Resolving Genetic Functions within Microbial Populations: In Situ Analyses Using rRNA and mRNA Stable Isotope Probing Coupled with Single-Cell Raman-Fluorescence In Situ Hybridization.

Huang, Wei E.; Ferguson, Andrew; Singer, Andrew C. ORCID: https://orcid.org/0000-0003-4705-6063; Lawson, Kathryn; Thompson, Ian P.; Kalin, Robert M.; Larkin, Michael J.; Bailey, Mark J.; Whiteley, Andrew S.. 2009 Resolving Genetic Functions within Microbial Populations: In Situ Analyses Using rRNA and mRNA Stable Isotope Probing Coupled with Single-Cell Raman-Fluorescence In Situ Hybridization. Applied and Environmental Microbiology, 75 (1). 234-241. https://doi.org/10.1128/AEM.01861-08

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Abstract/Summary

Prokaryotes represent one-half of the living biomass on Earth, with the vast majority remaining elusive to culture and study within the laboratory. As a result, we lack a basic understanding of the functions that many species perform in the natural world. To address this issue, we developed complementary population and single-cell stable isotope (13C)-linked analyses to determine microbial identity and function in situ. We demonstrated that the use of rRNA/mRNA stable isotope probing (SIP) recovered the key phylogenetic and functional RNAs. This was followed by single-cell physiological analyses of these populations to determine and quantify in situ functions within an aerobic naphthalene-degrading groundwater microbial community. Using these culture-independent approaches, we identified three prokaryote species capable of naphthalene biodegradation within the groundwater system: two taxa were isolated in the laboratory (Pseudomonas fluorescens and Pseudomonas putida), whereas the third eluded culture (an Acidovorax sp.). Using parallel population and single-cell stable isotope technologies, we were able to identify an unculturable Acidovorax sp. which played the key role in naphthalene biodegradation in situ, rather than the culturable naphthalene-biodegrading Pseudomonas sp. isolated from the same groundwater. The Pseudomonas isolates actively degraded naphthalene only at naphthalene concentrations higher than 30 µM. This study demonstrated that unculturable microorganisms could play important roles in biodegradation in the ecosystem. It also showed that the combined RNA SIP-Raman-fluorescence in situ hybridization approach may be a significant tool in resolving ecology, functionality, and niche specialization within the unculturable fraction of organisms residing in the natural environment.

Item Type:	Publication - Article
Digital Object Identifier (DOI):	https://doi.org/10.1128/AEM.01861-08
Programmes:	CEH Topics & Objectives 2009 - 2012 > Biodiversity > BD Topic 2 - Ecological Processes in the Environment
UKCEH and CEH Sections/Science Areas:	Hails
ISSN:	0099-2240
Additional Information. Not used in RCUK Gateway to Research.:	Open Access paper. Follow official URL for full text.
NORA Subject Terms:	Biology and Microbiology
Date made live:	12 Nov 2009 12:45 +0 (UTC)
URI:	https://nora.nerc.ac.uk/id/eprint/8293

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