Methane oxidation coupled to nitrate reduction under hypoxia by the Gammaproteobacterium Methylomonas denitrificans, sp. nov. type strain FJG1

Abstract

Obligate methanotrophs belonging to the Phyla Proteobacteria and Verrucomicrobia require oxygen for respiration and methane oxidation; nevertheless, aerobic methanotrophs are abundant and active in low oxygen environments. While genomes of some aerobic methanotrophs encode putative nitrogen oxide reductases, it is not understood whether these metabolic modules are used for NOx detoxification, denitrification or other purposes. Here we demonstrate using microsensor measurements that a gammaproteobacterial methanotroph Methylomonas denitrificans sp. nov. strain FJG1(T) couples methane oxidation to nitrate reduction under oxygen limitation, releasing nitrous oxide as a terminal product. Illumina RNA-Seq data revealed differential expression of genes encoding a denitrification pathway previously unknown to methanotrophs as well as the pxmABC operon in M. denitrificans sp. nov. strain FJG1(T) in response to hypoxia. Physiological and transcriptome data indicate that genetic inventory encoding the denitrification pathway is upregulated only upon availability of nitrate under oxygen limitation. In addition, quantitation of ATP levels demonstrates that the denitrification pathway employs inventory such as nitrate reductase NarGH serving M. denitrificans sp. nov. strain FJG1(T) to conserve energy during oxygen limitation. This study unravelled an unexpected metabolic flexibility of aerobic methanotrophs, thereby assigning these bacteria a new role at the metabolic intersection of the carbon and nitrogen cycles.

Methylotrophs in natural habitats: current insights through metagenomics

“…While labeled dinitrogen is measured in NC10-dominated microcosms fed 15 N-nitrite, it is possible that not only NC10 bacteria but also other organisms in the enrichment culture contributed to this activity. On the contrary, in experiments with pure cultures of M. denitrificans, also lacking genes for nitrous oxide reduction, evolution of nitrous oxide could be seen, in agreement with predictions from the genomic sequence (Kits et al 2015).…”

“…While at this moment, the potential role of dinitrogen fixation in the fitness of Methylobacter is not obvious, its ability to denitrify presents a mechanism by which it may be able to outcompete Methylosarcina during hypoxia. Methane oxidation coupled to nitrate reduction has been recently demonstrated during hypoxia in a related methanotroph, Methylomonas denitrificans (Kits et al 2015).…”

“…Their propensity to cope well with hypoxic situations has been previously reported King 1994, 1995). While the ability to denitrify presents one mechanism for coping with hypoxia (Kits et al 2015), active Methylococcaceae have also been detected in anoxic environments devoid of nitrate. In this case, methane oxidation was proposed to be linked to oxygenic photosynthesis (Milucka et al 2015).…”

Determining Roles of Accessory Genes in Denitrification by Mutant Fitness Analyses

“…Under the growth conditions tested, however, nirK mutants had no phenotype (Table 2). Although it has been claimed that the presence of one of these nitrite reductase homologs in a given organism precludes the presence of the other (12,39,40), this is obviously not true (13). In fact, P. stutzeri strains BAL361, ATCC 14405, CCUG 29243, DSM 10701, F13, RCH2, and T13, as well as members of 37 other species, representing five bacterial phyla, one archaeal phylum (Euryarchaeota), and one green alga (Chlamydomonas), also contain genes encoding proteins of both types, according to InterPro (see Table S5 in the supplemental material).…”

“…These two proteins are phylogenetically unrelated and have been reported to never occur in the same organism (12), although this was recently shown not to be the case (13). NirS contains the specialized heme d 1 , and several accessory genes (nirDEFGHJL) are involved in related cofactor maturation (6,14).…”