A reanalysis of phospholipid fatty acids as ecological biomarkers for methanotrophic bacteria

Paul L. E. Bodelier; Marie-Jose Bar Gillisen; Kees Hordijk; Jaap S. Sinninghe Damste; W. Irene C. Rijpstra; Jan A. J. Geenevasen; Peter F. Dunfield

doi:10.1038/ismej.2009.6

A reanalysis of phospholipid fatty acids as ecological biomarkers for methanotrophic bacteria

Paul L. E. Bodelier, Marie-Jose Bar Gillisen, Kees Hordijk, Jaap S. Sinninghe Damste, W. Irene C. Rijpstra, Jan A. J. Geenevasen, Peter F. Dunfield

Research output: Contribution to journal › Article › Academic › peer-review

Abstract

Aerobic methane-oxidizing bacteria (MB) are the primary terrestrial sinks for the greenhouse gas methane. A distinct characteristic of MB is the presence of specific phospholipid ester-linked fatty acids (PLFA) in their membranes that differentiate them from each other and also from all other organisms. These distinct PLFA patterns facilitate microbial ecology studies. For example, the assimilation of C from methane into PLFA can be traced in environmental samples using stable isotope (C-13) probing (SIP), which links the activity of MB to their community composition in situ. However, the phylogenetic resolution of this method is low because of a lack of PLFA profiles from cultured MB species. In this study, PLFA profiles of 22 alphaproteobacterial (type II) MB were analysed after growth on methane, methanol or both substrates together. Growth on different substrates did not affect the PLFA profiles of the investigated strains. A number of Methylocystis strains contained novel C18:2 fatty acids (omega 7c, 12c and omega 6c, 12c) that can be used as diagnostic biomarkers. The detection of these novel PLFA, combined with the analyses of multiple type II strains, increased the phylogenetic resolution of PLFA analysis substantially. Multivariate analysis of the expanded MB PLFA database identified species groups that closely reflected phylogenies based on 16S rRNA and pmoA gene sequences. The PLFA database therefore provides a robust framework for linking identity to activity in MB communities with a higher resolution than was previously possible. The ISME Journal (2009) 3, 606-617; doi:10.1038/ismej.2009.6; published online 5 February 2009

Original language	English
Pages (from-to)	606-617
Number of pages	12
Journal	ISME Journal
Volume	3
Issue number	5
DOIs	https://doi.org/10.1038/ismej.2009.6
Publication status	Published - May 2009
Externally published	Yes

Funding

We thank Peter Nichols, John Bowman and Mette Svenning for providing data of non-publicly available details of MOB PLFA profiles. Sergey Stoliar and Mary Lidstrom are kindly thanked for providing reference cultures. This study was part of the ESF-Eurodiversity programme (ERAS-CT-2003-98049, 6th EU-framework programme) and was financially supported by grants from the Netherlands Organization for Scientific Research (NWO; Grant no. 855.01.108), and the Max-Planck Society.

Funders	Funder number
ESF-Eurodiversity programme	ERAS-CT-2003-98049
Netherlands Organization for Scientific Research (NWO)	855.01.108
Administrative Headquarters of the Max Planck Society
Division Of Ocean Sciences; Directorate For Geosciences	0802004

Keywords

Plfa
Biomarkers
Fatty acids
Methane
Methanotrophs

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10.1038/ismej.2009.6

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abstract = "Aerobic methane-oxidizing bacteria (MB) are the primary terrestrial sinks for the greenhouse gas methane. A distinct characteristic of MB is the presence of specific phospholipid ester-linked fatty acids (PLFA) in their membranes that differentiate them from each other and also from all other organisms. These distinct PLFA patterns facilitate microbial ecology studies. For example, the assimilation of C from methane into PLFA can be traced in environmental samples using stable isotope (C-13) probing (SIP), which links the activity of MB to their community composition in situ. However, the phylogenetic resolution of this method is low because of a lack of PLFA profiles from cultured MB species. In this study, PLFA profiles of 22 alphaproteobacterial (type II) MB were analysed after growth on methane, methanol or both substrates together. Growth on different substrates did not affect the PLFA profiles of the investigated strains. A number of Methylocystis strains contained novel C18:2 fatty acids (omega 7c, 12c and omega 6c, 12c) that can be used as diagnostic biomarkers. The detection of these novel PLFA, combined with the analyses of multiple type II strains, increased the phylogenetic resolution of PLFA analysis substantially. Multivariate analysis of the expanded MB PLFA database identified species groups that closely reflected phylogenies based on 16S rRNA and pmoA gene sequences. The PLFA database therefore provides a robust framework for linking identity to activity in MB communities with a higher resolution than was previously possible. The ISME Journal (2009) 3, 606-617; doi:10.1038/ismej.2009.6; published online 5 February 2009",

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A reanalysis of phospholipid fatty acids as ecological biomarkers for methanotrophic bacteria

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