Oxic Environments Research Articles

The bacterial strains JAM1T and GP59 of the species Methylophaga nitratireducenticrescens differ in their expression profiles of denitrification genes in oxic and anoxic cultures

Background Strain JAM1T and strain GP59 of the methylotrophic, bacterial species Methylophaga nitratireducenticrescens were isolated from a microbial community of the biofilm that developed in a fluidized-bed, methanol-fed, marine denitrification system. Despite of their common origin, both strains showed distinct physiological characters towards the dynamics of nitrate (${\mathrm{NO}}_{3}^{-}$) reduction. Strain JAM1T can reduce ${\mathrm{NO}}_{3}^{-}$ to nitrite (${\mathrm{NO}}_{2}^{-}$) but not ${\mathrm{NO}}_{2}^{-}$ to nitric oxide (NO) as it lacks a NO-forming ${\mathrm{NO}}_{2}^{-}$ reductase. Strain GP59 on the other hand can carry the complete reduction of ${\mathrm{NO}}_{3}^{-}$ to N2. Strain GP59 cultured under anoxic conditions shows a 24-48h lag phase before ${\mathrm{NO}}_{3}^{-}$ reduction occurs. In strain JAM1T cultures, ${\mathrm{NO}}_{3}^{-}$ reduction begins immediately with accumulation of ${\mathrm{NO}}_{2}^{-}$. Furthermore, ${\mathrm{NO}}_{3}^{-}$ is reduced under oxic conditions in strain JAM1T cultures, which does not appear in strain GP59 cultures. These distinct characters suggest differences in the regulation pathways impacting the expression of denitrification genes, and ultimately growth. Methods Both strains were cultured under oxic conditions either with or without ${\mathrm{NO}}_{3}^{-}$, or under anoxic conditions with ${\mathrm{NO}}_{3}^{-}$. Transcript levels of selected denitrification genes (nar1 and nar2 encoding ${\mathrm{NO}}_{3}^{-}$ reductases, nirK encoding ${\mathrm{NO}}_{2}^{-}$ reductase, narK12f encoding ${\mathrm{NO}}_{3}^{-}$/${\mathrm{NO}}_{2}^{-}$transporter) and regulatory genes (narXL and fnr) were determined by quantitative reverse transcription polymerase chain reaction. We also derived the transcriptomes of these cultures and determined their relative gene expression profiles. Results The transcript levels of nar1 were very low in strain GP59 cultured under oxic conditions without ${\mathrm{NO}}_{3}^{-}$. These levels were 37 times higher in strain JAM1T cultured under the same conditions, suggesting that Nar1 was expressed at sufficient levels in strain JAM1T before the inoculation of the oxic and anoxic cultures to carry ${\mathrm{NO}}_{3}^{-}$ reduction with no lag phase. Transcriptomic analysis revealed that each strain had distinct relative gene expression profiles, and oxygen had high impact on these profiles. Among denitrification genes and regulatory genes, the nnrS3 gene encoding factor involved in NO-response function had its relative gene transcript levels 5 to 10 times higher in strain GP59 cultured under oxic conditions with ${\mathrm{NO}}_{3}^{-}$ than those in both strains cultured under oxic conditions without ${\mathrm{NO}}_{3}^{-}$. Since NnrS senses NO, these results suggest that strain GP59 reduced ${\mathrm{NO}}_{3}^{-}$ to NO under oxic conditions, but because of the oxic environment, NO is oxidized back to ${\mathrm{NO}}_{3}^{-}$ by flavohemoproteins (NO dioxygenase; Hmp), explaining why ${\mathrm{NO}}_{3}^{-}$ reduction is not observed in strain GP59 cultured under oxic conditions. Conclusions Understanding how these two strains manage the regulation of the denitrification pathway provided some clues on how they response to environmental changes in the original biofilm community, and, by extension, how this community adapts in providing efficient denitrifying activities.

Characterization and solubility measurement of synthetic uranophane and sklodowskite under oxic groundwater conditions

Naturally occurring uranyl silicates can serve as solubility-limiting solid phases (SLSPs) of U(VI) in the oxic environment of granitic groundwater, which is likely to occur in crystalline host rock media in Korea. In this study, two synthetic uranyl silicates, uranophane (Ca[UO2SiO3OH]2·5H2O) and sklodowskite (Mg[UO2SiO3OH]2·6H2O) were prepared and used to measure the U(VI) solubility in simulated groundwater (sGW), mimicking the composition of samples collected from the underground research tunnel at the Korea Atomic Energy Research Institute (KAERI). The solid- and solution-phase species involved were examined in detail using various characterization methods. According to the powder X-ray diffraction pattern and elemental analysis results, the synthetic mineral phases, which were identified as uranophane-α and sklodowskite having layered crystal structures, were retained intact in sGW; however, in 0.1 M NaClO4, emergence of other solid phases was observed. Enhanced FTIR and Raman spectroscopic data, particularly in the regions of 790–860 and 940–1020 cm−1 for the UO22+ and SiO44− ions, respectively, enable monitoring the changes in the solid phases. Ternary Ca–U(VI)-tricarbonato complexes were identified as the dominant dissolved U(VI) species in sGW using time-resolved laser-induced luminescence spectroscopy. Furthermore, the solubility constant of uranophane was calculated (log Ks,0° = 10.3 ± 0.4) and compared with the predicted values based on our geochemical modeling analysis and previously reported ones.

Microbial acidification by N, S, Fe and Mn oxidation as a key mechanism for deterioration of subsea tunnel sprayed concrete

The deterioration of fibre-reinforced sprayed concrete was studied in the Oslofjord subsea tunnel (Norway). At sites with intrusion of saline groundwater resulting in biofilm growth, the concrete exhibited significant concrete deterioration and steel fibre corrosion. Using amplicon sequencing and shotgun metagenomics, the microbial taxa and surveyed potential microbial mechanisms of concrete degradation at two sites over five years were identified. The concrete beneath the biofilm was investigated with polarised light microscopy, scanning electron microscopy and X-ray diffraction. The oxic environment in the tunnel favoured aerobic oxidation processes in nitrogen, sulfur and metal biogeochemical cycling as evidenced by large abundances of metagenome-assembled genomes (MAGs) with potential for oxidation of nitrogen, sulfur, manganese and iron, observed mild acidification of the concrete, and the presence of manganese- and iron oxides. These results suggest that autotrophic microbial populations involved in the cycling of several elements contributed to the corrosion of steel fibres and acidification causing concrete deterioration.

Volcanism and turbidity current events as drivers of the evolution of benthic redox conditions: Organic matter enrichment in the Chang 7 member, Upper Triassic Yanchang formation, Ordos Basin, North China

Depositional events have a significant impact on the terrestrial redox conditions and provide evidence for studying the organic matter enrichment. The objective of this study was to evaluate the influence of volcanic and turbidity current events on benthic redox conditions during the Upper Triassic Chang 7 member (Ch7) of the Ordos Basin. To address these issues, the varying sedimentological settings, paleoredox conditions, and relationships between the redox environment and depositional events were investigated via sedimentary analysis of the profiles, microscopic analysis, organic geochemical analysis, and elemental geochemical data. The fine-grained sediments in the Chang 73 submember (Ch73) consist of abundant organic matter, collophanite, and framboidal pyrite. However, in the upper part of the Ch7 member, there was a decrease in organic matter, a decrease in the number of microorganisms, and an increase in pyrite size, indicating that the oxic environment is not favorable for organic matter enrichment. The element and geochemical proxies show similar vertical variations and redox changes. Volcanic activity can bring substantial amounts of material or elements to the basin. The enrichment of Hg and S exhibited considerable variation, ranging from 8.7 to 274.4 ppb and from 0.16 to 4.53 wt%, respectively, which influenced the organic matter accumulation through the flourishing and death of microorganisms and redox changes in the benthic environment of the terrestrial basin. As the lake basin shrinks, the Ti and Al contents increase with increasing frequency of turbidity current events, and the terrestrial debris transported to the lake basin gradually increases while carrying large amounts of oxygen and affecting sedimentation rates, contributing to the destruction of the reducing conditions of the benthic environment, subsequently, influencing organic matter accumulation. These results will be helpful in understanding the effect of multiple depositional events on organic matter enrichment in lacustrine basins.

Effect of Oxidation on Vivianite Dissolution Rates and Mechanism.

The interest in the mineral vivianite (Fe3(PO4)2·8H2O) as a more sustainable P resource has grown significantly in recent years owing to its efficient recovery from wastewater and its potential use as a P fertilizer. Vivianite is metastable in oxic environments and readily oxidizes. As dissolution and oxidation occur concurrently, the impact of oxidation on the dissolution rate and mechanism is not fully understood. In this study, we disentangled the oxidation and dissolution of vivianite to develop a quantitative and mechanistic understanding of dissolution rates and mechanisms under oxic conditions. Controlled batch and flow-through experiments with pristine and preoxidized vivianite were conducted to systematically investigate the effect of oxidation on vivianite dissolution at various pH-values and temperatures. Using X-ray absorption spectroscopy and scanning transmission X-ray microscopy techniques, we demonstrated that oxidation of vivianite generated a core-shell structure with a passivating oxidized amorphous Fe(III)-PO4 surface layer and a pristine vivianite core, leading to diffusion-controlled oxidation kinetics. Initial (<1 h) dissolution rates and concomitant P and Fe release (∼48 h) decreased strongly with increasing degree of oxidation (0-≤ 100%). Both increasing temperature (5-75 °C) and pH (5-9) accelerated oxidation, and, consequently, slowed down dissolution kinetics.

Study of the Geological Context of the 7th–6th Century BC Phoenician Era Shipwreck “Mazarrón 2” (Murcia, Spain)

The Mazarrón 2 shipwreck was found in 1994 on the beach of Playa de la Isla (Mazarrón, Murcia, Spain). This finding is extremely important because the boat and its lead cargo were still in a reasonable conservation state and, therefore, provided new data on naval construction, commercial goods, navigation routes, and the relationships between the Phoenicians and the local population in the 7th–6th century BC. Currently, the shipwreck remains underwater, protected by a metallic coffer. In the last 2 years, a Preliminary Studies Project has been carried out, supported by national and regional public institutions. This research aims to know the shipwreck’s conservation state and to determine the extraction and conservation methods at the Museo Nacional de Arqueología Subacuática ARQVA (Cartagena, Spain), where the conservation and restoration treatment will be conducted. The sampling strategy and analytical study included not only wood and other materials from the shipwreck and its cargo but also the seawater and the seabed materials in the vicinity of the shipwreck. This paper presents the results of the geochemical study of the archeological site. The applied methodology included physico-chemical tests, X-ray diffraction, optical microscopy, FTIR spectroscopy, field-emission scanning electron microscopy coupled with X-ray microanalysis, and X-ray microscopy. The results indicated that, despite the wreck being buried at a shallow depth (less than 50 cm) in a marine environment with a water column of 2–2.5 m, influenced by complex coastal dynamics that favor an oxic environment, early diagenetic processes like the formation of pyrite framboids are particularly intense in the pores and internal channels of the wreck’s wood, where a different dysoxic–anoxic environment prevails. These processes have been the main mechanisms to have affected the wreck and are related to the biogeochemistry of sediments. The sediments have been confirmed to be closely related to the geological context of the Mazarrón region. The conducted study found no significant evidence of pollution due to the lead cargo.

Isotopically light Mo in sediments of methane seepage controlled by the benthic Fe–Mn redox shuttle process

Methane seepage has been extensively observed in various continental margin settings. It has profound effects on the marine redox environment and the molybdenum (Mo) cycles in marine sediments. Therefore, there has been much recent attention on the redox-sensitive behavior of Mo in methane seepage environments. However, the characteristics of the Mo isotope composition in the cold-seep system remain poorly understood. In this study, we performed geochemical analyses, including Mo content and isotope composition, on sediment samples (core QDN-MS6) from the “Haima” cold-seep deposit area in the South China Sea. The analysis reveals a significant concentration of authigenic pyrite in the mid-section of QDN-MS6 core (373–403 cm). Moreover, the δ34S value in this interval is notably elevated with high total sulfur/total organic carbon ratio. Additionally, the sediments in the mid-section exhibits substantial enrichment in Mo (enrichment factors of Mo ranging from 5.29 to 39.32). This implies that the sediments in the mid-section are influenced by sulfate-driven anaerobic oxidation of methane. Most notably, the sediments in the mid-section displayed distinct low δ98Mo values (with an average of −0.7‰). After careful consideration, we ruled out the influence of organic matter, an oxic environment, a weakly sulfidic environment, and incomplete removal of thiopolybdate as contributing factors. Based on δ56Fe-Fe/Al ratios, (Mo–U) enrichment factors, and As enrichment factors, we propose that the “benthic Fe-Mn redox shuttle process” is the primary cause of the observed light δ98Mo signatures in sediments. This newly identified mechanism sheds light on Mo isotope cycling in methane seepage environments and enhances our understanding of the Mo isotope cycling process.

Enrichment pattern of tungsten in sediments under methane seepage environments: Applicability as a proxy for tracing and reconstructing (paleo-)methane seepage

The release of hydrogen sulfide by sulfate-driven anaerobic oxidation of methane (SD-AOM) during methane seepage activities has a strong impact on the evolution of marine redox conditions and the cycles of redox-sensitive elements (e.g. Mo and U). Consequently, the sedimentary enrichment or depletion of these elements is often used to trace and reconstruct (paleo-)methane seepage activity. In recent years, tungsten (W) has shown promise as an indicator of marine redox changes, but its applicability to trace methane seepage activity is unknown. This study identified significant differences in the W content of sediments in methane seepage environments compared to suboxic environments not influenced by methane seepage and oxic environments in the South China Sea. The sediments subjected to methane seepage were characterized by low W contents, similar to those of euxinic Black Sea sapropels. It is believed that the sulfidic environment resulting from SD-AOM is the primary cause of W depletion in sediments subjected to methane seepage. By examining W's interaction with its twin element, Mo, we present WMo enrichment patterns in various environments. In methane seepage environment (sulfidic environments), sediments had high MoEF (> 10) and low WEF (< 2) with a high Mo/W molar ratio (> 10); in suboxic environments not influenced by methane seepage, sediments exhibited a WMo enrichment pattern similar to the UCC (the MoEF and WEF values are predominantly below 1 and 2, respectively, with a low Mo/W molar ratio, <1.5); in oxic environments (enrichment of FeMn (oxy)hydroxides), sediments exhibited high MoEF (2 < MoEF < 10) and high WEF (> 2), with a medium Mo/W molar ratio (1.5–10). This further indicates that the Mo/W molar ratio has great potential in tracing and reconstructing (paleo-)methane seepage activities.

The adsorption of cerium on synthetic δ-MnO2: Implications for Ce uptake behavior of hydrogenetic and early diagenetic ferromanganese nodules from the Western Pacific

Cerium (Ce) anomalies can be used to distinguish diagenetic and hydrogenetic nodules, making them an important discriminator for the genesis of marine ferromanganese nodules. To understand the enrichment and adsorption mechanisms of Ce in different types of ferromanganese nodules, we conducted mineralogical and geochemical studies on ferromanganese nodule layers formed through both hydrogenetic and early diagenetic processes as well as adsorption experiments on synthetic δ-MnO2 to monitor the Ce uptake during the different processes. The major and trace element contents of natural ferromanganese nodule layers were investigated by SEM, EPMA and LA-ICP-MS analysis. The marine nodule studied in this study consisted of a core of fish tooth and a rim that could be divided into the hydrogenetic (type I) and early diagenetic (type II) layers based on their mineralogy and Mn/Fe ratios. The Mn oxide mineral assemblage is composed of todorokite, buserite, birnessite, and vernadite (δ-MnO2) and occurred in both type I and II layers. The type I layer has laminated structures with a low Mn/Fe ratio (1.1–3.2; averaging at 1.7), and low Cu, Ni and Mg contents consistent with a hydrogenetic genesis. The type II layer has a columnar and stromatolitic structure with a high Mn/Fe ratio (5.1–54.0; averaging at 23.3) and high Cu, Ni and Mg contents that are similar to early diagenetic nodules. The ΣREE contents in type I and type II layers are 1405–3506 ppm (averaging at 2091 ppm) and 199–1232 ppm (averaging at 674 ppm), respectively, indicating that the REE is enriched in the hydrogenetic type I layers. Strong positive Ce anomalies are present type I layers ranging from 1.2 to 2.5 (averaging 1.9), but only slightly positive are seen in type II ranging from 0.4 to 2.4 (averaging at 1.0). Synthetic experiments to monitor the Ce uptake process show that Ce can be adsorbed onto δ-MnO2 with the XRD and FTIR patterns suggesting that the structure of δ-MnO2 did not change significantly, consistent with Ce behavior in hydrogenetic nodules. The results suggest that Ce is predominantly concentrated in hydrogenetic nodules in an oxic environment, whereas in the early diagenetic layer, there is less oxidation and fixation of Ce due to the suboxic conditions. Our findings are consistent with Ce anomalies in marine Fe-Mn nodules being the result of Mn oxide oxidation adsorption and then fixation (oxidation) after adsorption.

Purple is the new green: biopigments and spectra of Earth-like purple worlds

ABSTRACT With more than 5500 detected exoplanets, the search for life is entering a new era. Using life on Earth as our guide, we look beyond green landscapes to expand our ability to detect signs of surface life on other worlds. While oxygenic photosynthesis gives rise to modern green landscapes, bacteriochlorophyll-based anoxygenic phototrophs can also colour their habitats and could dominate a much wider range of environments on Earth-like exoplanets. Here, we characterize the reflectance spectra of a collection of purple sulfur and purple non-sulfur bacteria from a variety of anoxic and oxic environments. We present models for Earth-like planets where purple bacteria dominate the surface and show the impact of their signatures on the reflectance spectra of terrestrial exoplanets. Our research provides a new resource to guide the detection of purple bacteria and improves our chances of detecting life on exoplanets with upcoming telescopes. Our biological pigment data base for purple bacteria and the high-resolution spectra of Earth-like planets, including ocean worlds, snowball planets, frozen worlds, and Earth analogues, are available online, providing a tool for modellers and observers to train retrieval algorithms, optimize search strategies, and inform models of Earth-like planets, where purple is the new green.

Organic geochemistry of the middle Paleozoic Ora Formation in Iraq: Implications for source rock assessment and hydrocarbon potentiality

The Ora Formation (late Devonian–early Carboniferous) is thought to be a potential source rocks for the Paleozoic petroleum system of Iraq. The source potential from the Ora Formation is evaluated for the first time ever in this study from western and northern Iraq which integrates data from organic geochemistry including Total Organic Carbon (TOC) analysis, HAWK pyrolysis, gas chromatography (GC), and gas chromatography mass spectrometry (GC-MS) and mineralogical X-ray diffraction and scanning electron microscopy. The shale and muddy carbonate succession within the Ora Formation from surface section in northernmost Iraq and subsurface section from two wells (Akkas-1 and Akkas −3) from western Iraq have been employed to assess the source rock potentiality, thermal maturity, kerogen type, organic content, and depositional environment. In addition to organic geochemical analyses, mineralogical XRD and SEM-EDS were used to support the paleoenvironmental interpretation of the Ora Formation. The results from TOC and HAWK analyses reveal that the Ora Formation ranges from poor to good as a source rock. However, the HAWK data suggests that the surface samples from northernmost Iraq are highly mature, highly weathered, or both. Kerogen analysis revealed that the Ora Formation contains immature type III and mixed II-III kerogens. Low TOC values were attributed to factors such as significant clastic input, weathering effects, and the prevailing oxic environment during deposition. The presence of detrital influx of quartz and feldspars, along with the occurrence of illite and kaolinite clay minerals, suggest a detrital input with weathering influence under hot arid and warm humid conditions. Biomarker analysis of the light hydrocarbons using GC and GC-MS revealed that these light hydrocarbons were generated from marine planktonic algae sources, possibly with some contributions from terrestrial and/or microbially reworked organic matter. These high mature light hydrocarbons in subsurface section were originated from anoxic marine shale source rocks. They were most likely from the Cambro-Ordovician Khabour Formation and were contaminated from another source.

Constraints of Sedimentary Environment on Shale Organic Matter Enrichment: Insights from Elemental Geochemistry and Multiple Factor Analysis.

The organic-rich shale of the Wufeng-Longmaxi formation is an important section for shale gas exploration. The traditional univariate or bivariate analysis causes researchers to have great controversy about its enrichment mechanism. This study explores the combination of multiple factor analysis (MFA) and element geochemistry to calculate the contribution rate of a paleoenvironment to organic matter enrichment and clarify the main controlling factors of organic matter enrichment. Research has shown that there is generally high productivity from the Wufeng (O3w)-Longmaxi formation (S1l) deposition. The degree of terrigenous clastic input and weathering during the period of the O3w is relatively low, and sedimentary water restriction is strong, mainly developing an anoxic-dysoxic sedimentary environment. During the deposition of S1l1, the input intensity and weathering of terrigenous debris were slightly enhanced, and the increase of the water column led to the development of an anoxic environment at the bottom of the water layer. During the S1l2+3 period, the degree of terrigenous debris and weathering is the largest, and the high oxygen content of the water column is mainly a normal oxic environment. An MFA calculation shows that the paleoproductivity and paleoredox environment of the organic-rich shale section have the highest contribution rate of about 59.57% to the enrichment of organic matter, which is higher than that of paleoclimate conditions and terrigenous clastic input, indicating that the enrichment of organic matter is mainly controlled by paleoproductivity and the preservation environment. This study provides a basis for the application of MFA in element geochemistry and can serve as a model for other studies.

Marine redox fluctuations during the Marinoan glaciation

The proliferation of eukaryotes preceding the Cryogenian Marinoan glaciation (650–635 Ma) and the subsequent radiation of early animals imply a conceivable linkage between global glaciation and complex life evolution. However, the marine redox condition remains enigmatic during the Cryogenian, impeding our understanding of the role of O2 on this biological innovation. To fill this gap, we comprehensively reported mineralogy, iron isotope (δ56Fe), and iron speciation in the Cryogenian Nantuo Formation at Liulongshan, South China. This section encompasses glacial marine and non-glacial deposits, where the redbeds situated in the middle of the section, in conjunction with the diamictites adjacent to them, divide the Nantuo Formation into three distinct glacial sedimentary cycles. Micro-particle hematite within the Nantuo Formation indicates that the primary Fe-oxide was authigenic and trapped in water column. Furthermore, the Fe isotopic compositions of these authigenic components (δ56FeHR) calculated by mass balance equation reveal the redox state of the ocean coinciding with dynamic glaciation. The lower diamictite shows an increasing trend of δ56FeHR, Fe/Al, and FeHR/FeT, indicative of gradually more anoxic seawater conditions coupled with ice advance. Although redbeds intervals exhibit higher FeHR/FeT ratios (∼ 0.51), traditionally indicative of anoxic environments, our integration of mineralogical evidence suggested that the increased Feox content in redbeds might represent increased oxidation of Fe(II) at the redox chemocline, rather than the redox conditions of the bottom waters. This interpretation is consistent with the observed decreasing trend in our Fe isotope data, as well as the sedimentological evolution. Subsequently, the positive and increasing δ56FeHR values suggest that the oceanic redox conditions shifted to anoxic as the second glacial episode re-emerged. These findings suggest dynamic fluctuations in the redox condition of the ocean during the Marinoan Ice Age. Specifically, the formation of the redbeds may reflect a locally oxic environment. A modern analogy resembling this situation is blood falls, where the oxidation of iron-rich brine plumes under the Antarctic ice sheets. Such subglacial environments could have potentially provided a habitable “refuge” for early life to survive during the Neoproterozoic glaciation.

X-ray chemical imaging for assessing redox microsites within soils and sediments

Redox reactions underlie several biogeochemical processes and are typically spatiotemporally heterogeneous in soils and sediments. However, redox heterogeneity has yet to be incorporated into mainstream conceptualizations and modeling of soil biogeochemistry. Anoxic microsites, a defining feature of soil redox heterogeneity, are non-majority oxygen depleted zones in otherwise oxic environments. Neglecting to account for anoxic microsites can generate major uncertainties in quantitative assessments of greenhouse gas emissions, C sequestration, as well as nutrient and contaminant cycling at the ecosystem to global scales. However, only a few studies have observed/characterized anoxic microsites in undisturbed soils, primarily, because soil is opaque and microsites require µm-cm scale resolution over cm-m scales. Consequently, our current understanding of microsite characteristics does not support model parameterization. To resolve this knowledge gap, we demonstrate through this proof-of-concept study that X-ray fluorescence (XRF) 2D mapping can reliably detect, quantify, and provide basic redox characterization of anoxic microsites using solid phase “forensic” evidence. First, we tested and developed a systematic data processing approach to eliminate false positive redox microsites, i.e., artefacts, detected from synchrotron-based multiple-energy XRF 2D mapping of Fe (as a proxy of redox-sensitive elements) in Fe-“rich” sediment cores with artificially injected microsites. Then, spatial distribution of FeII and FeIII species from full, natural soil core slices (over cm-m lengths/widths) were mapped at 1–100 µm resolution. These investigations revealed direct evidence of anoxic microsites in predominantly oxic soils such as from an oak savanna and toeslope soil of a mountainous watershed, where anaerobicity would typically not be expected. We also revealed preferential spatial distribution of redox microsites inside aggregates from oak savanna soils. We anticipate that this approach will advance our understanding of soil biogeochemistry and help resolve “anomalous” occurrences of reduced products in nominally oxic soils.

Geochemical insights into secular changes in the depositional environment of ferromanganese nodules in the western North Pacific

Understanding Earth's surface dynamics and biological evolution requires deciphering past marine environmental changes. Hydrogenetic ferromanganese nodules formed by the direct precipitation of Fe–Mn oxide/hydroxide from seawater could record the marine environment at the time of deposition, as in the case of ferromanganese crusts. In this study, petrological and geochemical analyses were conducted on ferromanganese nodules collected from the Japanese Exclusive Economic Zone around Minamitorishima Island in the western North Pacific Ocean. Additionally, the results were compared with those of ferromanganese crusts distributed in the same area to elucidate the secular changes in the depositional environment. The mineralogical features (consisting solely of Fe-vernadite with an absence of 10 Å Mn oxide) and the geochemical characteristics (including positive Ce-anomaly and negative Y-anomaly in rare-earth element patterns, high Co contents, and low Cu and Ni contents) of the nodules suggest that the studied nodules are of a hydrogenetic origin. From the inside to the outside of the nodule, the Mn/Fe and Y/Ho ratios decrease while the Th/U ratio increases, indicating a changing depositional environment over time. A similar trend was observed in ferromanganese crusts from the nearby Takuyo-Daigo Seamount. Furthermore, similar compositional changes were observed on the surfaces of the crust samples (uppermost 1–3 mm), which correlated with depth-related changes in seawater oxygen concentrations. Therefore, the observed cross-sectional changes in the chemical compositions of the nodules and crusts may reflect changes in seawater-dissolved oxygen concentrations over time. The Mn/Fe and Y/Ho trends indicate a shift towards a less oxic environment with increasing age while maintaining the current depth profile, implying an expansion of the oxygen minimum zone (OMZ). Moreover, the observed Ni and Cu enrichment, together with the changes in the Mn/Fe and Y/Ho ratios, suggest that the expansion of the OMZ was caused by increased surface ocean productivity.

Denitrification in low oxic environments increases the accumulation of nitrogen oxide intermediates and modulates the evolutionary potential of microbial populations.

Denitrification in oxic environments occurs when a microorganism uses nitrogen oxides as terminal electron acceptors even though oxygen is available. While this phenomenon is well-established, its consequences on ecological and evolutionary processes remain poorly understood. We hypothesize here that denitrification in oxic environments can modify the accumulation profiles of nitrogen oxide intermediates with cascading effects on the evolutionary potentials of denitrifying microorganisms. To test this, we performed laboratory experiments with Paracoccus denitrificans and complemented them with individual-based computational modelling. We found that denitrification in low oxic environments significantly increases the accumulation of nitrite and nitric oxide. We further found that the increased accumulation of these intermediates has a negative effect on growth at low pH. Finally, we found that the increased negative effect at low pH increases the number of individuals that contribute to surface-associated growth. This increases the amount of genetic diversity that is preserved from the initial population, thus increasing the number of genetic targets for natural selection to act upon and resulting in higher evolutionary potentials. Together, our data highlight that denitrification in low oxic environments can affect the ecological processes and evolutionary potentials of denitrifying microorganisms by modifying the accumulation of nitrogen oxide intermediates.

Aliphatic Biomarker Signatures of Crude Oil from Tarakan Subbasin, Tarakan Basin, North Kalimantan, Indonesia

Organic geochemical studies of crude oil from Pamusian Field, Tarakan Subbasin, Tarakan Basin, North Kalimantan, have been done. Biomarker aliphatic hydrocarbon fractions were identified using a combined gas chromatography-mass spectrometer (GC - MS). Identified biomarkers consist of n-alkane groups, isoprenoids, bicyclic sesquiterpenoids, and pentacyclic triterpenoids. The most abundant aliphatic hydrocarbon biomarker is pristane followed by n-C19. The existence of n-alkanes shows a homologous (n-C16- n-C30) with a unimodal distribution type. The abundance of n-C19 is higher than other n-alkanes, supported by LHCPI value of 2.03, as an indicator of organic matter derived from microbial organisms. The amount of long chain n-alkanes (n-C25- n-C30) is almost the same as medium chain n-alkanes (n-C19 - n-C24) indicating the source of organic compounds is not only from microbial organisms, but also from terrestrial higher plants. The presence of 8β (H)-drimane compounds together with homodrimane shows the presence of bacterial input on the formation of oil from organic compounds. Ratio of Pr/Ph is 3.76, ratio of drimane/homodrimane is 1.058, ratio of Pr/n-C17 is 34.41, and ratio of Ph/n-C18 is 16.02 indicating the source of organic compounds came from terrestrial higher plants deposited in the oxic environment, and disposed to increase biodegradation. The CPI value is 0.95, and the highest amount of 17α (H), 21β (H)-hopane compounds suggest that Tarakan Subbasin oil was mature, and the source of organic compounds was derived from bacteria Keywords: Tarakan Basin, organic geochemistry, aliphatic hydrocarbon fraction, CPI

Arsenic methylation and microbial communities in paddy soils under alternating anoxic and oxic conditions

Arsenic (As) methylation in soils affects the environmental behavior of As, excessive accumulation of dimethylarsenate (DMA) in rice plants leads to straighthead disease and a serious drop in crop yield. Understanding the mobility and transformation of methylated arsenic in redox-changing paddy fields is crucial for food security. Here, soils including un-arsenic contaminated (N-As), low-arsenic (L-As), medium-arsenic (M-As), and high-arsenic (H-As) soils were incubated under continuous anoxic, continuous oxic, and consecutive anoxic/oxic treatments respectively, to profile arsenic methylating process and microbial species involved in the As cycle. Under anoxic-oxic (A-O) treatment, methylated arsenic was significantly increased once oxygen was introduced into the incubation system. The methylated arsenic concentrations were up to 2–24 times higher than those in anoxic (A), oxic (O), and oxic-anoxic (O-A) treatments, under which arsenic was methylated slightly and then decreased in all four As concentration soils. In fact, the most plentiful arsenite S-adenosylmethionine methyltransferase genes (arsM) contributed to the increase in As methylation. Proteobacteria (40.8%–62.4%), Firmicutes (3.5%–15.7%), and Desulfobacterota (5.3%–13.3%) were the major microorganisms related to this process. These microbial increased markedly and played more important roles after oxygen was introduced, indicating that they were potential keystone microbial groups for As methylation in the alternating anoxic (flooding) and oxic (drainage) environment. The novel findings provided new insights into the reoxidation-driven arsenic methylation processes and the model could be used for further risk estimation in periodically flooded paddy fields.

Disentangling artificial and natural benthic weathering in organic rich Baltic Sea sediments

Enhanced mineral dissolution in the benthic environment is currently discussed as a potential technique for ocean alkalinity enhancement (OAE) to reduce atmospheric CO2 levels. This study explores how biogeochemical processes affect the dissolution of alkaline minerals in surface sediments during laboratory incubation experiments. These involved introducing dunite and calcite to organic-rich sediments from the Baltic Sea under controlled conditions in an oxic environment. The sediment cores were incubated with Baltic Sea bottom water. Findings reveal that the addition of calcite increased the benthic alkalinity release from 0.4 μmol cm−2 d−1 (control) to 1.4 μmol cm−2 d−1 (calcite) as well as other weathering products such as calcium. However, these enhanced fluxes returned to lower fluxes after approximately 4 weeks yet still higher than the un-amended controls. Microbial activity appeared to be the primary driver for lowering pore water pH and thus enhanced weathering. In several sediment cores, pH profiles taken at the start of the experiments indicated activity of sulfur oxidizing Beggiatoa spp, which was verified by RNA-profiling of 16S rRNA genes. The pH profiles transitioned to those commonly associated with the activity of cable bacteria as the experiments progressed. The metabolic activity of cable bacteria would explain the significantly lower pH values (~5.6) at sediment depths of 1–3 cm, which would favor substantial calcite dissolution. However, a high abundance of cable bacteria was not reflected in 16S rRNA sequence data. Total alkalinity (TA) fluxes in these cores increased by a factor of ~3, with excess TA/calcium ratios indicating that the enhanced flux originated from calcite dissolution. The dissolution of dunite or the potential formation of secondary minerals could not be identified due to the strong natural flux of silicic acid, likely due to biogenic silica dissolution. Furthermore, no accumulation of potentially harmful metals such as nickel was observed, as highlighted as a potential risk in other studies concerning OAE. Given the complexity of sediment chemistry and changes of the benthic conditions induced by the incubation, it remains challenging to distinguish between natural and enhanced mineral weathering. Further investigation, including the identification of suitable tracers for mineral dissolution, are necessary to assess the feasibility of benthic weathering as a practical approach for OAE and climate change mitigation.

Hydrocarbon generation potential and organic matter accumulation patterns in organic-rich shale during the mesoproterozoic oxygenation event: evidence from the Xiamaling formation shale

A significant deposition of black shales occurred during the Mesoproterozoic Oxygenation Event (MOE). In order to investigate the hydrocarbon generation potential and organic matter enrichment mechanism of these shale deposits, we studied the Xiamaling Formation shale in the North China region as a representative sample of the Mesoproterozoic shale. The research involved organic petrology, organic geochemistry, mineralogy, and elemental geochemistry. The following observations were made: (1) The depositional environment of the Xiamaling Formation shale can be categorized as either oxic or anoxic, with the former having shallow depositional waters and high deposition rates, while the latter has deeper depositional waters and slower deposition rates. (2) Anoxic shales exhibited significantly better hydrocarbon generation potential compared to shales deposited in oxic environments, although the latter still demonstrated high hydrocarbon generation potential. (3) Shales deposited in anoxic environments displayed higher paleoproductivity compared to those deposited in oxic environments. The high deposition rate in oxic environments slowed the decomposition and mineralization of organic matter, leading to the formation of high-quality shales. In contrast, the strong paleoproductivity, along with favorable preservation conditions, accounted for the high hydrocarbon potential of anoxic shales.