title: Overcoming the anaerobic hurdle in phenotypic microarrays: generation and visualization of growth curve data for Desulfovibrio vulgaris Hildenborough.
abstract: Growing anaerobic microorganisms in phenotypic microarrays (PM) and 96-well microtiter plates is an emerging technology that allows high throughput survey of the growth and physiology and/or phenotype of cultivable microorganisms. For non-model bacteria, a method for phenotypic analysis is invaluable, not only to serve as a starting point for further evaluation, but also to provide a broad understanding of the physiology of an uncharacterized wild-type organism or the physiology/phenotype of a newly created mutant of that organism. Given recent advances in genetic characterization and targeted mutations to elucidate genetic networks and metabolic pathways, high-throughput methods for determining phenotypic differences are essential. Here we outline challenges presented in studying the physiology and phenotype of a sulfate-reducing anaerobic delta proteobacterium, Desulfovibrio vulgaris Hildenborough. Modifications of the commercially available OmniLog system (Hayward, CA) for experimental setup, and configuration, as well as considerations in PM data analysis are presented. Also highlighted here is data viewing software that enables users to view and compare multiple PM data sets. The PM method promises to be a valuable strategy in our systems biology approach to D. vulgaris studies and is readily applicable to other anaerobic and aerobic bacteria.
authors.affiliation: Ecology Department, Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA. seborglin@lbl.gov
authors.forename: Sharon
authors.initials: S
authors.lastname: Borglin
authors.forename: Dominique
authors.initials: D
authors.lastname: Joyner
authors.forename: Janet
authors.initials: J
authors.lastname: Jacobsen
authors.forename: Aindrila
authors.initials: A
authors.lastname: Mukhopadhyay
authors.forename: Terry C
authors.initials: TC
authors.lastname: Hazen
mesh_terms: D049109:Cell Proliferation; D011232:Chemical Precipitation; D003470:Culture Media; D003625:Data Collection / Q000379:methods; D003628:Database Management Systems; D016969:Desulfovibrio vulgaris / Q000254:growth & development* / Q000502:physiology*; D058085:Iron Compounds; D046228:Microarray Analysis / Q000295:instrumentation* / Q000379:methods*; D010641:Phenotype; D015203:Reproducibility of Results; D013053:Spectrophotometry / Q000379:methods; D013431:Sulfates / Q000378:metabolism
chemical_list: D003470:Culture Media; D058085:Iron Compounds; D013431:Sulfates