IntroductionUnderstanding how environmental conditions influence early decay processes remains a central challenge in taphonomy, particularly regarding the relative roles of aerobic and anaerobic regimes. Because microorganisms drive soft-tissue decomposition, this study examines how contrasting oxygen conditions affect microbial community structure, metabolic potential, and the minerals formed during fish decay.MethodsFish decay experiments were conducted under controlled aerobic and anaerobic conditions. O2, pH, and H2S were monitored using microprobe measurements, and water chemistry was characterized through major ion analyses. Microbial community composition was assessed using 16S rRNA gene sequencing, and from this, metabolic potential was predicted using PICRUSt2. SEM-EDS and XRD were used to identify the precipitate minerals.ResultsOxygen availability resulted in markedly distinct microbial assemblages and decay trajectories. Anaerobic conditions were associated with lower pH and elevated hydrogen sulfide concentrations, whereas aerobic conditions maintained higher pH. Predicted metabolic functions were broadly conserved between treatments. Aerobic decay was characterized by higher DIC, lower DOC, and enrichment of genes linked to complete organic matter oxidation, including β-oxidation pathways. In contrast, anaerobic decay exhibited higher DOC, lower DIC, and increased abundances of genes associated with fermentation and carbohydrate metabolism, consistent with incomplete degradation. Mineralogical analyses identified magnesium phosphates and sodium sulfates in both treatments.DiscussionEnvironmental oxygen availability strongly controls microbial metabolism and decay dynamics. Aerobic microbial communities promoted more extensive tissue decomposition, whereas anaerobic communities favored slower, fermentation-dominated decay. The early mineral phases identified in both treatments likely represent precursors to diagenetic minerals and provide new insights into mineralization pathways that may contribute to exceptional fossil preservation.

The combined preservation of soft tissues, biomineralized structures, and molecular biomarkers is rare; yet, such finds offer key insights into ancient physiology, ecology, and taphonomy. We integrate organic geochemical analyses with high-resolution micro-mineral imaging of a three-dimensionally preserved Cretaceous pterosaur wing phalanx from Brazil to reveal steroid biomarkers and multi-stage mineralization pathways underlying its preservation. A localized redox shift toward acidic, oxidative conditions around the carcass played a central role. Microbial decay generated acidity that promoted early phosphate mineralization (fluorapatite), stabilizing tissues. This fluorapatite is associated with barite and celestite indicating a microenvironment with enhanced microbial sulfate production. Following phosphatization, three phases of carbonate mineralization encapsulated organic compounds, protecting them from diagenetic alteration. Molecular analyses report steroids in pterosaurs, with δ13C values indicating a fish- and cephalopod-based diet, highlighting early mineralization as key to long-term biomolecule preservation.

AbstractAmbergris, a rare and valuable by-product of sperm whales, is prized for its distinctive fragrance and may offer insights into whale metabolism and diet. However, identifying ambergris, particularly when recovered as jetsam, is challenging owing to sample heterogeneity and the effects of environmental weathering. Traditional identification techniques, including visual inspection, odour analysis and chemical profiling (e.g. gas chromatography–mass spectrometry and Fourier transform infrared spectroscopy), can confirm chemical composition, but cannot determine biological origin. DNA metabarcoding presents a complementary approach for verifying ambergris by detecting species-specific DNA, such as DNA from Physeter macrocephalus, in environmental samples. This study assessed the effectiveness of DNA metabarcoding alongside chemical profiling by analysing curated ambergris specimens from the Western Australian Museum. DNA concentrations varied across samples, with several yielding P. macrocephalus DNA, confirming their origin. However, some samples lacked detectable DNA, probably owing to degradation or possible misidentification. Chemical analysis identified key biomarkers, such as ambrein, in most samples, supporting their classification as ambergris. The findings highlight the value of combining DNA metabarcoding with traditional chemical methods to improve the reliability of ambergris identification.

Exceptional preservation of ichthyosaur fossils in the Toarcian (similar to 183-180 Ma) Posidonia Shale of southwest Germany was previously attributed to sustained anoxia or euxinic conditions that excluded aerobic scavengers and promoted early diagenetic mineralization. Here we show a partial ichthyosaur specimen within a carbonate concretion that contained three distinct biogeochemical compartments - the host shale, concretion matrix, and fossil bones - reflecting contrasting redox conditions during decomposition and early diagenesis. Under euxinic conditions, sulfate-reducing bacteria in the sediment generated isotopically light bicarbonate, which precipitated as the micritic calcite of the concretion. The bones uniquely preserve highly degraded, heavy carbon-enriched organic matter and heavy sulfur-enriched barite infilling the marrow cavities. We hypothesize this barite was produced by sulfur-oxidizing bacteria that anaerobically metabolized sulfide to sulfate. These results demonstrate that coupled microbial redox processes and carbonate cementation occurred within microenvironments associated with ichthyosaur bodies that enabled their three-dimensional preservation during the Early Jurassic.

Many antibiotics originate from soil-inhabiting Actinobacteria, especially from the diverse genus Streptomyces. However, the emergence of antibiotic resistance poses a significant global challenge to treating infectious diseases. Therefore, the search for Actinobacteria, particularly from less-explored environments, as potential sources of novel antimicrobial compounds, is of great importance. This study sampled various biofilms growing on cave structures within Deer Cave and Lagang Cave, located in the UNESCO World Heritage Site of Gunung Mulu National Park (GMNP; Sarawak, Malaysia). From this relatively untapped niche in caves, we identified and screened actinobacterial isolates for their potential antimicrobial properties against drug-resistant Pseudomonas aeruginosa and Staphylococcus aureus strains. Of 48 isolates, 24 showed inhibition of one or both drug-resistant strains in the antimicrobial assays conducted using cross-streak and agar well diffusion methods. The ethyl acetate extracts containing potential secondary metabolites demonstrated effective inhibition, particularly against the drug-resistant Gram-negative P. aeruginosa. In contrast, the supernatants obtained from aerobic cultivation exhibited comparatively better activity against Gram-positive S. aureus strains. 16S rRNA gene sequencing analysis of the isolates revealed that all except one isolate belonged to the genus Streptomyces. Maximum likelihood bootstrap tree analysis strongly supported the correct clustering of the Streptomyces isolates with well-known bioactive compound producers, such as S. gardneri, S. laurentii, and S. zaomyceticus. Notably, Deer Cave Isolate D3-12 exhibited inhibitory activity against both drug-resistant strains and, therefore, represents a promising candidate for future studies involving the characterization of its bioactive compounds. The remaining actinobacterial isolate exhibited 100% sequence homology to soil-inhabiting Rhodococcus pedecola, known for its antibacterial properties. These findings suggest that the caves of GMNP harbor untapped ecological niches of diverse cave-dwelling Actinobacteria, which may serve as sources of antimicrobial compounds effective against emerging antibiotic-resistant pathogens.

A growing international demand for tea tree oil (TTO) has increased the need for methods to verify authenticity and origin. While several approaches exist to detect adulteration in commercial TTO, methods to determine geographic origin have not yet been established. In this study, gas chromatography isotope ratio mass spectrometry (GC-irMS) was used to conduct the first compound-specific isotope analysis of terpinen-4-ol and gamma-terpinene in authentic and oxidised Australian TTO from New South Wales (n = 13). Across authentic samples, the mean delta & sup1;& sup3;C values for gamma-terpinene and terpinen-4-ol were-30.4 +/- 0.50 parts per thousand and -31.3 +/- 0.37 parts per thousand respectvely. Oxidation increased delta & sup1;& sup3;C values for gamma-terpinene but did not affect terpinen-4-ol. Analysis of locally and internationally sourced commercial samples showed that these isotope values did not distinguish adulterated oils. Although some sample groupings suggested a possible relationship with growing region, broader international sampling is needed to evaluate provenance more reliably.

Short-term observations suggest that environmental changes affect the diversity and composition of soil fungi, significantly influencing forest resilience, plant diversity, and soil processes. However, time-series experiments should be supplemented with geobiological archives to capture the long-term effects of environmental changes on fungi-soil-plant interactions, particularly in undersampled, floristically diverse tropical forests. We recently conducted trnL-P6 amplicon sequencing to generate a sedimentary ancient DNA (sedaDNA) record of the regional catchment vegetation of the tropical waterbody Lake Towuti (Sulawesi, Indonesia), spanning over one million years (Myr) of the lake's developmental history. In this study, we performed 18SV9 amplicon sequencing to create a parallel paleofungal record to (a) infer the composition, origins, and functional guilds of paleofungal community members and (b) determine the extent to which downcore changes in fungal community composition reflect the late Pleistocene evolution of the Lake Towuti catchment. We identified at least 52 members of Ascomycota (predominantly Dothiodeomycetes, Eurotiomycetes, and Leotiomycetes) and 12 members of Basidiomycota (primarily Agaricales and Polyporales). Spearman correlation analysis of the relative changes in fungal community composition, geochemical parameters, and paleovegetation assemblages revealed that the overwhelming majority consisted of soil organic matter and wood-decaying saprobes, except for a necrotrophic phytopathogenic association between Mycosphaerellaceae (Cadophora) and wetland herbs (Alocasia) in more-than-1-Myr-old silts and peats deposited in a pre-lake landscape, dominated by small rivers, wetlands, and peat swamps. During the lacustrine stage, vegetation that used to grow on ultramafic catchment soils during extended periods of inferred drying showed associations with dark septate endophytes (Ploettnerulaceae and Didymellaceae) that can produce large quantities of siderophores to solubilize mineral-bound ferrous iron, releasing bioavailable ferrous iron needed for several processes in plants, including photosynthesis. Our study showed that sedaDNA metabarcoding paired with the analysis of geochemical parameters yielded plausible insights into fungal-plant-soil interactions, and inferred changes in the paleohydrology and catchment evolution of tropical Lake Towuti, spanning more than one Myr of deposition.

Sauropod dinosaurs were abundant and diverse across much of the globe throughout the Jurassic and Cretaceous periods and include the largest terrestrial animals of all time. Since the discovery of the first near-complete skeletons in the late 19th century, sauropods have been almost universally interpreted as herbivorous. However, our concept of their diet is based on indirect evidence and inference since no sauropod fossilized gut contents (cololites) are known. Here, we describe a cololite associated with a specimen of the sauropod Diamantinasaurus matildae from the mid-Cretaceous (∼101-94 Ma) Winton Formation of Queensland, Australia. The cololite is hosted within an indurated rock layer, localized to the abdominal region, and closely and consistently associated with a layer of mineralized skin. Conifer pinnules, angiosperm leaves, and seed-fern fruiting bodies are preserved within, as are chemical biomarkers consistent with gymnosperms and angiosperms. This Diamantinasaurus cololite provides the first direct, empirical evidence in sauropods of herbivory, demonstrating generalist feeding, low- to high-level browsing, and minimal oral processing of food. The longevity of the clade Sauropoda was underpinned by the persistence through time of generalist feeders like Diamantinasaurus that were capable of feeding at a range of heights on a variety of different plant species.

Paraloid (R) resins, particularly Paraloid (R) B-72, are widely used in palaeontological preparation to stabilise fossils. However, their presence may interfere with organic geochemical analyses. To evaluate this, standard biomarker extraction protocols were applied to pure Paraloid (R) B-72, to a fossil bone previously treated with the resin, and to commercial grade acetone commonly used as its solvent. The resin was mobilised by dichloromethane-containing solvent mixtures during extraction and fractionation. Despite this, saturated and aromatic biomarkers were successfully isolated since the polyacrylate resin is insoluble in non-polar solvents. Paraloid (R) B-72 predominately eluted into the aromatic and polar fractions, but did not significantly impact saturated biomarker profiles. Insoluble residues isolated from these fractions analysed by flash pyrolysis-gas chromatography-mass spectrometry revealed compounds mainly from the resin. Microwave assisted solvent extraction appears to effectively separate Paraloid (R) B-72 from fossils, as no resin-derived monomers were detected in the extracted fossil pyrolysate. This suggests that the insoluble organic fraction of resin-stabilised fossils can be reliably studied using biomarker techniques with minimal interference. Time-of-flight secondary ion mass spectrometry (ToF-SIMS) analysis produced abundant organic fragments from Paraloid (R) B-72, but mapping specific oxygen-bearing peaks associated with the resin may allow researchers to distinguish regions containing indigenous organics from those contaminated by the consolidant. These findings indicate that, with appropriate analytical approaches, both soluble and insoluble organic fractions of Paraloid (R)-treated fossils can yield valid biomarker data, enabling chemical analysis of specimens previously deemed unsuitable due to conservation treatments.

Molecular parameters based on the relative abundance of various sterane isomers contribute valuable information about sources and thermal history of organic-matter-rich sediments. However, this application is limited for 5 beta- and 5 alpha-steranes due to their co-elution on common gas chromatography (GC) columns: e.g., relative retention index of 5 beta 20R and 5 alpha 20S cholestanes on Agilent DB1 columns = 28.081 and 28.065, respectively. Selected ion monitoring (SIM) and tandem (MS/MS) mass spectral protocols were developed to improve the analytical resolution of these compounds, exploiting slight differences in mass fragmentation patterns. Protocols were optimised on a 1:1 mixture of authentic 5 alpha 20R and 5 beta 20R cholestane standards (5 alpha 20R in place of 5 alpha 20S). Parameters offering 5 alpha:5 beta selectivity (e.g., SIM: 149/151 Da; MRM: [149 -> 79]/[151 -> 79]) were tested on a suite of 5 alpha 20R:5 beta 20R standards and show an excellent correlation (R-2 > 0.99) with substrate composition. The capacity to quantify the relative contribution of co-eluting 5 alpha 20S and 5 beta 20R in more complex samples was tested by analyses of a crude oil (Blina-4, Canning Basin, Western Australia) known to have high abundances of C27-29 5 alpha 20S steranes (20S/[20S + 20R] approximate to 0.5) and spiked with 5 beta 20R cholestane. The relative proportions of 5 alpha 20S and 5 beta 20R were determined using 5 alpha 20R:5 beta 20R calibration curves with good consistency and accuracy. Values deviated from the target when either analyte was particularly dominant (>= 80 %), probably due to differences in ion density compared to the resolved standards. This issue may be improved with further method refinement and the true sterane deconvolution value offered by this approach will become apparent with further application to a diverse range of samples.

Organic analyses of past organisms enhance our understanding of Earth's evolutionary history, complementing the macrofossil record. Biomolecular remains are typically vulnerable to diagenetic mineralisation, but can persist in exceptional depositional settings such as Lagerstätten. Their preservation is usually linked to anoxic conditions that exclude aerobic degraders. However, we report intact skin tissue of the fossil fish Diplomystus dentatus from the Fossil Basin Lagerstätte (USA), preserved through phosphate permineralisation in an oxygen-enriched microenvironment. Notably, only the skin with scales retained tissue integrity, and this organic material was closely associated with fluorapatite absent from the surrounding matrix. Geochemical analyses revealed higher oxidation states in the skin than in vertebrae and bones, likely due to early degradation of the fatty acid-rich dermis. Redox-sensitive biomarkers and isotopic data (δ15N) indicated a less reducing environment in the skin region compared to bones and the eye, yet more reducing than the surrounding sediment. This localised oxygen enrichment fostered sulphide-oxidising bacteria, evidenced by mineral sulphates (barite) found only in the skin. Phosphatisation was likely driven by dermal breakdown and the release of H+, reducing alkalinity and enabling phosphate mineralisation over the carbonate system.

Diagenetically mineralized fossil tissues represent invaluable paleobiological evidence of past life. Lipid biomarkers may be identified alongside fossils, yet the relationship between localized, diagenetic mineral precipitation, and lipid preservation remains underexplored. Coprolites (fossilized feces) attract a unique diversity of early diagenetic minerals including carbonates and phosphates, within individual samples, mediating molecular preservation of soluble lipid biomarkers alongside exceptional morphological preservation. Analysis of a well-preserved coprolite from the Carboniferous (307 ± 0.1 Ma) Mazon Creek assemblage, USA via time of flight-secondary ion mass spectrometry (ToF-SIMS) spatial compound mapping demonstrated the association of 5α,14α,17α(H) 20R cholestane, a C27 dietary sterane, with iron carbonate (and some pyrite) rather than phosphate minerals. Furthermore, Raman spectroscopic fingerprinting of a suite of organic-rich fossils spanning a number of biological species and preserved across the Mazon Creek site and other depositional settings was utilized to explore whether the localized preservation of steroids in carbonate phases represents a lagerstätten-specific or generalizable pattern. Our spectroscopic analyses demonstrate a significant positive correlation between signatures of lipid biomarkers and carbonates rather than phosphates across all soft-part samples at the Mazon Creek site and throughout Phanerozoic time and space. Early diagenetic carbonate measurably immobilizes otherwise labile lipid biomarkers and shields them against diagenetic stressors. Localized preservation identifies carbonate phases as a preferential resource for lipid-based biological information and reveals organomineral associations as a new frontier in understanding the survival of molecules in deep time.

Studying past ecosystems from ancient environmental DNA preserved in lake sediments (sedaDNA) is a rapidly expanding field. This research has mainly involved Holocene sediments from lakes in cool climates, with little known about the suitability of sedaDNA to reconstruct substantially older ecosystems in the warm tropics. Here, we report the successful recovery of chloroplast trnL (UAA) sequences (trnL-P6 loop) from the sedimentary record of Lake Towuti (Sulawesi, Indonesia) to elucidate changes in regional tropical vegetation assemblages during the lake's Late Quaternary paleodepositional history. After the stringent removal of contaminants and sequence artifacts, taxonomic assignment of the remaining genuine trnL-P6 reads showed that native nitrogen-fixing legumes, C3 grasses, and shallow wetland vegetation (Alocasia) were most strongly associated with >1-million-year-old (>1 Ma) peats and silts (114-98.8 m composite depth; mcd), which were deposited in a landscape of active river channels, shallow lakes, and peat-swamps. A statistically significant shift toward partly submerged shoreline vegetation that was likely rooted in anoxic muddy soils (i.e., peatland forest trees and wetland C3 grasses (Oryzaceae) and nutrient-demanding aquatic herbs (presumably Oenanthe javanica)) occurred at 76 mcd (~0.8 Ma), ~0.2 Ma after the transition into a permanent lake. This wetland vegetation was most strongly associated with diatom ooze (46-37 mcd), thought to be deposited during maximum nutrient availability and primary productivity. Herbs (Brassicaceae), trees/shrubs (Fabaceae and Theaceae), and C3 grasses correlated with inorganic parameters, indicating increased drainage of ultramafic sediments and laterite soils from the lakes' catchment, particularly at times of inferred drying. Downcore variability in trnL-P6 from tropical forest trees (Toona), shady ground cover herbs (Zingiberaceae), and tree orchids (Luisia) most strongly correlated with sediments of a predominantly felsic signature considered to be originating from the catchment of the Loeha River draining into Lake Towuti during wetter climate conditions. However, the co-correlation with dry climate-adapted trees (i.e., Castanopsis or Lithocarpus) plus C4 grasses suggests that increased precipitation seasonality also contributed to the increased drainage of felsic Loeha River sediments. This multiproxy approach shows that despite elevated in situ temperatures, tropical lake sediments potentially comprise long-term archives of ancient environmental DNA for reconstructing ecosystems, which warrants further exploration.

The oil spill resulting from the grounding of the MV Wakashio on a reef off the coast of Mauritius in July 2020 was the world's first major spillage of Very Low Sulfur Fuel Oil (VLSFO) since the implementation of a Global Sulfur Cap from January 2020. In this study, we examine sediments collected in March 2023 from two Mauritius mangrove systems. Analyses by both gas chromatography-mass spectrometry and comprehensive two-dimensional gas chromatography confirmed, by comparison of molecular biomarkers, the presence of Wakashio VLSFO in one of the mangrove systems. The spilled oil had undergone extensive weathering resulting in substantial losses of toxic mono- and polycyclic aromatic compounds. Applying WebGNOME-ADIOS oil spill models to compare the fate of Wakashio VLSFO with traditional fuels suggests that more of the VLSFO would evaporate, naturally disperse, and undergo sedimentation compared to traditional fuels that were more likely to remain floating.

Exceptionally well-preserved fossil specimens in the Fossil Basin of the Green River Formation (GRF) have made it the subject of extensive paleontological study, but the organic molecular framework that evolved during a key paleoclimatic and fossil-bearing interval during the early Eocene is poorly understood. Whereas the organic geochemistry of the larger co-eval GRF basins has been extensively characterized, our molecular understanding of the fossil-bearing layers in the Fossil Basin and the drivers of the exceptional fossilization therein remain unresolved. To bridge this gap, sediments from the famous 18 ''-layer the fossiliferous horizon that is extensively quarried for exceptional soft-tissue fossils were sampled for organic and isotopic geochemical characterisation. The results show that the Fossil Basin sedimentary archive is geochemically distinct from other GRF basins, as exemplified by the absence of the classical biomarker beta-carotane and minimal evidence for the large green algal blooms that predominate in the other GRF lake basins. Photic zone euxinia (PZE), anoxia, and a freshwater cap enabled development of a productive and diverse ecosystem. Salinity and density stratification prevented vertical mixing of the water column and supported preservation of decaying carcasses. In contrast to other GRF basins, the small areal extent and ellipsoid shape of the Fossil Basin focussed terrestrial and freshwater inputs into the lake, resulting in ideal conditions for preservation of an exceptional fossil record.

Environmental contamination of aquatic systems by per- and polyfluoroalkyl substances (PFAS) has generated significant health concerns. Remediation of contaminated sites such as the fire-fighting emergency training grounds that use aqueous film-forming foams is a high priority. Phytoremediation may help play a part in removing PFAS from such contaminated waters. We investigated the potential of the water fern Azolla filiculoides, which is used for phytoremediation of a wide range of contaminants, to uptake seven common PFAS (perfluorobutanoic acid [PFBA], perfluorobutane sulfonic acid [PFBS], perfluoroheptanoic acid [PFHpA], perfluorohexanoic acid [PFHxA], perfluorohexane sulfonic acid [PFHxS], perfluorooctanoic acid [PFOA], and perfluoropentanoic acid [PFPeA]), during a 12-day exposure to environmentally relevant concentrations delivered as equimolar mixtures: low (∑PFAS = 0.0123 ± 1.89 μmol L-1), medium (∑PFAS = 0.123 ± 2.88 μmol L-1), and high (∑PFAS = 1.39 μmol L-1) treatments, equivalent to approximately 5, 50, and 500 µg L-1 total PFAS, respectively. The possible phytotoxic effects of PFAS were measured at 3-day intervals using chlorophyll a content, photosystem II efficiency (Fv/Fm), performance index, and specific growth rate. The PFAS concentrations in plant tissue and water were also measured every 3 days using ultra-high-performance liquid chromatography-tandem mass spectrometry. Treatments with PFAS did not lead to any detectable phytotoxic effects. All seven PFAS were detected in plant tissue, with the greatest uptake occurring during the first 6 days of exposure. After 12 days of exposure, a maximum bioconcentration factor was recorded for PFBA of 1.30 and a minimum of 0.192 for PFBS. Consequently, the application of Azolla spp. as a stand-alone system for phytoremediation of PFAS in aquatic environments is not sufficient to substantially reduce PFAS concentrations. Environ Toxicol Chem 2024;43:2157-2168. © 2024 The Author(s). Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC.