Spectral characterisation of eight glycerolipids and their detection in natural samples using time-of-flight secondary ion mass spectrometry

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

The preservation of biosignatures on Mars is largely associated with extensive deposits of clays formed under mild early Noachian conditions (> 3.9 Ga). They were followed by widespread precipitation of acidic sulfates considered adverse for biomolecule preservation. In this paper, an exhaustive mass spectrometry investigation of ferric subsurface materials in the Rio Tinto gossan deposit (~ 25 Ma) provides evidence of well-preserved molecular biosignatures under oxidative and acidic conditions. Time of flight secondary ion mass spectrometry (ToF–SIMS) analysis shows a direct association between physical-templating biological structures and molecular biosignatures. This relation implies that the quality of molecular preservation is exceptional and provides information on microbial life formerly operating in the shallow regions of the Rio Tinto subsurface. Consequently, low-pH oxidative environments on Mars could also record molecular information about ancient life in the same way as the Noachian clay-rich deposits.

The Molecular Record of Metabolic Activity in the Subsurface of the Río Tinto Mars Analog

In the subsurface, the interplay between microbial communities and the surrounding mineral substrate, potentially used as an energy source, results in different mineralized structures. The molecular composition of such structures can record and preserve information about the metabolic pathways that have produced them. To characterize the molecular composition of the subsurface biosphere, we have analyzed some core samples by time-of-flight secondary ion mass spectrometry (ToF-SIMS) that were collected in the borehole BH8 during the operations of the Mars Analog and Technology Experiment (MARTE) project. The molecular analysis at a micron-scale mapped the occurrence of several inorganic complexes bearing PO₃^-, SO_{x(2 to 4)}^-, NO_x(2,3)^-, FeO_x(1,2)^-_, SiO₂^-, and Cl^-. Their distribution correlates with organic molecules that were tentatively assigned to saturated and monounsaturated fatty acids, polyunsaturated fatty acids, saccharides, phospholipids, sphingolipids, and potential peptide fragments. SO_x^- appear to be mineralizing some microstructures larger than 25 microns, which have branched morphologies, and that source SO₃-bearing adducts. PO₃-rich compounds occur in two different groups of microstructures which size, morphology, and composition are different. While a group of >40-micron sized circular micronodules lacks organic compounds, an ovoidal microstructure is associated with m/z of other lipids. The NO₂^-/NO₃^- and Cl^- ions occur as small microstructure clusters (<20 microns), but their distribution is dissimilar to the mineralized microstructures bearing PO₃^-, and SO₃^-. However, they have a higher density in areas with more significant enrichment in iron oxides that are traced by different Fe-bearing anions like FeO₂^-. The distribution of the organic and inorganic negative ions, which we suggest, resulted from the preservation of at least three microbial consortia (PO₄^--, and NO₂^--/NO₃^--mineralizers PO₄-lipid bearing microstructures), would have resulted from different metabolic and preservation pathways.

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

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.

Kidney Lipidomics by Mass Spectrometry Imaging: A Focus on the Glomerulus

Lipid disorders have been associated with glomerulopathies, a distinct type of renal pathologies, such as nephrotic syndrome. Global analyses targeting kidney lipids in this pathophysiologic context have been extensively performed, but most often regardless of the architectural and functional complexity of the kidney. The new developments in mass spectrometry imaging technologies have opened a promising field in localized lipidomic studies focused on this organ. In this article, we revisit the main works having employed the Matrix Assisted Laser Desorption Ionization Time of Flight (MALDI-TOF) technology, and the few reports on the use of TOF-Secondary Ion Mass Spectrometry (TOF-SIMS). We also present a first analysis of mouse kidney cortex sections by cluster TOF-SIMS. The latter represents a good option for high resolution lipid imaging when frozen unfixed histological samples are available. The advantages and drawbacks of this developing field are discussed.

Extreme (13)C depletion of carbonates formed during oxidation of biogenic methane in fractured granite

Precipitation of exceptionally ¹³C-depleted authigenic carbonate is a result of, and thus a tracer for, sulphate-dependent anaerobic methane oxidation, particularly in marine sediments. Although these carbonates typically are less depleted in ¹³C than in the source methane, because of incorporation of C also from other sources, they are far more depleted in ¹³C (δ¹³C as light as −69‰ V-PDB) than in carbonates formed where no methane is involved. Here we show that oxidation of biogenic methane in carbon-poor deep groundwater in fractured granitoid rocks has resulted in fracture-wall precipitation of the most extremely ¹³C-depleted carbonates ever reported, δ¹³C down to −125‰ V-PDB. A microbial consortium of sulphate reducers and methane oxidizers has been involved, as revealed by biomarker signatures in the carbonates and S-isotope compositions of co-genetic sulphide. Methane formed at shallow depths has been oxidized at several hundred metres depth at the transition to a deep-seated sulphate-rich saline water. This process is so far an unrecognized terrestrial sink of methane.

Precipitation of ¹³C-depleted authigenic carbonate is a tracer of sulphate-dependent anaerobic methane oxidation, particularly in marine sediments. Here, the authors present extremely ¹³C-depleted carbonates from deep granitoid rocks suggesting the presence of microbial sulphate reducers and methane oxidisers.

ToF-SIMS of tissues: "lessons learned" from mice and women

The ability to image cells and tissues with chemical and molecular specificity could greatly expand our understanding of biological processes. The subcellular resolution mass spectral imaging capability of time of flight secondary ion mass spectrometry (ToF-SIMS) has the potential to acquire chemically detailed images. However, the complexities of biological systems combined with the sensitivity of ToF-SIMS require careful planning of experimental methods. Tissue sample preparation methods of formalin fixation followed by paraffin embedding (FFPE) and OCT embedding are compared. Results show that the FFPE can potentially be used as a tissue sample preparation protocol for ToF-SIMS analysis if a cluster ion pre-sputter is used prior to analysis and if nonlipid related tissue features are the features of interest. In contrast, embedding tissue in OCT minimizes contamination and maintains lipid signals. Various data acquisition methodologies and analysis options are discussed and compared using mouse breast and diaphragm muscle tissue. Methodologies for acquiring ToF-SIMS 2D images are highlighted along with applications of multivariate analysis to better identify specific features in a tissue sections when compared to H&E images of serial sections. Identification of tissue features is necessary for researchers to visualize a molecular map that correlates with specific biological features or functions. Finally, lessons learned from sample preparation, data acquisition, and data analysis methods developed using mouse models are applied to a preliminary analysis of human breast tumor tissue sections.

Characterization of freeze-fractured epithelial plasma membranes on nanometer scale with ToF-SIMS

Time-of-flight secondary ion mass spectrometry (ToF-SIMS) was used to characterize the freeze-fracturing process of human epithelial PANC-1 and UROtsa cells. For this purpose, phosphatidylcholine, sphingomyelin, phosphatidylethanolamine, and phosphatidylserine standard samples were investigated to find specific signals with both high specificity and signal intensity. The results were used to investigate single cells of subconfluent cell layers prepared with a special silicon wafer sandwich preparation technique. This freeze-fracturing technique strips cell membranes off the cells, isolating them on opposing silicon wafer substrates. Criteria were found for defining regions with stripped off cell membranes and, on the opposing wafer, complementary regions with the remaining cells. Measured ethanolamine/choline and serine/choline ratios in these regions clearly showed that in the freeze-fracturing process, the lipid bilayer of the plasma membrane is split along its central zone. Accordingly, only the outer lipid monolayer is stripped off the cell, while the inner lipid monolayer remains attached to the cell on the opposing wafer, thus allowing detailed analysis of a single lipid monolayer. Furthermore, it could be shown that using different washing procedures did not influence the transmembrane lipid distribution. Under optimized preparation conditions, it became feasible to detect lipids with a lateral resolution of approximately 100 nm. The data indicate that ToF-SIMS would be a very useful technique to study with very high lateral resolution changes in lipid composition caused, for example, by lipid storage diseases or pharmaceuticals that interfere with the lipid metabolism.

Applicability of ToF-SIMS for monitoring compositional changes in bone in a long-term animal model

Time-of-flight secondary ion mass spectrometry (ToF-SIMS) is a well-established technique in material sciences but has not yet been widely explored for implementation in life sciences. Here, we demonstrate the applicability and advantages of ToF-SIMS analysis for the study of minerals and biomolecules in osseous tissue. The locally resolved analysis of fragment ions deriving from the sample surface enables imaging and differentiation of bone tissue and facilitates histology on non-stained cross sections. In a rat model, bilateral ovariectomy combined with either a multi-deficiency diet or steroid treatment was carried out to create osteoporotic conditions. We focused our study on the Ca content of the mineralized tissue and monitored its decline. Calcium mass images of cross sections show the progressive degenerative changes in the bone. We observed a decreased Ca concentration in the edge region of the trabeculae and a decline in the Ca/P ratio. Additionally, we focused on the non-mineralized matrix and identified fragment ions that are characteristic for the collagen matrix. We observed trabeculae with wide ranges of non-mineralized collagen for the diet group owing to an impaired mineralization process. Here, the advantage of coeval monitoring of collagen and minerals indicated an osteomalacic model rather than an osteoporotic one.

Time-of-flight secondary ion mass spectrometry-based molecular distribution distinguishing healthy and osteoarthritic human cartilage

Osteoarthritis (OA) is a pathology that ultimately causes joint destruction. The cartilage is one of the principal affected tissues. Alterations in the lipid mediators and an imbalance in the metabolism of cells that form the cartilage (chondrocytes) have been described as contributors to the OA development. In this study, we have studied the distribution of lipids and chemical elements in healthy and OA human cartilage. Time of flight-secondary ion mass spectrometry (TOF-SIMS) allows us to study the spatial distribution of molecules at a high resolution on a tissue section. TOF-SIMS revealed a specific peak profile that distinguishes healthy from OA cartilages. The spatial distribution of cholesterol-related peaks exhibited a remarkable difference between healthy and OA cartilages. A distinctive colocalization of cholesterol and other lipids in the superficial area of the cartilage was found. A higher intensity of oleic acid and other fatty acids in the OA cartilages exhibited a similar localization. On the other hand, CN(-) was observed with a higher intensity in the healthy samples. Finally, we observed an accumulation of calcium and phosphate ions exclusively in areas surrounding the chondrocyte in OA tissues. To our knowledge, this is the first time that TOF-SIMS revealed combined changes in the molecular distribution in the OA human cartilage.

Ancient microbial activity recorded in fracture fillings from granitic rocks (Äspö Hard Rock Laboratory, Sweden)

Fracture minerals within the 1.8-Ga-old Äspö Diorite (Sweden) were investigated for fossil traces of subterranean microbial activity. To track the potential organic and inorganic biosignatures, an approach combining complementary analytical techniques of high lateral resolution was applied to drill core material obtained at -450 m depth in the Äspö Hard Rock Laboratory. This approach included polarization microscopy, time-of-flight secondary ion mass spectrometry (ToF-SIMS), confocal Raman microscopy, electron microprobe (EMP) and laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS). The fracture mineral succession, consisting of fluorite and low-temperature calcite, showed a thin (20-100 μm), dark amorphous layer lining the boundary between the two phases. Microscopic investigations of the amorphous layer revealed corrosion marks and, in places, branched tubular structures within the fluorite. Geochemical analysis showed significant accumulations of Si, Al, Mg, Fe and the light rare earth elements (REE) in the amorphous layer. In the same area, ToF-SIMS imaging revealed abundant, partly functionalized organic moieties, for example, C(x)H(y)⁺, C(x)H(y)N⁺, C(x)H(y)O⁺. The presence of such functionalized organic compounds was corroborated by Raman imaging showing bands characteristic of C-C, C-N and C-O bonds. According to its organic nature and the abundance of relatively unstable N- and O- heterocompounds, the organic-rich amorphous layer is interpreted to represent the remains of a microbial biofilm that established much later than the initial cooling of the Precambrian host rock. Indeed, δ¹³C, δ¹⁸O and ⁸⁷Sr/⁸⁶Sr isotope data of the fracture minerals and the host rock point to an association with a fracture reactivation event in the most recent geological past.

Detecting the presence of denatured human serum albumin in an adsorbed protein monolayer using TOF-SIMS

We demonstrate the application of time-of-flight secondary ion mass spectrometry (TOF-SIMS) in conjunction with multivariate statistics to differentiate trace levels of denatured proteins in adsorbed monolayers; specifically, human serum albumin (HSA) on oxidized silicon substrates. Subtle differences in protein conformation due to thermal denaturation of HSA, unable to be determined by dynamic light scattering nor circular dichroism, were differentiated by TOF-SIMS. The fragmentation pattern is highly sensitive to protein conformation, allowing assessment of relative amounts of proteins in mixtures and quantifying amounts of denatured protein in a sample. Discussion is presented on ascribing orientation and conformational differences between samples based upon TOF-SIMS spectra. This has implications for detecting denatured protein in biotechnology and medical applications.

Lipid mapping of colonic mucosa by cluster TOF-SIMS imaging and multivariate analysis in cftr knockout mice

The cftr knockout mouse model of cystic fibrosis (CF) shows intestinal obstruction; malabsorption and inflammation; and a fatty acid imbalance in intestinal mucosa. We performed a lipid mapping of colon sections from CF and control (WT) mice by cluster time of flight secondary-ion mass spectrometry (TOF-SIMS) imaging to localize lipid alterations. Data were processed either manually or by multivariate statistical methods. TOF-SIMS analysis showed a particular localization for cholesteryl sulfate at the epithelial border, C16:1 fatty acid in Lieberkühn glands, and C18:0 fatty acid in lamina propria and submucosa. Significant increases in vitamin E (vE) and C16:0 fatty acid in the epithelial border of CF colon were detected. Principal component analysis (PCA) and partitioning clustering allowed us to characterize different structural regions of colonic mucosa according to variations in C14:0, C16:0, C16:1, C18:0, C18:1, C18:2, C20:3, C20:4, and C22:6 fatty acids; phosphatidylethanolamine, phosphatidylcholine, and phosphatidylinositol glycerolipids; cholesterol; vitamin E; and cholesteryl sulfate. PCA on spectra from Lieberkühn glands led to separation of CF and WT individuals. This study shows for the first time the spatial distribution of lipids in colonic mucosa and suggests TOF-SIMS plus multivariate analyses as a powerful tool to investigate disease-related tissue spatial lipid signatures.