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Analysis of methanotroph community composition using a pmoA-based microbial diagnostic microarray
journal contribution
posted on 2023-05-19, 07:39 authored by Stralise-Pavese, N, Abell, GCJ, Bodrossy, LMicrobial 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).
History
Publication title
Nature ProtocolsVolume
6Issue
5Pagination
609-624ISSN
1754-2189Department/School
Tasmanian Institute of Agriculture (TIA)Publisher
Nature Publishing GroupPlace of publication
United StatesRights statement
Copyright 2011 Nature America, Inc.Repository Status
- Restricted