Cultivation of methanotrophic bacteria in opposing gradients of methane and oxygen

Abstract

In sediments, methane-oxidizing bacteria live in opposing gradients of methane and oxygen. In such a gradient system, the fluxes of methane and oxygen are controlled by diffusion and consumption rates, and the rate-limiting substrate is maintained at a minimum concentration at the layer of consumption. Opposing gradients of methane and oxygen were mimicked in a specific cultivation set-up in which growth of methanotrophic bacteria occurred as a sharp band at either c. 5 or 20 mm below the air-exposed end. Two new strains of methanotrophic bacteria were isolated with this system. One isolate, strain LC 1, belonged to the Methylomonas genus (type I methantroph) and contained soluble methane mono-oxygenase. Another isolate, strain LC 2, was related to the Methylobacter group (type I methantroph), as determined by 16S rRNA gene and pmoA sequence similarities. However, the partial pmoA sequence was only 86% related to cultured Methylobacter species. This strain accumulated significant amounts of formaldehyde in conventional cultivation with methane and oxygen, which may explain why it is preferentially enriched in a gradient cultivation system.

Methanotrophic bacteria in oilsands tailings ponds of northern Alberta

“…Nitrogen is not limited in the ponds, in fact some nitrifying bacteria were detected (Supplementary Figure S2). However, the high ammonia/ammonium concentrations up to 17 mg l À 1 should require that methanotrophic species have mechanisms to deal with the toxic byproducts of ammonia oxidation by pMMO (Stein and Klotz, 2011 (Amaral and Knowles, 1995;Henckel et al, 1999;Henckel et al, 2000, van Bodegom et al, 2001Horz et al, 2002;Pester et al, 2004;Bussmann et al, 2006). Methane and O 2 levels certainly affect methanotroph communities, but the effect is probably sitespecific and difficult to generalize.…”

Anaerobic Oxidation of Methane in Sediments of Lake Constance, an Oligotrophic Freshwater Lake

“…These primers amplified only novel NC10-related pmoA genes and no known pmoA genes of aerobic methanotrophs from our samples. PCR targeting the pmoA gene was performed using primer A189f (21), together with one of the newly designed primers and the PCR program described previously (6). Two to 20 ng of extracted DNA was used for all PCRs.…”

A new cell morphotype among methane oxidizers: a spiral-shaped obligately microaerophilic methanotroph from northern low-oxygen environments

“…It belonged to the phylogenetic cluster containing PmoA sequences from gammaproteobacterial methanotrophs and formed a novel, genus-level lineage, which was only distantly related (81-86% amino acid identity) to the PmoA cluster defined by the genera Methylococcus, Methylocaldum and Methylogaea (Figure 2a). Notably, this PmoA lineage included a number of sequences obtained in cultivation-independent studies from various freshwater environments, that is, peatlands, lake sediments, boreal forest and alpine fen soils (Pester et al, 2004;Jaatinen et al, 2005;Bussmann et al, 2006;Danilova and Dedysh, 2014;Cheema et al, 2015;Danilova et al, 2015). This PmoA lineage is also addressed as OSC (Organic Soil Cluster) cluster of uncultivated methanotrophs, which occur predominantly in peatlands and in some upland soils (Knief, 2015).…”