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Analysis of methanotroph community composition using a pmoA-based microbial diagnostic microarray

Citation

Stralise-Pavese, N and Abell, GCJ and Bodrossy, L, Analysis of methanotroph community composition using a pmoA-based microbial diagnostic microarray, Nature Protocols, 6, (5) pp. 609-624. ISSN 1754-2189 (2011) [Refereed Article]

Copyright Statement

Copyright 2011 Nature America, Inc.

DOI: doi:10.1038/nprot.2010.191

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).

Item Details

Item Type:Refereed Article
Keywords:DNA, bacterial, Methylococcaceae, oligonucleotide array sequence analysis oxygenases, soil microbiology
Research Division:Biological Sciences
Research Group:Genetics
Research Field:Genetics not elsewhere classified
Objective Division:Expanding Knowledge
Objective Group:Expanding Knowledge
Objective Field:Expanding Knowledge in the Biological Sciences
Author:Bodrossy, L (Dr Levente Bodrossy)
ID Code:118630
Year Published:2011
Web of Science® Times Cited:24
Deposited By:Tasmanian Institute of Agriculture
Deposited On:2017-07-14
Last Modified:2017-08-28
Downloads:0

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