A novel mechanism for the anaerobic degradation of non-methane hydrocarbons in archaea

Abstract

Crude oil and natural gas are formed due to the degradation of the organic matter in deep subsurface layers. From there, they can migrate towards the sediment surface, where they represent an energy source for microbial communities. Anaerobic methanotrophic archaea (ANME) are the main responsible of anaerobic oxidation of methane in anoxic environments. For methane oxidation, they use a reversal of the methanogenesis, whose key enzyme is the methyl-coenzyme M reductase (MCR). However, little is known about the role of archaea in the anaerobic oxidation of other hydrocarbons. Apart from ANME, only three archaea are described as anaerobic hydrocarbons degraders, although the three use mechanisms of bacterial origin. The aim of my thesis is to shed light on the role of archaea in anaerobic hydrocarbon degradation. In Chapter II, we describe a new pathway to degrade butane and propane in two archaeal strains of the newly described clade Candidatus Syntrophoarchaeum, which we cultivated in consortia with syntrophic partner bacteria. Using meta-omics approaches, we discovered that Ca. Syntrophoarchaeum use before uncharacterized divergent MCRs to activate butane and propane. The produced alkyl-CoM units are then fully oxidized using a combination of different pathways and the reducing equivalents are transferred to the partner bacteria for sulfate reduction. Chapter III reports about archaea harbouring similar mcr genes in oil seeps of the Gulf of Mexico. Archaea of the D-C06 clade were especially abundant in these environments and we could visualize them in oil droplets without any associated bacteria. Metagenomic analyses revealed that D-C06 had a machinery for alkane degradation similar to Ca. Syntrophoarchaeum, including a divergent mcr gene. Strikingly they also contained a complete methanogenesis pathway with a canonical mcr copy. Therefore, we hypothesize that D-C06 are degrading hydrocarbons coupled to methane production in a single cell. Chapter IV focuses on the physiology of Ca. Syntrophoarchaeum using different substrate incubations, temperature growth studies and transcriptomics. Growth was detected only on butane and propane. While two Ca. Syntrophoarchaeum strains were found in butane enrichments, only one was detected in the propane cultures. Analysis of the expression of mcr genes revealed certain links between substrates and MCR enzymes. The knowledge for culturing these anaerobic hydrocarbondegrading organisms is summarized in a detailed protocol in Chapter V, which may help in the cultivation of similar archaeal clades in the future. In summary, my thesis describes a novel pathway in archaea to degrade hydrocarbons anaerobically. The key element is highly divergent MCRs that are capable to activate multi-carbon alkanes. This constitutes a genuine archaeal mechanism, previously unknown. Genomic analyses have revealed that this pathway can be found in different archaeal clades like Ca. Syntrophoarchaeum or DC06 with different lifestyles. These archaea are detected in diverse hydrocarbon-rich environments like oil and gas seeps and deep reservoirs. This indicates a so far unexplored role of these groups in hydrocarbon degradation that should be addressed in future research.