Open Access Research article

Niche differentiation in nitrogen metabolism among methanotrophs within an operational taxonomic unit

Sven Hoefman1, David van der Ha2, Nico Boon2, Peter Vandamme1, Paul De Vos13 and Kim Heylen1*

Author Affiliations

1 Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium

2 Laboratory of Microbial Ecology and Technology (LabMET), Ghent University, Coupure Links 653, B-9000 Ghent, Belgium

3 BCCM/LMG Bacteria Collection, Ghent, Belgium

For all author emails, please log on.

BMC Microbiology 2014, 14:83  doi:10.1186/1471-2180-14-83

Published: 4 April 2014



The currently accepted thesis on nitrogenous fertilizer additions on methane oxidation activity assumes niche partitioning among methanotrophic species, with activity responses to changes in nitrogen content being dependent on the in situ methanotrophic community structure Unfortunately, widely applied tools for microbial community assessment only have a limited phylogenetic resolution mostly restricted to genus level diversity, and not to species level as often mistakenly assumed. As a consequence, intragenus or intraspecies metabolic versatility in nitrogen metabolism was never evaluated nor considered among methanotrophic bacteria as a source of differential responses of methane oxidation to nitrogen amendments.


We demonstrated that fourteen genotypically different Methylomonas strains, thus distinct below the level at which most techniques assign operational taxonomic units (OTU), show a versatile physiology in their nitrogen metabolism. Differential responses, even among strains with identical 16S rRNA or pmoA gene sequences, were observed for production of nitrite and nitrous oxide from nitrate or ammonium, nitrogen fixation and tolerance to high levels of ammonium, nitrate, and hydroxylamine. Overall, reduction of nitrate to nitrite, nitrogen fixation, higher tolerance to ammonium than nitrate and tolerance and assimilation of nitrite were general features.


Differential responses among closely related methanotrophic strains to overcome inhibition and toxicity from high nitrogen loads and assimilation of various nitrogen sources yield competitive fitness advantages to individual methane-oxidizing bacteria. Our observations proved that community structure at the deepest phylogenetic resolution potentially influences in situ functioning.

Methylomonas methanica; Methylomonas koyamae; Methylomonas lenta; Strain dependency; Nitrogen assimilation; Detoxification