Geobiology最新文献

The widespread, stepwise oxygenation of Earth's atmosphere in the Precambrian led to a transformation of the global carbon (C) and nitrogen (N) cycles. While the temporal evolution of these nutrient cycles has been studied extensively in marine environments, lacustrine environments are understudied. This study first examines how water column oxygen conditions impact sedimentary carbon (δ¹³C_org) and nitrogen (δ¹⁵N) isotope signals in modern lakes. Subsequently, we use these patterns to interpret past changes in the geological record of lacustrine δ¹⁵N during atmospheric oxygenation. The compiled modern lake sediment dataset reveals average (± standard deviation) δ¹⁵N values of +2.9‰ ± 3.2‰ and δ¹³C_org values of −25.99‰ ± 3.77‰, as well as thresholds in δ¹³C_org for oxic versus anoxic conditions, and in δ¹⁵N for circumneutral versus alkaline pH conditions. In contrast to the stepwise oxygenation of the atmosphere, the lacustrine δ¹⁵N record does not directly reflect major oxygenation events, but instead increases gradually in response to the evolution of new aerobic N metabolic pathways, with a notable shift in the Phanerozoic. While we found that intrasite variability at a single modern anoxic lake is expected to remain within ~5‰ for δ¹⁵N, alkaline lakes in both the ancient and modern deviate from this range. We observe δ¹⁵N > +10‰ for approximately half of total ancient alkaline lake sediments and some modern lake sediments. This is consistent with previous applications of enriched δ¹⁵N as a basicity proxy. The lacustrine δ¹⁵N record aligns well with the evolution of microbial metabolic pathways in addition to providing information pertaining to environmental conditions of the depositional setting.

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.

Large-scale geological processes shape microbial habitats and drive the evolution of life on Earth. During the Oligocene, convergence between Africa and Europe led to the opening of the Western Mediterranean Basin, a deep-ocean system characterized by fluid venting, oxygen depletion, and the absence of benthic fauna. In this extreme, inhospitable seafloor environment, fusiform objects known as Tubotomaculum formed, whose origin has long remained controversial. We show that these enigmatic mineralizations consist of nanosized, poorly crystalline, phosphorus-rich Mn-Fe compounds produced through microbial mediation. They preserve carbonaceous material together with morphological, chemical, and mineralogical biosignatures, including high Mn oxidation state (3.9 ± 0.15), cell envelopes, extracellular polymeric substances (EPS), cell-EPS partitioning of redox-sensitive Mn and Fe, cluster-assembled microbial cells, microbialite-like and branching structures, and channel networks for nutrient transport. Geochemical signatures indicate precipitation under suboxic to anoxic, non-sulfidic (post-oxic) conditions from mixed seawater–hydrothermal fluids, with exposure on the seafloor prior to burial. The fusiform architecture of these self-organized microbial populations suggests shaping by nutrient-rich bottom currents associated with venting activity. This study provides a detailed glimpse into initial benthic colonization of the nascent Western Mediterranean Basin and establishes Tubotomaculum as a model for investigating biomineralization and microbial adaptation in extreme environments, with implications for the search for life beyond Earth.

The discovery of cholestane in animal fossils from the Ediacaran (571–541 million years ago) has generated much excitement, but it is not the only interesting biomarker recovered. Coprostane, a geologically stable form of coprostanol, has also been found in Ediacaran rocks. This is surprising, since coprostanol is typically used in modern settings as an environmental biomarker for humans and other mammals, who produce the compound with help from bacteria in their gut. The prevailing hypothesis is that an abundance of coprostane in some Ediacaran fossils—particularly Dickinsonia—represents the degradation of the organism's cholesterol by bacteria in the microbial mat, comparable to what is seen in modern vertebrate corpses as they decompose. However, this hypothesis assumes coprostanol-producing bacteria were absent in the guts of Ediacaran organisms, and to date no one has tested whether such bacteria exist in modern invertebrates. In this study, we assembled 115 metagenomes to look for evidence of coprostanol-producing enzymes in invertebrate microbiomes. Ultimately, we did not find any evidence for the enzyme in any invertebrate microbiomes, supporting the hypothesis that coprostane is not a gut biomarker for Ediacaran animals. However, a reassessment of coprostane/cholestane ratios shows Dickinsonia was unique in coprostanol enrichment, with ratio levels comparable to waste polluted marine waters and modern vertebrate feces. While we cannot rule out the possibility of contamination, we prefer a novel interpretation of the coprostane signature in dickinsoniomorph fossils, where the elevated level of coprostanol comes from digestion of the microbial mat and concentration of the biologically inert compound. If correct, the elevated coprostanol signal provides new insights into the feeding strategy of these enigmatic animals.

Microbial processes in marine sediments drive changes in redox conditions, ultimately controlling the cycling of elements between the dissolved and solid phases. The microbial community driving these cycles depends on trace metals, but it can also be inhibited at elevated metal concentrations. During diagenesis, many trace elements are released from iron (Fe) and manganese (Mn) (oxyhydr)oxides, potentially affecting microbial metabolisms. Here we present results from geochemical and microbiological analyses of samples collected during R/V Polarstern Expedition PS119 to the East Scotia Ridge. The sediments are dominantly diatomaceous ooze with high contents of reactive Fe and Mn (oxyhydr)oxides and increased trace metal contents from nearby hydrothermal vents. Two multi-corer cores were sampled immediately after collection at five specific sediment depths (three splits each), sealed anaerobically in incubation bags, and analyzed in 4-month intervals post collection for major, minor, and trace metals and 16S rRNA gene sequencing. By isolating the sediment from overlying seawater during the incubation process, we simulated the in situ diagenetic processes of Fe and Mn oxide reduction. Our data show that Mn and trace metals, especially Mo, Ni, Tl, and Cu, are mobilized during early diagenesis. Analysis of 16S rRNA genes revealed shifts in the microbial community from Nitrososphaera and Nanoarchaeia to Bacteroidia and Bacilli alongside a marked decrease in richness, Pielou's evenness, and Shannon alpha diversity during the eight-month incubations. We statistically correlate the microbial community shift with the changes in porewater trace metal concentrations, revealing that Mn, Co, Ag, and Tl are driving the microbial compositions in these samples. In this organic matter limited but Fe and Mn (oxyhydr)oxide rich system, we simulate deeper diagenesis to peer into the role of changing Fe, Mn, and trace metal cycles and highlight the role of Fe and Mn (oxyhdyr)oxides as shuttles for trace metals to the deep biosphere. By identifying key metals that are diagenetically cycled and affect the in situ microbial community, we reveal feedbacks between metals and microbial communities that play important roles in biogeochemical cycles on Earth, provide insight into the origin and potential evolution of metabolic pathways in the deep biosphere, and offer clues that may aid in our understanding of Earth's history and potentially beyond.

In Arctic polar deserts, rocks can be extensively colonized by phototrophic hypolithic communities that exploit periglacial sorting processes to grow beneath opaque rocks. These communities are distinguished by green bands that are distinctly and abruptly separated from the black-pigmented communities on the rock surface (epiliths). We used 16S and 18S rDNA culture-independent methods to address the hypothesis that the two communities are different. Although both communities were dominated by cyanobacterial species (Chroococcidiopsis and Nostoc spp.), we found that the hypolithic and epilithic habitats host distinct microbial communities. We found that eukaryotic hypolithic and epilithic communities were statistically similar but that the hypolithic habitats contained tardigrade DNA, showing that the more clement subsurface habitat supports animal life in contrast to the surface of the rocks. These results reveal the distinctive communities and sharp demarcations that can develop across small spatial scales in the Earth's rocky extreme environments.

Interface environments between extreme and neutrophilic conditions are often hotspots of metabolic activity and taxonomic diversity. In serpentinizing systems, the mixing of high pH fluids with meteoric water, and/or the exposure of these fluids to the atmosphere can create interface environments with distinct but related metabolic activities and species. Investigating these systems can provide insights into the factors that stimulate microbial growth, and/or what attributes may be limiting microbial physiologies in native serpentinized fluids. To this aim, changes in geochemistry and microbial communities were investigated for different interface environments at Ney Springs—a marine-like terrestrial serpentinization system where the main serpentinized fluids have been well characterized geochemically and microbially. We found that reduced sulfur species from Ney Springs had large impacts on the community changes observed at interface environments. Oxygen availability at outflow environments resulted in a relative increase in the taxa observed that were capable of sulfur oxidation, and in some cases light-driven sulfur oxidation. A combination of cultivation work and metagenomics suggests these groups seem to predominantly target sulfur intermediates like polysulfide, elemental sulfur, and thiosulfate as electron donors, which are present and abundant to various degrees throughout the Ney system. Fluid mixing with meteoric water results in more neutral pH systems which in turn select for different sulfur-oxidizing taxa. Specifically, we see blooms of taxa that are not typically observed in the primary Ney fluids, such as Halothiobacillus in zones where fluids mix underground with meteoric water (~pH 10) or the introduction of Thiothrix into the nearby creek as fluids enter at the surface (~pH 8). This work points to the potential importance of oxidants for stimulating microbial respiration at Ney Springs, and the observation that these serpentinized fluids act as an important source of reduced sulfur, supporting diverse taxa around the Ney Springs system.

Carbonaceous particles that concentrate arsenic in microbialites as old as ~3.5 Ga are similar to As-rich organic globules in modern microbialites. The former particles have been interpreted as tracers of As cycling by early microbial metabolisms. However, it is unclear if arsenic accumulation is a consequence of biological activity or passive postmortem binding of arsenic by organic matter during diagenesis in volcanically influenced, As-rich environments. Here, we address this uncertainty by evaluating the concentrations, speciation, and detectability of As in active or heat-killed biofilms formed by cyanobacteria or anoxygenic photosynthetic microbes exposed to environmentally relevant concentrations of As(III) or As(V) (50 μM to 3 mM). The genomes or metagenomes of these biofilms contain genes involved in detoxifying or energy-yielding As metabolisms. Biomass accumulates As from the solution in a concentration-dependent manner and with a preference for oxidized As(V) over As(III). Autoclaved biomass accumulates As even more strongly than active biomass, likely because living biofilms actively detoxify As. Active biofilms oxidize and reduce As and accumulate both As(III) and As(V), whereas a small fraction of As(V) can be reduced in inactive biofilms that bind As during diagenesis. Arsenic enrichments in the biomass are detectable by X-ray based spectroscopy techniques (XRF, EPMA-WDS) that are commonly used to analyze geological materials. These findings enable the reconstruction of past active and passive interactions of microbial biomass with arsenic in fossilized microbial biofilms and microbialites from the early Earth.

Changes in δ¹³C value of bulk sedimentary organic matter (OM) throughout Earth's history are thought to reflect carbon cycle perturbations, but as sedimentary OM may derive from multiple sources, it could also record other processes. We measured δ¹³C of microscale components of shale OM using nano-EA-IRMS to investigate drivers of large-magnitude carbon isotope excursions (CIE) in the late Tonian Chuar Group, USA. Components included organic-walled microfossils, kerogen, graphite, and macerate size-fractions. Microfossils δ¹³C has a broad range within samples, but average values vary little throughout stratigraphy and are decoupled from bulk δ¹³C_org, showing that these positive CIEs are not driven by secular changes in the carbon cycle. Instead, our fine-scale approach identified enriched components that can account for the CIE: exogenous clasts of kerogen and graphite, a finer macerate fraction, and abundant Eosynechococcus—a bloom-forming phytoplankter. The presence of these ¹³C-enriched particles indicates that the positive CIE signals were driven by a combination of allochthonous input/enhanced productivity, as well as thermal alteration. Fine-scale measurements can tease apart contributors to bulk δ¹³C_org records and offer insights into the Proterozoic carbon cycle.