Organic-rich shales as archive and resource for microbial extremophiles

Abstract

Organic-rich shales of sedimentary basins are the most abundant carbon-rich rocks throughout the world, formed as a consequence of different geological events. The repetitive sedimentation of the mudstones, clay particles, biological organic matter, microbial decomposition of the organic matter, and evaporation formed organic-rich shales of diverse origins in different geological eras. These organic-rich shales are an important source of gas, oil, and occasionally precious metals such as copper, gold, silver, uranium. Moreover, these shales may also provide environmental microbial communities with the sole source of carbon from their organic component. Unlike the air-exposed black shales in subterrestrial environments, deep-sea subsurface black shales are colonized by anaerobic halotolerant bacteria and methanogens. The subterrestrial organic-rich shales enrich completely different microbial communities belonging mainly to aerobic/microaerophilic chemoorganotroph and chemolithotroph categories. The subterrestrial black shales provide essential organics characterized as kerogen and bitumen, accessible for microbial growth through fractures and microfissures. DNA analysis performed on the various black shales of different origins confirmed the microbial colonization by Firmicutes, Actinobacteria, and Proteobacteria communities. The inhabitant microorganisms are supposed to devour the hydrocarbons as a sole carbon source. Their contribution to the global carbon cycle, remediation of hydrocarbons, and facilitation of oil recovery from shales are being validated. In this study, the inhabitant microbial diversity of the subterrestrial organic-rich environments was metagenomically investigated to identify if the colonized microbiota is specialized to degrade hydrocarbons and could cope with different environmental stress factors. It was further established by analysing microbial colonization of organic-rich shales with or without high heavy metal contents. In the first chapter, the organic-rich shale samples with low metal content from Monte San Giorgio were analysed. The microbial structure inhabiting the organic component of the shale was distinguished from that of the rocky shale surface and limestone rocks. Furthermore, the enrichment effect of the media of choice on the native shale and limestone microbiome gave insights into the metabolic capabilities of the oligotrophic versus fastidious communities. The organics of the shale are not easily degradable and accessible carbon sources which facilitate the specialized oligotrophic microorganisms to colonize slowly. The functional profiling of the inhabitant microbiota clearly shows the ability to degrade complex aromatic hydrocarbon compounds. The second chapter explored the native microbial communities in the metalliferous organic-rich shale of Marsberg Kilianstollen copper mine. The low temperature, toxic copper-enriched leachate, and low availability of organics adapted heavy metal resistant consortia that could also degrade the complex hydrocarbons. Ktedonobacteria biofilm formed near the acid mine drainage in Kilian copper mine was further investigated to reveal functional pathways from the metagenome-assembled genomes (MAGs). Due to the common observation of Ktedonobacteria high abundance in the cold Marberg Kilianstollen, Germany and other extreme hot springs environment Sasso Pisano, Italy, the diversity of newly discovered Ktedonobacteria in these ecosystems was further elucidated. The inhabiting Ktedonobacteria strains were found to be phylogenetically distinct at Marsberg and Sasso Pisano. However, it is hypothesized that they show functional conservation for the carbon monoxide oxidation (Cox operons), heavy metal resistance, aromatic compounds metabolism, and sporulation mechanisms.