Geobiology最新文献

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.

Upper Messinian carbonates recently recorded in the Salento Peninsula (southern Italy, central Mediterranean) contain microbial facies, including textures never previously described in the Late Miocene of the Mediterranean. This study focuses on the geometry and internal fabrics of a 3 × 28 m build-up of coalescent dendrolite and thrombolite, to examine its formation and the possible microbes involved, and to reconstruct its growth dynamics and related palaeoenvironmental conditions. Salento dendrolites have centimetric dendritic growth forms with a microlaminated, originally aragonitic, microstructure. The thrombolites, in contrast, are characterized by larger mesoclots with arborescent, anastomose growth patterns and a distinctive microfabric of small, originally calcitic, spheroids with a sparry nucleus surrounded by acicular crystals. Bio-geochemical analyses (UV epifluorescence, micro-Raman spectroscopy and SEM-EDS) reveal the presence of organic matter intimately associated with both dendrolite and thrombolite textures, supporting a biotic origin. The sedimentary context and microfabrics suggest that cyanobacteria may have played a major role in the formation of these structures, together with heterotrophic microbes, mainly sulfate-reducing bacteria, in the dendrolite. Build-up geometries, stratigraphic setting, and analysis of the associated sediment suggest that the dendrolite-thrombolite framework developed in a small, shallow-water lagoon, under moderate to high energy, variable salinity, and possibly high sedimentation rate. Salento dendrolite-thrombolite build-up appears to be the only known example of large microbial bioconstruction made by microlaminated dendrolites.

Microscopic tubules and filaments composed of iron minerals occur in various rock types of all ages. Although typically lacking carbonaceous matter, many are reasonably interpreted as the remains of filamentous microorganisms coated with crystalline iron oxyhydroxides. Iron-oxidizing bacteria (IOB) acquire such a coating naturally during life. However, recent debates about purported microfossils have highlighted the potential for self-organized nonbiological mineral growth (particularly in chemical gardens) to form compositionally and morphologically similar tubules. How can biogenic and abiogenic iron-mineral tubules be differentiated? Here, we use optical and electron microscopy and Mössbauer spectroscopy to compare the composition, microtexture, and morphology of ferruginous chemical gardens and iron-mineralized sheaths of bacteria in the genus Leptothrix. Despite broad morphological similarity, we find that Leptothrix exhibits a narrower range of filament diameters and lower filament tortuosity than chemical gardens. Chemical gardens produced from a ferrous salt also tend to incorporate Fe²⁺ whereas Leptothrix sheaths predominantly do not. Finally, the oxyhydroxides formed in Leptothrix sheaths tend to be smoother and denser on the inward-facing side, rougher and sparser on the outward side, whereas for chemical garden tubules the reverse is true. Some of these differences show promise for the diagnosis of natural samples.

Silicification of microfossils is an important taphonomic process that provides a record of microbial life across a range of environments throughout Earth history. However, questions remain regarding the mechanism(s) by which silica precipitated and preserved delicate organic material and detailed cellular morphologies. Constraining the different mechanisms of silica precipitation and identifying the common factors that allow for microfossil preservation is the key to understanding ancient microbial communities and fossil-preserving mechanisms. Here, we use synchrotron ptychographic X-ray computed tomography (PXCT) as a novel technique to analyze microfossils from the Cretaceous Barra Velha Formation and better characterize their diverse morphologies and preservation styles. Through this technique, we generate 2D and 3D reconstructions that illustrate the microfossils and silica-organic textures at nanometer resolution. At this resolution, we identify previously uncharacterized silica textures and organic-silica relationships that help us relate findings from modern silicifying environments and experimental work to the fossil record. Additionally, we identify primary morphological differences among the microfossils as well as preservational variability that may have been driven by physiological and/or biochemical differences between the different organisms that inhabited the Cretaceous pre-salt basin. These findings help us to better characterize the diversity and complexity of the microbiota in this ancient basin as well as taphonomic processes and biases that may have driven microfossil preservation in this and other silicifying environments throughout Earth history.

Shallow-marine environments are thought to have been pivotal to the spreading, perhaps even the origin, of early life on Earth. The shallow-marine Archean sedimentary record of early life, however, is biased towards carbonates; nearshore siliciclastic environments have not received proportional attention. Here we describe densely laminated, silicified and dolomitized fossil calcareous mounds in tidal-facies sandstones of the Archean Moodies Group (ca. 3.22 Ga) in the Barberton Greenstone Belt, Eswatini. They vary between (1) cm- to dm-scale, isolated, club- to pedestal-shaped, nodular mounds on top of and within the conduits of fluid-escape structures, and (2) mm- to cm-scale, undulatory and wavily laminated structures, interbedded with well-bedded silt- and sandstones. Geochemical indicators of a possible biogenic origin were largely obliterated by local hydrothermal alteration and regional lower-greenschist-facies metamorphism: In situ SIMS δ¹³C_carb isotope analyses from several traverses across the best-preserved laminae of a mound and δ³⁴S_VCDT values from diagenetic rims of nearby detrital pyrite grains yield ambiguous isotopic evidence about biologic processing; TOC of putative laminae is too low to measure δ¹³C_org, and Raman spectroscopy of finely dispersed carbonaceous particles and of kerogenous laminae indicate mean maximum metamorphic temperature of ca. 500°C. Textural and regional evidence, however, suggests that the carbonate laminae represent metabolic products of microbial communities that took advantage of sand volcanoes from which nutrient-rich fluids erupted episodically. We base this inference on the habitable depositional setting on a wave- or current-swept photic-zone tidal platform, the stromatolitic morphologies in two and three dimensions, the occurrence of in-situ kerogen, the carbonate mineralogy, and the presence of comparable mound structures elsewhere in the Moodies Group. Although the metabolic strategies utilized by the microorganisms remain unknown, this occurrence places a novel ecologic niche in the Paleoarchean microbial colonization of coastal regions.