Leveraging genome-scale metabolic models to understand aerobic methanotrophs

Abstract

Genome-scale metabolic models (GEMs) are valuable tools serving systems biology and metabolic engineering. However, GEMs are still an underestimated tool in informing microbial ecology. Since their first application for aerobic gammaproteobacterial methane oxidizers less than a decade ago, GEMs have substantially increased our understanding of the metabolism of methanotrophs, a microbial guild of high relevance for the natural and biotechnological mitigation of methane efflux to the atmosphere. Particularly, GEMs helped to elucidate critical metabolic and regulatory pathways of several methanotrophic strains, predicted microbial responses to environmental perturbations, and were used to model metabolic interactions in cocultures. Here, we conducted a systematic review of GEMs exploring aerobic methanotrophy, summarizing recent advances, pointing out weaknesses, and drawing out probable future uses of GEMs to improve our understanding of the ecology of methane oxidizers. We also focus on their potential to unravel causes and consequences when studying interactions of methane-oxidizing bacteria with other methanotrophs or members of microbial communities in general. This review aims to bridge the gap between applied sciences and microbial ecology research on methane oxidizers as model organisms and to provide an outlook for future studies.

Keywords: metabolic modelling; methane oxidisers; systems biology.

Figure 1

Phylogenetic diversity of methanotrophs that perform aerobic methane oxidation. Names in bold indicate strains that have a reconstructed GEM. The tree, based on a concatenated protein alignment of 71 marker genes (Supplementary S1), was created using anvi’o [138] with third-party software: HMMER [139], Prodigal [140], and MUSCLE [141] as sequence aligner. The phylogenetic tree was generated using IQ-TREE with a maximum likelihood approach and the WAG model with 1000 bootstrap iterations [142, 143]. The genome of Nitrosomonas europaea ATCC 19718 (GCA_000009145) was used as an outgroup. Microbial genomes and associated metadata were obtained from the NCBI (https://www.ncbi.nlm.nih.gov/data-hub/genome/). Black, dark grey, light grey, and white circles at nodes denote 100%, >90%, >70%, and > 50% bootstrap support, respectively. Organisms for which a GEM has been constructed are highlighted in bold. Colored circles indicate the source of a sequenced genome.

Figure 2

Genealogy of methanotroph GEM models. The diagram shows the evolution and genealogy of GEMs of methanotrophic microorganisms since the reconstruction of the GEM for Methylomicrobium buryatense 5GB1 [42]. Each box represents a single metabolic model and includes the species name and the number of reactions incorporated (NA indicates that the article or supplementary materials did not specify the number of reactions.) Two GEMs with a white square in the lower right corner were reconstructed based on a GEM of the methylotroph Methylobacterium extorquens AM1 [144].