detection of Arboviruses, Arthropods, and Bloodmeals

“…Recent work has demonstrated that some detection platforms are conducive for use in the field. [5][6][7] The ElectraSense microarray platform, developed by CustomArray, Inc. (CustomArray, Inc., Bothell, WA) was identified to fit our specifications for effective field deployment. This platform relies on electrochemical detection (ECD) of a reaction that occurs after the capture probe hybridizes to the target sequence and allows for the development of compact microarray readers for potential field use.…”