title: Analysis of methanotroph community composition using a pmoA-based microbial diagnostic microarray.
abstract: Microbial diagnostic microarrays (MDMs) are highly parallel hybridization platforms containing multiple sets of immobilized oligonucleotide probes used for parallel detection and identification of many different microorganisms in environmental and clinical samples. Each probe is approximately specific to a given group of organisms. Here we describe the protocol used to develop and validate an MDM method for the semiquantification of a range of functional genes--in this case, particulate methane monooxygenase (pmoA)--and we give an example of its application to the study of the community structure of methanotrophs and functionally related bacteria in the environment. The development and validation of an MDM, following this protocol, takes ∼6 months. The pmoA MDM described in detail comprises 199 probes and addresses ∼50 different species-level clades. An experiment comprising 24 samples can be completed, from DNA extraction to data acquisition, within 3 d (12-13 h bench work).
authors.affiliation: AIT-Austrian Institute of Technology, Bioresources Unit, Seibersdorf, Austria.
authors.forename: Nancy
authors.initials: N
authors.lastname: Stralis-Pavese
authors.forename: Guy C J
authors.initials: GC
authors.lastname: Abell
authors.forename: Angela
authors.initials: A
authors.lastname: Sessitsch
authors.forename: Levente
authors.initials: L
authors.lastname: Bodrossy
mesh_terms: D004269:DNA, Bacterial / Q000235:genetics*; D008772:Methylococcaceae / Q000235:genetics* / Q000302:isolation & purification*; D020411:Oligonucleotide Array Sequence Analysis; D010105:Oxygenases / Q000235:genetics*; D012988:Soil Microbiology
chemical_list: D004269:DNA, Bacterial; D010105:Oxygenases; C021555:methane monooxygenase