Identification, functioning, and molecular signatures of thermophilic archaea involved in anaerobic hydrocarbon oxidation

The aim of my PhD project is to culture and describe novel thermophilic microorganisms, in particular archaea, that thrive on hydrocarbons in the absence of molecular oxygen. The basis for my cultivation are sediment samples from the Guaymas Basin in the Gulf of California, retrieved ruing the RV Atlantis cruise AT42-05 (November-December 2018). In this tectonically active spreading center, geothermally heated fluids rise up through a thick layer of organic-rich sediment, which causes the pyrolytic cleavage of biomolecules into bioaccessible compounds such as linear (n-) alkanes and aromatic hydrocarbons. The anaerobic oxidation of these hydrocarbons may be coupled to the reduction of sulfate, which is abundantly present in the Guaymas Basin. My experiments are based on anoxic sediment slurries prepared with artificial seawater medium including sulfate as electron acceptor.

Previous studies cultured archaea that activate short-chain alkanes such as ethane, propane, and butane and completely oxidize them to CO₂. These archaea thrive at up to 50°C and form consortia with specific sulfate-reducing partner bacteria. To explore additional alkane-degrading archaea, I have supplied sediment slurries with medium-chain n-alkanes (C₆ (hexane) – C₁₄ (tetradecane)) as electron donors. First metagenomic analyses suggest the growth of novel alkane degraders that contain specific highly divergent methyl-coenzyme M reductases (MCRs). They associate with a specific, previously undescribed sulfate-reducing partner bacterium belonging to the Thermodesulfobacteria. Our data suggest that MCR-catalyzed reactions are more diverse and distributed among the domain Archaea than previously believed. Substrates of these organisms may include a variety of hydrocarbons, such as medium- and long-chain alkanes.

Unsubstituted aromatic hydrocarbons (AHs) are toxic products of the complete combustion of organic material such as fossil fuels. In my second project, I study the anaerobic degradation of AHs in marine sediments. Therefore, the sediment slurries were supplemented with four unsubstituted aromatic hydrocarbons (AHs) as electron donors. Due to their high stability and hydrophobicity, the majority of AHs end up in marine sediments. This is concerning, since many AHs have carcinogenic, mutagenic and toxic impacts and can bioaccumulate through food webs. Microbial degradation is the main route by which these pollutants are removed from sediments. While aerobic AH degradation is well studied, little is known about the mechanisms of anaerobic oxidation of unsubstituted AHs.

For both cultures, sulfide production rates are observed as markers of metabolic activity. Successful enrichments from both cultivation experiments are analyzed in physiological experiments, and in a variety of -omics approaches, metabolite analyzes and in situ hybridization to characterize the microorganisms present in the cultures and elucidate their metabolic capacities.

In addition to these cultivation experiments, I characterize the membrane lipids of these and other alkane-oxidizing archaea that were recently enriched in our group from Guaymas Basin sediments (Candidatus Syntrophoarchaeum, Candidatus Ethanoperedens, and a hexadecane-degrading Hadesarchaeon) using state-of-the-art mass spectrometry techniques. Since the membrane lipid composition varies between different archaeal groups, certain core lipids can serve as biomarkers for past and present archaeal activity, providing information on factors like distribution of microbial biomass and prevailing species. Describing specific lipid signatures for these novel archaea will enable their detection in various environments and therefore provide evidence on their spatial and temporal distribution. Some of these enrichment cultures originate from different temperature regimes. Therefore, further information on the temperature-dependency of the membrane lipid composition in alkane-degrading archaea will be gained. This work is carried out in collaboration with the Hinrichs Lab for Organic Geochemistry at MARUM.

Contacts: Hannah Zehnle, Gunter Wegener