title: Development and validation of an open source O2-sensitive gel for physiological profiling of soil microbial communities.
abstract: Community level physiological profiling is a simple, high-throughput technique for assessing microbial community physiology. Initial methods relying on redox-dye based detection of respiration were subject to strong enrichment bias, but subsequent development of a microtiter assay using an oxygen-quenched dye reduced this bias and improved the versatility of the approach. Commercial production of the oxygen microplates recently stopped, which led to the present effort to develop and validate a system using a luminophore dye (platinum tetrakis pentafluorophenyl) immobilized at the bottom of wells within a 96 well microtiter plate. The technique was used to analyze three well-characterized Florida soils: oak saw palmetto scrub, coastal mixed hardwood, and soil from an agricultural field used to grow corn silage. Substrate induced respiration was monitored by measuring respiration rates in soils under basal conditions and comparing to soils supplemented with nitrogen and various carbon sources (mannose, casein, asparagine, coumaric acid). All data was compared to a previously available commercial assay. There were no significant differences in the maximum peak intensity or the time to peak response for all soils tested (p<0.001, α=0.05). The experimental assay plates can be reused on soils up to four times (based on a deviation of less than 5%), where the commercial assay should not be reused. The results indicate that the new oxygen-based bioassay is a cost effective, open source tool for functional profiling of microbial communities.
authors.affiliation: Agricultural & Biological Engineering, University of Florida, Gainesville, FL, USA. Electronic address: emclamor@ufl.edu.
authors.forename: E S
authors.initials: ES
authors.lastname: McLamore
authors.affiliation: Microbiological and Chemical Exposure Assessment Research Division, U.S. Environmental Protection Agency, Cincinnati, OH, USA. Electronic address: garland.jay@epamail.epa.gov.
authors.forename: J L
authors.initials: JL
authors.lastname: Garland
authors.affiliation: Department of Soil and Water Science, University of Florida, Gainesville, FL, USA. Electronic address: echo13@ufl.edu.
authors.forename: C
authors.initials: C
authors.lastname: Mackowiak
authors.affiliation: Agricultural & Biological Engineering, University of Florida, Gainesville, FL, USA. Electronic address: aureliendesaunay@ufl.edu.
authors.forename: A
authors.initials: A
authors.lastname: Desaunay
authors.affiliation: Agricultural & Biological Engineering, University of Florida, Gainesville, FL, USA. Electronic address: ngarland929@ufl.edu.
authors.forename: N
authors.initials: N
authors.lastname: Garland
authors.affiliation: Agricultural & Biological Engineering, University of Florida, Gainesville, FL, USA. Electronic address: pchaturvedi@ufl.edu.
authors.forename: P
authors.initials: P
authors.lastname: Chaturvedi
authors.affiliation: Agricultural & Biological Engineering, University of Florida, Gainesville, FL, USA. Electronic address: mtaguchi@whitney.ufl.edu.
authors.forename: M
authors.initials: M
authors.lastname: Taguchi
authors.affiliation: Agricultural & Biological Engineering, University of Florida, Gainesville, FL, USA. Electronic address: kmj08@ufl.edu.
authors.forename: K
authors.initials: K
authors.lastname: Dreaden
authors.affiliation: Kennedy Space Center, Space Life Sciences Laboratory, Kennedy Space Center, USA. Electronic address: john.a.catechis@nasa.gov.
authors.forename: John
authors.initials: J
authors.lastname: Catechis
authors.affiliation: Agricultural & Biological Engineering, University of Florida, Gainesville, FL, USA. Electronic address: jullman@ufl.edu.
authors.forename: J L
authors.initials: JL
authors.lastname: Ullman
mesh_terms: D001681:Biological Assay / Q000379:methods*; D002244:Carbon / Q000378:metabolism; D005431:Florida; D008828:Microbiological Techniques / Q000379:methods*; D064307:Microbiota / Q000502:physiology*; D009584:Nitrogen / Q000378:metabolism; D010100:Oxygen / Q000378:metabolism*; D012988:Soil Microbiology
chemical_list: D002244:Carbon; D009584:Nitrogen; D010100:Oxygen
keywords: Assay; Oxygen quenched dye; Physiological profiling; Substrate induced respiration