title: Development and assessment of whole-genome oligonucleotide microarrays to analyze an anaerobic microbial community and its responses to oxidative stress.
abstract: The application of DNA microarray technology to investigate multiple-species microbial communities presents great challenges. In this study, we reported the design and quality assessment of four whole genome oligonucleotide microarrays for two syntroph bacteria, Desulfovibrio vulgaris and Syntrophobacter fumaroxidans, and two archaeal methanogens, Methanosarcina barkeri, and Methanospirillum hungatei, and their application to analyze global gene expression in a four-species microbial community in response to oxidative stress. In order to minimize the possibility of cross-hybridization, cross-genome comparison was performed to assure all probes unique to each genome so that the microarrays could provide species-level resolution. Microarray quality was validated by the good reproducibility of experimental measurements of multiple biological and analytical replicates. This study showed that S. fumaroxidans and M. hungatei responded to the oxidative stress with up-regulation of several genes known to be involved in reactive oxygen species (ROS) detoxification, such as catalase and rubrerythrin in S. fumaroxidans and thioredoxin and heat shock protein Hsp20 in M. hungatei. However, D. vulgaris seemed to be less sensitive to the oxidative stress as a member of a four-species community, since no gene involved in ROS detoxification was up-regulated. Our work demonstrated the successful application of microarrays to a multiple-species microbial community, and our preliminary results indicated that this approach could provide novel insights on the metabolism within microbial communities.
authors.affiliation: Microbiology Department, Pacific Northwest National Laboratory, Richland, WA 99352, USA. johannes.scholten@pnl.gov
authors.forename: Johannes C M
authors.initials: JC
authors.lastname: Scholten
authors.forename: David E
authors.initials: DE
authors.lastname: Culley
authors.forename: Lei
authors.initials: L
authors.lastname: Nie
authors.forename: Kyle J
authors.initials: KJ
authors.lastname: Munn
authors.forename: Lely
authors.initials: L
authors.lastname: Chow
authors.forename: Fred J
authors.initials: FJ
authors.lastname: Brockman
authors.forename: Weiwen
authors.initials: W
authors.lastname: Zhang
mesh_terms: D001421:Bacteria, Anaerobic / Q000235:genetics / Q000378:metabolism*; D001426:Bacterial Proteins / Q000378:metabolism*; D002874:Chromosome Mapping / Q000379:methods; D004867:Equipment Design; D019544:Equipment Failure Analysis; D020869:Gene Expression Profiling / Q000379:methods; D016680:Genome, Bacterial / Q000235:genetics*; D006360:Heat-Shock Proteins / Q000378:metabolism*; D020411:Oligonucleotide Array Sequence Analysis / Q000295:instrumentation* / Q000379:methods; D018384:Oxidative Stress / Q000502:physiology*
chemical_list: D001426:Bacterial Proteins; D006360:Heat-Shock Proteins