Diverse electron sources support denitrification under hypoxia in the obligate methanotroph Methylomicrobium album strain BG8

Abstract

Aerobic methane-oxidizing bacteria (MOB) are a diverse group of microorganisms that are ubiquitous in natural environments. Along with anaerobic MOB and archaea, aerobic methanotrophs are critical for attenuating emission of methane to the atmosphere. Clearly, nitrogen availability in the form of ammonium and nitrite have strong effects on methanotrophic activity and their natural community structures. Previous findings show that nitrite amendment inhibits the activity of some cultivated methanotrophs; however, the physiological pathways that allow some strains to transform nitrite, expression of gene inventories, as well as the electron sources that support this activity remain largely uncharacterized. Here we show that Methylomicrobium album strain BG8 utilizes methane, methanol, formaldehyde, formate, ethane, ethanol, and ammonia to support denitrification activity under hypoxia only in the presence of nitrite. We also demonstrate that transcript abundance of putative denitrification genes, nirS and one of two norB genes, increased in response to nitrite. Furthermore, we found that transcript abundance of pxmA, encoding the alpha subunit of a putative copper-containing monooxygenase, increased in response to both nitrite and hypoxia. Our results suggest that expression of denitrification genes, found widely within genomes of aerobic methanotrophs, allow the coupling of substrate oxidation to the reduction of nitrogen oxide terminal electron acceptors under oxygen limitation. The present study expands current knowledge of the metabolic flexibility of methanotrophs by revealing that a diverse array of electron donors support nitrite reduction to nitrous oxide under hypoxia.

Communal metabolism by Methylococcaceae and Methylophilaceae is driving rapid aerobic methane oxidation in sediments of a shallow seep near Elba, Italy

“…S5). These orthologues also encode copper‐dependent monooxygenases, which are potentially involved in methane oxidation under oxygen limited and nitrite‐rich conditions (Kits et al ., ,b). Potentially linked to these putative alternative pMMOs, several MAGs contained genes involved in denitrification, such as narG and napABC , encoding nitrate reductases, and nirS , encoding nitrite reductase.…”

Metagenomic Binning Recovers a Transcriptionally Active Gammaproteobacterium Linking Methanotrophy to Partial Denitrification in an Anoxic Oxygen Minimum Zone

“…Indeed, the abundance of OPU3-like OTUs has been shown to increase with decreasing oxygen further off the Costa Rican coast (Tavormina et al, 2013). However, the activity of methanotrophic denitrifiers in the OMZ water column may also be driven strongly by nitrite conditions; for example, in Methylomicrobium album, transcription of methanotrophy genes and nitrous oxide production via denitrification was dependent on both nitrite availability and low oxygen conditions, whereas denitrification gene transcription was stimulated only by nitrite availability (Kits et al, 2015a). In the GD, the distribution of OPU3 amplicons and transcriptional activity, notably those of GD_7, mirror that of the nitrite profile (Figure 2).…”

Methanotrophy under Versatile Conditions in the Water Column of the Ferruginous Meromictic Lake La Cruz (Spain)

“…We found, however, microbiological/molecular (i.e., CARD-FISH, sequencing) evidence for the presence of aerobic gamma-MOB at anoxic depths (Figures 3, 4). It has been shown recently that some of these bacteria can couple methane oxidation to nitrate/nitrite reduction under oxygen limitation, although trace amounts of oxygen are probably still required for the initial oxidation of methane to methanol (Kits et al, 2015a,b). This metabolic switch would provide gamma-MOB with a competitive advantage in an environment with fluctuating O 2 conditions (i.e., transient sub-micromolar O 2 concentrations) and could explain why zones of aerobic MO and nitrate/nitrite-dependent methane oxidation appear to overlap in the environment (Deutzmann et al, 2014).…”

“…Since aerobic gamma-MOB are, with regards to their metabolic requirements, more versatile than previously believed (Kits et al, 2015a,b), it is conceivable that both Mn(IV) and Fe(III) could serve as viable electron acceptors in the respiratory chain, in addition to O 2 and nitrate or nitrite (Kits et al, 2015a,b). …”

“…In shallow lakes with light penetration below the oxycline, aerobic MO may be coupled to in situ production of oxygen by photosynthesis (Milucka et al, 2015; Oswald et al, 2015; Brand et al, 2016). Additionally, MO (by facultative aerobic MOB) may be coupled to denitrification under oxygen limitation (Kits et al, 2015a,b). Methylomirabilis oxyfera (phylum NC 10), for example, has been shown to couple nitrite reduction to NO with methane oxidation, where O 2 is produced intracellularly by NO dismutation and used to oxidize methane aerobically (Ettwig et al, 2010).…”