Archive of bacterial community in anhydrite crystals from a deep-sea basin provides evidence of past oil-spilling in a benthic environment in the Red Sea

In deep-sea sediment, the microbes present in anhydrite crystals after mild hydrothermal activities are markers of the past environment. In this study, this hypothesis was tested by analyzing the metagenome of an anhydrite crystal sample from a hydrothermal and hypersaline sediment core sampled from the Atlantis II Deep in the Red Sea. The 16S/18S rRNA genes in the metagenome were assigned to Bacteria, Archaea, Fungi and even invertebrate species. The dominant species in the crystals was an alkane-degrading Alcanivorax bacterium, which was not detected in the adjacent sediment layer. Using a genome-binning method, a draft genome of the Alcanivorax bacterium was separated from the metagenome. Phylogenetic and genomic analyses revealed that this species was a close relative of Alcanivorax borkumensis Sk2. The draft genome contained all the functional genes for alkane utilization and the reduction of nitrogen oxides. Fluorescence microscopy using 16S rRNA and marker gene probes revealed intact cells of the Alcanivorax bacterium in the crystals. Moreover, the metagenomes of the anhydrites and control sediment contained aromatic degradation pathways, which were mostly derived from Ochrobactrum sp. The estimated age of the anhydrite layer was between 750–770 years, which might span the event of hydrothermal eruption into the benthic floor. Altogether, these results support the presence of an oxic, oil-spilling benthic environment in the Atlantis II basin of the Red Sea in approximately the 14th century. The original microbial inhabitants underwent a dramatic selection process via drastic environmental changes following the formation of an overlying anoxic brine pool in the basin due to hydrothermal activities.