The long-term oxidative weathering of fossil organic matter and sulfide minerals of the subterrestrial Kupferschiefer black shale by lithobiontic microbial community - metaomics field studies

The role of microorganisms in the 12-year-long oxidative weathering of subterrestrial ~256-million-year-old fossil organic matter-rich and metal sulfide-containing Kupferschiefer black shale was studied. The phylogenetic diversity of the lithobiontic microbial community inhabiting the black shale was defined. The metagenome and metaproteome of the community was screened in order to identify the genes and enzymes respectively potentially responsible for long-term bioweathering of the black shale. The microorganisms and their metabolic processes crucial in the bioweathering of primary components of the Kupferschiefer were defined. The lithobiontic microbial community inhabiting the black shale was dominated by the following bacterial genera: Pseudomonas, Limnobacter, Yonghaparkia, Thiobacillus, Bradyrhyzobium. Sulfuricaulis limicola and Sulfurifustis variabilis species were also present. These bacteria together with some less abundant genera, such as Nitrospira, Microbacterium, Mesorhizobium, Methylobacterium and Sphingopyxis were indicated as crucial in the weathering of the black shale. Archaea and fungi, represented by Nitrososphaera and Aspergillus genera respectively, were detected for the first time on the surface of the black shale. Two microbial processes essential in the bioweathering of primary fossil organic matter and sulfide minerals present in the black shale were identified. The direct bioweathering of the fossil organic matter was based on oxidative enzymatic oxidation of aliphatic and aromatic compounds, mainly hydrocarbons. Chemoorganotrophic microorganisms, mostly bacteria, but also archaea and fungi are responsible for this process. Simultaneously, the inorganic reduced sulfur compounds were oxidized by neutrophilic and alkalophilic chemolitotrophic bacteria. The geochemical consequences of microbial activity were the oxidation of primary fossil organic matter and dissolution of sulfide minerals.