Preservation of Underground Microbial Diversity in Ancient Subsurface Deposits (>6 Ma) of the Rio Tinto Basement

Abstract

The drilling of the Rio Tinto basement has provided evidence of an underground microbial community primarily sustained by the Fe and S metabolism through the biooxidation of pyrite orebodies. Although the gossan is the microbial activity product, which dates back to the Oligocene (25 Ma), no molecular evidence of such activity in the past has been reported yet. A Time of Flight Secondary Ion Mass Spectrometry (ToF-SIMS) molecular analysis of a subsurface sample in the Peña de Hierro basement has provided novel data of the ancient underground microbial community. It shows that the microbial remains are preserved in a mineral matrix composed of laminated Fe-oxysulfates and K- and Na-bearing sulfates alternating with secondary silica. In such a mineral substrate, the biomolecule traces are found in five different microstructure associations, (1) <15 micron-sized nodular microstructures composed of POn(2≤n≤4)−, (2) <30 micron-size micronodules containing fatty acids, acylglycerides, and alkanol chains, (3) <20 micro-sized nodules containing NOn−(2≤n≤3) ions, (4) 40-micron size nodules with NH4+ and traces of peptides, and (5) >200-micron thick layer with N-bearing adducts, and sphingolipid and/or peptide traces. It suggests the mineralization of at least five microbial preserved entities with different metabolic capabilities, including: (1) Acidiphilium/Tessaracoccus-like phosphate mineralizers, (2) microbial patches preserving phosphate-free acylglycerides bacteria, (3) nitrogen oxidizing bacteria (e.g., Acidovorax sp.), (4) traces of heterotrophic ammonifying bacteria, and (5) sphingolipid bearing bacteria (e.g., Sphingomonadales, and δ-Proteobacteria) and/or mineralized biofilms. The primary biooxidation process acted as a preservation mechanism to release the inorganic ions that ultimately mineralized the microbial structures.

Unveiling microbial preservation under hyperacidic and oxidizing conditions in the Oligocene Rio Tinto deposit

“…ToF–SIMS is an analytic surface technique that characterizes the distribution of positive and negative ions in a sample. For this reason, it can provide essential information about the preservation of organic compounds, establishing a direct association between the mineral matrix and the occurrence of molecular biosignatures in the sample 106 . ToF–SIMS has a high detection level for different compounds, including contaminants that can potentially be attached to the thin section surface.…”

The Molecular Profile of Soil Microbial Communities Inhabiting a Cambrian Host Rock

“…21 + , respectively. The formation of the [M − H] − FA ions is also associated directly with the fragmentation process in the glycerides (Figure 10A-C), which is supported by sharing the same compound distribution with the different diglyceride cations [37]. Furthermore, it is likely that the formation of the acylium cations (R-CO + ) come from the diacylglyceride fragmentation and the loss of H + from detached FAs through the ToF-SIMS sample analysis or by natural degradation processes, which will be further discussed in the following section.…”

“…It is supported by the observation of positive m / z peaks like 211.21, 239.25, 241.22, 265.26, 267.28, 283.27, 299.27, 313.29, 341.30, and 371.36, which fit well with cations C 14 H 27 O + , C 16 H 31 O + , C 18 H 33 O + , C 15 H 29 O 2 + , C 18 H 35 O + , C 18 H 35 O 2 + , C 18 H 35 O 3 + , C 19 H 37 O 3 + , C 21 H 41 O 3 + , and C 23 H 47 O 3 + , respectively. The formation of the [M − H] − FA ions is also associated directly with the fragmentation process in the glycerides ( Figure 10 A–C), which is supported by sharing the same compound distribution with the different diglyceride cations [ 37 ]. Furthermore, it is likely that the formation of the acylium cations (R-CO + ) come from the diacylglyceride fragmentation and the loss of H + from detached FAs through the ToF-SIMS sample analysis or by natural degradation processes, which will be further discussed in the following section.…”

“…Furthermore, a multivariate analysis combining the spectral and spatial distribution in the sample was run to find correlations between fragment occurrence and molecular fragmentation patterns. Mass spectral acquisition and image analysis were performed within the ION-TOF Surface Lab software suit (version 7.0), including the overload of Red, Green, and Blue (RGB) images for molecular mapping [ 34 , 37 ]. The analysis of the molecular fragmentation pattern was completed through the Chemical online tool [ 38 ] and the open source mass spectrometry tool mMass [ 39 ].…”

Revealing sphingolipids composition in extracellular vesicles and paternal β-cells after persistent hyperglycemia

“…Time of Flight -Secondary Ion Mass Spectrometry is an example of an advanced physical method that can be successfully used in metabolomic and lipidomic researches. This technique has been successfully used for the characterization of lipids in biological samples and comparative analyzes of cells, tissues, organs, and even organisms [12][13][14]. In this study, we would like to focus on SPs composition in β-cells and their residues and metabolites secreted in the form of extracellular vesicles (EVs) using ToF-SIMS.…”