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Identification of Diazotrophic Microorganisms in Marine Sediment via Fluorescence In Situ Hybridization Coupled to Nanoscale Secondary Ion Mass Spectrometry (FISH-NanoSIMS)

Dekas, Anne E. and Orphan, Victoria J. (2011) Identification of Diazotrophic Microorganisms in Marine Sediment via Fluorescence In Situ Hybridization Coupled to Nanoscale Secondary Ion Mass Spectrometry (FISH-NanoSIMS). In: Research on Nitrification and Related Processes. Methods in Enzymology . No.486. Elsevier , Amsterdam, pp. 281-305. ISBN 9780123812940. https://resolver.caltech.edu/CaltechAUTHORS:20110518-083725900

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Abstract

Growing appreciation for the biogeochemical significance of uncultured microorganisms is changing the focus of environmental microbiology. Techniques designed to investigate microbial metabolism in situ are increasingly popular, from mRNA-targeted fluorescence in situ hybridization (FISH) to the "-omics" revolution, including metagenomics, transcriptomics, and proteomics. Recently, the coupling of FISH with nanometer-scale secondary ion mass spectrometry (NanoSIMS) has taken this movement in a new direction, allowing single-cell metabolic analysis of uncultured microbial phylogenic groups. The main advantage of FISH-NanoSIMS over previous noncultivation-based techniques to probe metabolism is its ability to directly link 16S rRNA phylogenetic identity to metabolic function. In the following chapter, we describe the procedures necessary to identify nitrogen-fixing microbes within marine sediment via FISH-NanoSIMS, using our work on nitrogen fixation by uncultured deep-sea methane-consuming archaea as a case study.


Item Type:Book Section
Related URLs:
URLURL TypeDescription
http://dx.doi.org/10.1016/B978-0-12-381294-0.00012-2 DOIArticle
ORCID:
AuthorORCID
Dekas, Anne E.0000-0001-9548-8413
Orphan, Victoria J.0000-0002-5374-6178
Additional Information:© 2011 Elsevier Inc. Available online 23 December 2010. We thank Christopher House, Yunbin Guan, John Eiler, Kendra Turk, Annelie Pernthaler, Sameer Walavalkar, Kevin McKeegan, Raj Singh, and Mark Ellisman for helping to develop and optimize the method. We thank James Howard, Sameer Walavalkar, and Eric Matson for sample and data contributions to this chapter. We also thank two anonymous reviewers for helpful suggestions. This research was supported by grants from the Department of Energy (Career award, #DE-SC0003940) and Gordon and Betty Moore Foundation (to VJO) and the National Science Foundation (graduate fellowship to AED).
Funders:
Funding AgencyGrant Number
Department of Energy (DOE)DE-SC0003940
Gordon and Betty Moore FoundationUNSPECIFIED
NSF Graduate Research FellowshipUNSPECIFIED
Series Name:Methods in Enzymology
Issue or Number:486
Record Number:CaltechAUTHORS:20110518-083725900
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20110518-083725900
Official Citation:Anne E. Dekas, Victoria J. Orphan, Identification of Diazotrophic Microorganisms in Marine Sediment via Fluorescence In Situ Hybridization Coupled to Nanoscale Secondary Ion Mass Spectrometry (FISH-NanoSIMS), In: Martin G. Klotz, Editor(s), Methods in Enzymology, Academic Press, 2011, Volume 486, Research on Nitrification and Related Processes, Part A, Pages 281-305, ISSN 0076-6879, ISBN 9780123812940, DOI: 10.1016/B978-0-12-381294-0.00012-2.
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:23702
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:31 May 2011 21:51
Last Modified:03 Oct 2019 19:58

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