Lipidomics and Comparative Metabolite Excretion Analysis of Methanogenic Archaea Reveal Organism-Specific Adaptations to Varying Temperatures and Substrate Concentrations

ABSTRACT Methanogenic archaea possess diverse metabolic characteristics and are an ecologically and biotechnologically important group of anaerobic microorganisms. Although the scientific and biotechnological value of methanogens is evident with regard to their methane-producing physiology, little is known about their amino acid excretion, and virtually nothing is known about the lipidome at different substrate concentrations and temperatures on a quantitative comparative basis. Here, we present the lipidome and a comprehensive quantitative analysis of proteinogenic amino acid excretion as well as methane, water, and biomass production of the three autotrophic, hydrogenotrophic methanogens Methanothermobacter marburgensis, Methanothermococcus okinawensis, and Methanocaldococcus villosus under varying temperatures and nutrient supplies. The patterns and rates of production of excreted amino acids and the lipidome are unique for each tested methanogen and can be modulated by varying the incubation temperature and substrate concentration, respectively. Furthermore, the temperature had a significant influence on the lipidomes of the different archaea. The water production rate was much higher, as anticipated from the rate of methane production for all studied methanogens. Our results demonstrate the need for quantitative comparative physiological studies connecting intracellular and extracellular constraints of organisms to holistically investigate microbial responses to environmental conditions. IMPORTANCE Biological methane production by methanogenic archaea has been well studied for biotechnological purposes. This study reveals that methanogenic archaea actively modulate their lipid inventory and proteinogenic amino acid excretion pattern in response to environmental changes and the possible utilization of methanogenic archaea as microbial cell factories for the targeted production of lipids and amino acids.