Anoxic Environments Research Articles

Tethered heme domains in a triheme cytochrome allow for increased electron transport distances.

Decades of research describe myriad redox enzymes that contain cofactors arranged in tightly packed chains facilitating rapid and controlled intra-protein electron transfer. Many such enzymes participate in extracellular electron transfer (EET), a process which allows microorganisms to conserve energy in anoxic environments by exploiting mineral oxides and other extracellular substrates as terminal electron acceptors. In this work, we describe the properties of the triheme cytochrome PgcA from Geobacter sulfurreducens. PgcA has been shown to play an important role in EET but is unusual in containing three CXXCH heme binding motifs that are separated by repeated (PT)x motifs, suggested to enhance binding to mineral surfaces. Using a combination of structural, electrochemical, and biophysical techniques, we experimentally demonstrate that PgcA adopts numerous conformations stretching as far as 180 Å between the ends of domains I and III, without a tightly packed cofactor chain. Furthermore, we demonstrate a distinct role for its domain III as a mineral reductase that is recharged by domains I and II. These findings show PgcA to be the first of a new class of electron transfer proteins, with redox centers separated by some nanometers but tethered together by flexible linkers, facilitating electron transfer through a tethered diffusion mechanism rather than a fixed, closely packed electron transfer chain.

Arsenic Methylation by a Sulfate-Reducing Bacterium from Paddy Soil Harboring a Novel ArsSM Fusion Protein.

Microbial arsenic (As) methylation is an important process of As biogeochemistry. Only a few As-methylating microorganisms have been isolated from paddy soil, hindering the mechanistic understanding of the process involved. We isolated 54 anaerobic and 32 aerobic bacteria from paddy soil with a high As methylation potential. Among the 86 isolates, 14 anaerobes, including 7 sulfate-reducing bacteria (SRB), but none of the aerobes were able to methylate arsenite [As(III)] or monomethylarsenite [MMA(III)] or both, suggesting that the As-methylating ability is much more prevalent in anaerobes than in aerobes. We performed a detailed investigation on As methylation by a SRB isolate, Solidesulfovibrio sp. TC1, and identified a novel bifunctional enzyme consisting of a fusion of As(III) S-adenosylmethionine (SAM) methyltransferase (ArsM) and a radical SAM protein. The enzyme (ArsSM) can catalyze As(III) methylation to MMA and DMA and subsequent adenosylation of DMA to form 5'-deoxy-5'-dimethylarsinoyl-adenosine (DDMAA), which is a key intermediate in the biosynthesis of arsenosugars. High concentrations of sulfide produced by SRB did not affect As(III) methylation to MMA but inhibited MMA methylation to DMA. Genes encoding ArsSM fusion proteins are widespread in anaerobes, particularly SRB, suggesting that ArsSM-carrying anaerobes may play an important role in As methylation in an anoxic environment.

Sedimentary Environment of the Permian Marine Shale in the Kaijiang‐Liangping Trough, Sichuan Basin, China: Implications for Organic Matter (OM) Accumulation

ABSTRACTThe Permian shales in the Kaijiang‐Liangping Trough within the Sichuan Basin represent a promising frontier for marine shale gas exploration, whereas there has been limited systematic research on their sedimentary environment and organic matter (OM) enrichment mechanisms. Therefore, we present total organic carbon (TOC) analysis, major/trace element analyses and scanning electron microscope experiments for the Permian marine shales from the trough to determine their paleoenvironmental conditions and influencing factors of OM enrichment. The results show that the paleoclimate changed from dry climate to humid and warm climate (P3w1 [the first member of the Wujiaping Formation]) and semi‐humid to semi‐arid climate (P3w2 [the second member of the Wujiaping Formation]) and P3d‐I (Dalong Formation‐I) and then to arid climate again during the shale deposition period from the P2g (Gufeng Formation) to the P3d‐II. The shales with the highest TOC contents (TOC > 3%, P3d‐I and P2g), lower TOC contents (TOC < 1%, P3w1 and P3w2) and higher TOC contents (1% < TOC < 2%, P3d‐II) were formed under the control of anoxic environment and high paleoproductivity, oxic‐suboxic environment and high paleoproductivity, anoxic‐euxinic environment and lower productivity, respectively. Only appropriate sedimentation rates promote OM enrichment. Terrestrial input, paleoclimate, volcanic activity and hydrothermal upwelling mainly indirectly affect OM accumulation by influencing paleoproductivity. The degree of redox conditions is the primary factor affecting OM enrichment, followed by paleoproductivity. Nonetheless, anoxic to euxinic environments are most appropriate for OM preservation. Weak volcanic activity can boost paleoproductivity, but severe volcanic activity might introduce excessive harmful compounds that limit organism survival, resulting in a fall in paleoproductivity. Additionally, element P brought by volcanic ashes doesn't contribute to OM accumulation.

Simultaneous Reduction and Methylation of Nanoparticulate Mercury: The Critical Role of Extracellular Electron Transfer.

Mercury nanoparticles are abundant in natural environments. Yet, understanding their contribution to global biogeochemical cycling of mercury remains elusive. Here, we show that microbial transformation of nanoparticulate divalent mercury can be an important source of elemental and methylmercury.Geobacter sulfurreducensPCA, a model bacterium predominant in anoxic environments (e.g., paddy soils), simultaneously reduces and methylates nanoparticulate Hg(II). Moreover, the relative prevalence of these two competing processes and the dominant transformation pathways differ markedly between nanoparticulate Hg(II) and its dissolved and bulk-sized counterparts. Notably, even when intracellular reduction of Hg(II) nanoparticles is constrained by cross-membrane transport (a rate-limiting step that also regulates methylation), the overall Hg(0) formation remains substantial due to extracellular electron transfer. With multiple lines of evidence based on microscopic and electrochemical analyses, gene knockout experiments, and theoretical calculations, we show that nanoparticulate Hg(II) is preferentially associated with c-type cytochromes on cell membranes and has a higher propensity for accepting electrons from the heme groups than adsorbed ionic Hg(II), which explains the surprisingly larger extent of reduction of nanoparticles than dissolved Hg(II) at relatively high mercury loadings. These findings have important implications for the assessment of global mercury budgets as well as the bioavailability of nanominerals and mineral nanoparticles.

Detection of heat transfer mechanism in biological systems and HIF-1 α inducing invasion of liver cancer cells in hypoxic environments by activating STAT3

HIF-1α, as a hypoxia-inducing factor, can promote the invasion and metastasis of cancer cells by activating downstream signaling pathways. However, different heat transfer mechanisms in biological systems have important effects on the survival and function of tumor cells. The aim of this study was to investigate how the mechanisms of heat transfer in biological systems affect HIF-1α-mediated STAT3 activation and further induce the invasion ability of liver cancer cells in anoxic environment. The expression and activation of HIF-1α and STAT3 in hepatocellular carcinoma cell lines were detected by establishing anoxic model. At the same time, thermal imaging and heat transfer analysis methods were used to evaluate the heat transfer characteristics of cells under different temperature and hypoxia conditions. The effects of HIF-1α and STAT3 on invasion of hepatocellular carcinoma cells were analyzed in combination with cell migration and invasion experiments. The results showed that the expression of HIF-1α was significantly increased and the STAT3 signaling pathway was activated under hypoxia. The abnormal change of the heat transfer mechanism of biological system accelerates the invasion ability of hepatocellular carcinoma cells. Inhibition of HIF-1α expression can significantly reduce the activation level of STAT3, thereby inhibiting cell migration and invasion. This study reveals the interaction between the biological heat transfer mechanism and HIF-1α-STAT3 signaling pathway under hypoxia environment, which provides a new potential target for the treatment of malignant tumors such as liver cancer, and emphasizes the importance of regulating the heat transfer mechanism.

3775-year-old wood burial supports "wood vaulting" as a durable carbon removal method.

Six-times more carbon dioxide (CO2) is removed each year by terrestrial photosynthesis than fossil fuel emissions. However, the carbon is mostly returned to the atmosphere by decomposition. We found a 3775-year-old ancient wood log buried 2 meters belowground that was preserved far beyond its expected lifetime. The wood had near-perfect preservation, with carbon loss less than 5% compared to a modern sample. The lack of decay is likely due to the low permeability of the compact clay soil at the burial site. Our observation suggests a hybrid nature-engineering approach for carbon removal by burying woody biomass in similar anoxic environments. We estimate a global sequestration potential of up to 10 gigatonnes CO2 per year with existing technology at a low cost of $30 to $100 per tonne after optimization.

Impact of chemical aging on pyrogenic carbon colloid facilitated transport and transformation of Cr (VI) in anoxic environments

Frequent wildfires have accumulated the pyrogenic carbon (PyC) colloids in the environment, where they undergo environmental aging processes. The altered properties of aged PyC colloids may affect their ability to facilitate transformation and transport of contaminants in post-fire environments, posing unknown threats to ecological security. This study investigated the effect of chemical aging on the PyC colloid-facilitated transformation and transport of chromium (Cr) using batch experiments, column experiments, and transport model simulations. Results showed that aged PyC colloids exhibited weaker electron-donating capacity, and the reduction of Cr (VI) to Cr (III) decreased from 37.6 % to 13.5 % with the increasing aging time. Although PyC colloid transport increased with aging time, the PyC colloid-facilitated Cr (III) transport decreased because of the weakened reduction of Cr (VI). The transport of PyC colloid-facilitated Cr (III) was weaker at low pH. The reactive solute transport model well simulated the aged PyC colloid-facilitated transformation and transport of Cr (VI). Our findings highlight the significance of aging processes and environmentally relevant conditions in influencing the PyC colloid-facilitated transformation and transport of Cr, which is crucial for assessing risks of wildfire-driven Cr pollution and the potential of PyC for in-situ pollution control.

Widespread occurrence of dissolved oxygen anomalies, aerobic microbes, and oxygen-producing metabolic pathways in apparently anoxic environments.

Nearly all molecular oxygen (O2) on Earth is produced via oxygenic photosynthesis by plants or photosynthetically active microorganisms. Light-independent O2 production, which occurs both abiotically, e.g., through water radiolysis, or biotically, e.g., through the dismutation of nitric oxide or chlorite, has been thought to be negligible to the Earth system. However, recent work indicates that O2 is produced and consumed in dark and apparently anoxic environments at a much larger scale than assumed. Studies have shown that isotopically light O2 can accumulate in old groundwaters; that strictly aerobic microorganisms are present in many apparently anoxic habitats; and that microbes and metabolisms that can produce O2 without light are widespread and abundant in diverse ecosystems. Analysis of published metagenomic data reveals that the enzyme putatively capable of nitric oxide dismutation (NOD) forms four major phylogenetic clusters and occurs in at least 16 bacterial phyla most notably the Bacteroidota. Similarly, a re-analysis of published isotopic signatures of dissolved O2 in groundwater suggests in-situ production in up to half of the studied ecosystems. Geochemical and microbiological data supports the conclusion that "dark oxygen" production is an important and widespread yet overlooked process in apparently anoxic environments with far-reaching implications for subsurface biogeochemistry and ecology.

Transport of reduced PBAT microplastics in saturated porous media: Synergistic effects of enhanced surface energy and roughness

Microplastic (MP) pollution presents significant global environmental challenges, exacerbated by reduction aging processes in anoxic environments, thereby increasing environmental risks and potential threats to human health. However, the mechanisms underlying the transport of reduced MPs remain poorly understood. In this study, laboratory-scale column experiments were conducted to investigate the transport behavior of polybutylene adipate terephthalate (PBAT), a common biodegradable MPs, and its reduced products obtained through the aging process mediated by two typical reducing agents, NaBH4 and Na2S, under varying conditions (ionic strength (IS), divalent cations, and low molecular weight organic acids (LMWOAs)). The results indicated that reduction aging improved the hydrophilicity of PBAT by increasing the surface roughness (roughness factor increased from 1.300 to 1.642) and surface energy (from 51.80 to 107.03 mN m−1), thereby increasing the mobility of reduced PBAT (with recovery rate increased from 53.77 % to 63.18 %). Increased IS decreased the mobility of reduced PBAT by decreasing the surface negative charge density. Divalent cations inhibited the mobility of both pristine and reduced PBAT in porous media, with pristine PBAT, containing more oxygen functional groups, exhibiting stronger inhibition. Furthermore, LMWOAs promoted the retention of reduced PBAT in porous media, which was dependent on the type of LMWOAs. This study revealed the alterations in MPs properties caused by reduction aging and their effects on transport mechanisms, offering new insights into the transport behavior and environmental risks of reduced MPs.

Nitrogen reducing mechanism by microporous aeration based on microbial population characteristics: water temperature factor

ABSTRACT The formation of black odour water is primarily attributed to the elevated concentration of organic pollutants, along with an excessive amount of nitrogen and phosphorus, ultimately leading to an anoxic aquatic environment. The water temperature influence mechanism on black-odorous water restoration by microporous aeration is still lacking depth study. This paper selected (15–18) ℃ (spring and autumn), (22–25) ℃ (summer), (8–11) ℃ (winter) as temperature conditions, and investigated temperature influence on nitrogen reduction. Researches showed that: (1) The removal rates of COD, NH4 +-N and TN were significantly positively correlated with temperature (r = 0.99, 0.96, 0.97), the lowest removal rates were 83.16%, 95.68%, 58.7% ((8–11) ℃), the highest values were 92.67%, 98.27%, 70.96% ((22–25) ℃), respectively. (2) At a temperature range of 22–25°C, the microbial community exhibited the highest levels of abundance, diversity, and uniformity. Notably, Proteobacteria dominated this temperature range with a relative abundance of 79.72%. Furthermore, temperature positively correlated with the majority of dominant bacterial species, suggesting that conditions at 22–25°C are highly conducive to the growth of most bacterial communities. Among these, Limnohabitans, Alsobacter, and Candidatus_Aquirestis, which possess key functions in denitrification and nitrogen removal, displayed significantly higher abundances. It explains the positive correlation between temperature and removal rates of COD, TN and NH4 +-N from microbial population’s perspective. Thus, the best temperature for repairing black-smelly water is (22–25) ℃. This study provides technical reference for mechanism research and practical application of microporous aeration.

Comparison between Co(II) and Ni(II) cycling at goethite-water interfaces: Interplay with Fe(II)-catalyzed recrystallization

Cobalt (Co) and nickel (Ni) are critical metals for modern renewable energy technologies as well as essential micronutrients for terrestrial plant health and marine primary production. Both metals are commonly surface-adsorbed onto and/or structurally-incorporated into iron (oxyhydr)oxide minerals, such as goethite (α-FeOOH), that are ubiquitously present in soils and sediments at the Earth’s surface. In sub- and anoxic environments, aqueous ferrous iron (Fe(II)) generated from dissimilatory Fe(III) reduction can induce the recrystallization of goethite and subsequently influences the speciation and mobilization of associated metals, e.g., Co(III) being reduced to Co(II). While it is generally considered that divalent Co and Ni behave similarly at goethite-water interfaces, there lacks a direct comparison of their cycling through goethite in response to Fe(II)-catalyzed recrystallization. Here, under circumneutral anoxic conditions with and without addition of aqueous Fe(II), we performed batch reaction experiments on Co(II)-substituted goethite and Co(II) and Ni(II) sorption experiments on pure goethite. The redox state and coordination environment of Co associated with goethite were determined using high energy resolution fluorescence detected X-ray absorption spectroscopy at the Co K-edge, and the distribution of solid-bound Co and Ni in goethite following sorption was revealed by sequential dissolution. Our results show that substitution of Co(II) for Fe(III) in goethite has less negative feedback on Fe(II)-catalyzed recrystallization than Ni(II), which may be related to their differing structural distortions as evidenced by EXAFS. In the absence of Fe(II), aqueous Co(II) is more favourably adsorbed onto and incorporated deeper into goethite than Ni(II), suggesting that Co(II) is more structurally compatible with goethite. The presence of Fe(II) markedly enhances the structural incorporation of both Co(II) and Ni(II) as a result of goethite recrystallization, which in turn can be inhibited by the accumulation of metals at the mineral surface. Furthermore, structurally-incorporated Co(II) is more difficult to be released back into solution (i.e. sum of aqueous and extract fractions) than Ni(II) during Fe(II)-catalyzed goethite recrystallization. Overall, our work highlights the significant differences between Co(II) and Ni(II) in their cycling at goethite-water interfaces and intricate interplay with Fe(II)-catalyzed recrystallization. This improves our understanding of their mobilization and distribution in anoxic goethite-rich systems and can provide useful insights for their enrichment and extraction from natural and artificial laterites generated from the enhanced weathering of ultramafic mine tailings.

Enhanced phosphorus removal from anoxic water using oxygen-carrying iron-rich biochar: Combined roles of adsorption and keystone taxa

Anthropogenic enrichment of phosphorus (P) in water environment can cause eutrophication, harmful algal blooms, and water quality deterioration. Adsorbents are often used for the removal and recovery of P from water, however, P is highly susceptible to re-release in anoxic benthic environments. As a response, this study prepared oxygen-carrying iron-rich biochar (O-Fe-BC) as an effective oxygen micro-nanobubble carrier (Q = 8.7024 cm³/g STP at 1.5 MPa) and P adsorbent (qm = 16.7097 mg P/g, q0.1 = 3.1974 mg P/g). Over the 90-day experimental period with O-Fe-BC, dissolved oxygen (DO) levels in the overlying water could maintain at ∼4 mg/L (peaking at ∼9.5 mg/L), and total phosphorus (TP) and soluble reactive phosphorus (SRP) levels decreased by over 96 %. The higher inorganic phosphorus content in the surface sediment-biochar mixture, along with the lower labile P and Fe concentration in the sediment pore water in the O-Fe-BC group compared to other groups, suggested the enhanced P immobilization. Further mechanism exploration revealed the combined roles of adsorption and microbial response, in which O-Fe-BC achieved efficient phosphate adsorption primarily through inner-sphere complexation via ligand exchange and keystone taxa (particularly Candidatus Electronema) played a crucial role in driving water chemistry divergence. Specially, these cable bacteria could provide large pools of Fe oxides in the surface sediment, binding with P to prevent its release, as supported by significant correlations between Ca. Electronema abundance and oxidation–reduction potential (ORP), TP, SRP, and sediment Fe-P variations. Additionally, a pot experiment with mung bean seedlings showed that the recovered O-Fe-BC significantly promoted the seed germination and growth, indicating its potential as a novel material for removing and recovering P from eutrophic waters. Taken together, our work provided a promising strategy for sustainable anoxia and P pollution mitigation, and also highlighted the indispensable roles of inner-sphere adsorption in P recovery and microbial keystone taxa in P cycling regulation.

Assessment of physicochemical properties and radioactivity in groundwater at households living in bac Lieu province, vietnam.

This paper presents findings on groundwater physiochemical composition and radioactivity levels in households in Bac Lieu province, Vietnam. Through discriminant analysis, it was observed that groundwater quality exhibits spatial variations corresponding to saline intrusion zones. The paired-samples T-tests revealed significantly different ratios of Ra-224, Ra-226, and Ra-228 isotopes between Na-Cl and Ca-Na-HCO3 water types. All three water types had a ratio of Ra-226/Ra-228 of approximately one, indicating the presence of groundwater aquifers beneath the crust and fluvial marine sediment. Furthermore, strong associations between sulfate and calcium suggest that CO2 enrichment in groundwater aquifers indicates anoxic aquatic environments. Twenty-five of the thirty-three evaluated samples exceeded the national technical regulations for domestic water quality with parameters such as chloride, sulfate, sodium, gross alpha, or total dissolved solids. Fifteen samples exceeded gross alpha's allowable contamination threshold of 0.1Bq/L. The combination of Ra-226 and Ra-228 did not surpass the U.S. Environmental Protection Agency's recommended limit of 0.185Bq/L. However, nineteen samples exhibited annual committed effective doses of radium isotopes for infants that exceeded the WHO recommendation of 0.1mSv/year.

Molecular basis of hyper-thermostability in the thermophilic archaeal aldolase MfnB

Methanogenic archaea are chemolithotrophic prokaryotes that can reduce carbon dioxide with hydrogen gas to form methane. These microorganisms make a significant contribution to the global carbon cycle, with methanogenic archaea from anoxic environments estimated to contribute > 500 million tons of global methane annually. Archaeal methanogenesis is dependent on the methanofurans; aminomethylfuran containing coenzymes that act as the primary C1 acceptor molecule during carbon dioxide fixation. Although the biosynthetic pathway to the methanofurans has been elucidated, structural adaptations which confer thermotolerance to Mfn enzymes from extremophilic archaea are yet to be investigated. Here we focus on the methanofuran biosynthetic enzyme MfnB, which catalyses the condensation of two molecules of glyceralde-3-phosphate to form 4‑(hydroxymethyl)-2-furancarboxaldehyde-phosphate. In this study, MfnB enzymes from the hyperthermophile Methanocaldococcus jannaschii and the mesophile Methanococcus maripaludis have been recombinantly overexpressed and purified to homogeneity. Thermal unfolding studies, together with steady-state kinetic assays, demonstrate thermoadaptation in the M. jannaschii enzyme. Molecular dynamics simulations have been used to provide a structural explanation for the observed properties. These reveal a greater number of side chain interactions in the M. jannaschii enzyme, which may confer protection from heating effects by enforcing spatial residue constraints.

Effects of exosomes and inflammatory response on tumor: a bibliometrics study and visualization analysis via CiteSpace and VOSviewer

BackgroundTumor is a new organism formed by abnormal hyperplasia of local tissue cells under the action of various tumorigenic factors. Inflammation plays a decisive role in inducing tumorigenesis, promoting tumor development, invasion and migration. More and more evidence indicate that exosomes are involved in regulating the formation of tumor microenvironment in the process of proinflammatory carcinogenesis, leading to the stimulation of anti-tumor immune response or systemic immunosuppression, and exosomes play a crucial role in the development of tumor.MethodsThe articles on tumor-derived exosomes and inflammatory responses from January 2005 to January 2024 were collected through Web of Science (WOS), and the inclusion criteria were “Article”, “Review Article” and “Early Access”. Articles obtained after excluding “Book Chapters”, “Editorial Material”, “Proceeding Paper”, “Meeting ” and “Retracted Publication”. Bibliometrics and visualization analysis were carried out on the obtained articles using CiteSpace6.2.R6 and VOSviewer1.6.20.ResultsTotal of 703 articles were included. The number of published documents showed a fluctuating growth trend year by year. A total of 61 countries have participated in the research on the effects of exosomes and inflammatory responses on tumors, among which China and the United States have the largest influence in this field. The obtained articles have been published in 60 journals around the world, among which PLOS ONE and NAT REV IMMUNOL are the journals with the most published articles and the highest co-citations respectively. The article from French author THERY C was cited the most (202 times). As a major researcher on the basic function of exosomes, THERY C established the gold standard for extraction, separation and identification of exosomes, and found that exosomes promote tumor metastasis through direct regulation of miRNA. Her research has had a huge impact on the field. Keyword co-occurrence analysis indicate that extracellular vesicles, inflammation, cancer, miRNAs, mesenchymal stem cells, drug delivery, gastric cancer and circulating endothelial microparticles are the research hotspot at present stage. The main keywords of the cluster analysis show that extracellular vesicles, human papilloma virus, myeloid cells, tumor macro-environment are the current research hotspots and frontier. The research hotspots have developed over time from the time chart of keywords and clustering, especially after 2016, exosomes have established extensive links with drug delivery, cancer treatment, inflammatory response and other fields. Tumor-derived exosomes stimulate receptor cells to secrete pro-inflammatory cytokines and growth factors, enabling immune and inflammatory cells to perceive the intracellular environment of cancer cells even when cancer cells do not express any tumor-specific antigens. For example, in anoxic environment, cancer cells can secrete exosomes containing pro-inflammatory factors to promote the invasion and metastasis of cancer cells. In the complex tumor microenvironment, both tumor cells and various stromal cells will secrete specific exosomes, and promote the development of tumors through various ways, so that tumor cells have drug resistance, and bring adverse effects on the clinical treatment of tumor patients. MicroRNAs and long noncoding RNA as hot keywords play important roles in regulating and mediating tumor development, and their specificity makes them important biomarkers for cancer prediction and diagnosis. Highlighting word analysis shows that microRNAs secreted by leukemia patients can effectively promote the proliferation of malignant cells and the development of cardiovascular diseases. At the same time, exosomes can induce the secretion of some microRNAs in patients, leading to cardiac repair and regeneration. Therefore, the detection and screening of microRNAs plays a crucial role in predicting the incidence of cardiovascular diseases in patients.ConclusionExosomes have attracted increasing attention due to their significant heterogeneity and ability to regulate the tumor immune microenvironment. However, tumor cell-derived exosomes accelerate tumor progression by enhancing immunosuppression and inflammation, increasing oxidative stress, and promoting angiogenesis, which may lead to poor prognosis.Graphical abstract

Geochemical distribution of major and trace elements in hydromorphic soil profiles developed on recent alluvium

Geochemical composition and distribution of major elements study is vital in terms of investigating the major soil forming compounds and to know the fate of trace elements in soils. Particle size distribution (PSD), pH, organic carbon (OC), and major and trace elements of hydromorphic soils formed on recent alluvium in Obafemi-Owode Local Government Area of Ogun state, Nigeria were analysed using standard procedures. Three profiles pits were dug based on the mapping units identified, and samples were collected for laboratory analysis. Data were subjected descriptive statistics and Pearson’ correlation coefficients using IBM SPSS version 27. The PSD was dominated by sand content, followed by clay and silt, and soil pH in KCl was strongly acid (3.17–4.30) and pH in H2O was moderately acid (4.74–5.80), while OC contents were low to moderate (1.22–6.69 g/kg). The major elemental results showed higher concentration of SiO2 (>50 %) connotes presence quartz, feldspar, and clay minerals. Manganese, Cu, Ba, Zr, and Zn have higher concentrations among the trace elements. Major elements ratios (SiO2/Al2O3, K2O/Al2O3) showed moderate weathering stage, while trace elements ratios (Ni/Co and Cu/Zn) revealed deposition under humid conditions and anoxic environment. The statistical analysis revealed that most elements have skewness closed to zero except MgO and K2O. Correlation coefficients between the elements are positive and significant (p < 0.05 and p < 0.01) indicating that their presence can be accounted for by similar lithology, though some have negative relationship which could be as a result of anthropogenic activities. The study found that elements were potential tracers for the presence of human activities and environmental changes.

The formation of tubular seep carbonate deciphered from mineralogical and geochemical characteristics: an example from the South China Sea

As a special type of seep carbonate, the many details concerning the formation mode and mechanism of tubular seep carbonates are rarely reported. Here, new geochemical and mineralogical data regarding tubular seep carbonate (SQW-65) are reported. Sample SQW-65 had anomalously negative δ13C values and positive δ18O values, which suggested the dissociation of gas hydrate. Additionally, almost all the sub-samples showed no Ce anomaly (Ce/Ce*average = 0.93), with obvious U enrichment (21.3&amp;lt; UEF &amp;lt;240.3), which indicates that the studied tubular seep carbonate was formed in an anoxic environment. Subsequently, the formation process of the studied tubular seep carbonate is further discussed according to the variability of mineralogical and geochemical characteristics from the rim to the core of the tubular formation. In the early stage of the studied tubular seep carbonate (periphery), owing to the influence of terrigenous components, the quartz and Ti content and Y/Ho ratio were high. However, with the formation of the periphery, the influence of terrigenous components was gradually weakened. In addition, from the rim to the core, the carbon and oxygen isotope values showed a “covariation” coupling relationship, an enrichment of U, and a reduction in total rare earth element content. This is because as the outer wall thickens and the internal fluid channel narrows, the intensity of the sulphate-driven anaerobic oxidation of methane and the associated precipitation rate of carbonate also increase.

Transcriptional regulation of the anaerobic 3-hydroxybenzoate degradation pathway in Aromatoleum sp. CIB

Phenolic compounds are commonly found in anoxic environments, where they serve as both carbon and energy sources for certain anaerobic bacteria. The anaerobic breakdown of m-cresol, catechol, and certain lignin-derived compounds yields the central intermediate 3-hydroxybenzoate/3-hydroxybenzoyl-CoA. In this study, we have characterized the transcription and regulation of the hbd genes responsible for the anaerobic degradation of 3-hydroxybenzoate in the β-proteobacterium Aromatoleum sp. CIB. The hbd cluster is organized in three catabolic operons and a regulatory hbdR gene that encodes a dimeric transcriptional regulator belonging to the TetR family. HbdR suppresses the activity of the three catabolic promoters (PhbdN, PhbdE and PhbdH) by binding to a conserved palindromic operator box (ATGAATGAN4TCATTCAT). 3-Hydroxybenzoyl-CoA, the initial intermediate of the 3-hydroxybenzoate degradation pathway, along with benzoyl-CoA, serve as effector molecules that bind to HbdR inducing the expression of the hbd genes. Moreover, the hbd genes are subject to additional regulation influenced by the presence of non-aromatic carbon sources (carbon catabolite repression), and their expression is induced in oxygen-deprived conditions by the AcpR transcriptional activator. The prevalence of the hbd cluster among members of the Aromatoleum/Thauera bacterial group, coupled with its association with mobile genetic elements, suggests acquisition through horizontal gene transfer. These findings significantly enhance our understanding of the regulatory mechanisms governing the hbd gene cluster in bacteria, paving the way for further exploration into the anaerobic utilization/valorization of phenolic compounds derived from lignin.

Depositional environments and thermal maturity of the hydrocarbon source rocks in the Devonian–Early carboniferous Ora Formation from palynological organic petrographic investigations in northern and western Iraq

The study investigates the palynofacies, organic matter character, and hydrocarbon generation potential of this rock unit, based on surface and subsurface samples from the Ora Formation type-section in extreme northern Iraq and the Akkas-3 well in western Iraq, respectively. Dark, mostly oxidized, gelified platy amorphous organic matter (AOM) dominates the palynological components in the surface section, in addition to a few rounded spores and structured phytoclasts. In contrast, palynomorphs, including Ambitisporites avitus, Aneurospora spp., Vallatisporites verrucosus, Acinosporites spp., Verrucosisporites nitidus and the algae Botryococcus, are predominant in studied samples from the Akkas-3 well. Statistical cluster analysis identified three palynofacies types in the surface section based on stratigraphic variations in the particulate organic matter. These vary from high amorphous organic matter (AOM), moderate phytoclast, and low palynomorph abundances that represent proximal suboxic–anoxic shelfal environments to moderate to good AOM and low to moderate palynomorph abundances that represent distal suboxic–anoxic or distal dysoxic–anoxic shelfal environments. The organic petrographic study of the outcrop section also revealed the strong effect of oxidation, where dispersed terrigenous and amorphous organic materials in the form of granular and gelified forms dominate and reflect a terrestrial origin of these components. In the subsurface section, a mixed terrestrial and less marine or lacustrine origin characterized the studied organic matter, where land plant spores (sporinite), in addition to vitrinite and inertinite, are dominant with a few scattered liptinite macerals. The difference in thermal maturity between the outcrop and subsurface samples is likely due to the higher tectonic burial of the outcrop samples that form part of the Northern Thrust Zone of Iraq. Nevertheless, higher abundances of AOM (oil-prone kerogen type II) accumulated in the northern outcrop type section. This might imply that the Ora Formation has a higher potential for hydrocarbon production north of the Akkas field.

Synergistic removal of bio-recalcitrant organic compounds and nitrate: Coupling photocatalysis and biodegradation to enhance the bioavailability of electron donors

Nitrate pollution poses significant threats to both aquatic ecosystems and human well-being, particularly due to eutrophication and increased risks of methemoglobinemia. Conventional treatment for nitrate-contaminated wastewater face challenges stemming from limited availability of carbon sources and the adverse impacts of toxins on denitrification processes. This study introduces an innovative Intimately Coupled Photocatalysis and Biodegradation (ICPB) system, which utilizes Ag3PO4/Bi4Ti3O12, denitrifying sludge, and polyurethane sponge within an anoxic environment. This system demonstrates remarkable efficacy in simultaneously removing bio-recalcitrant organic compounds (such as sulfamethoxazole) and nitrates, surpassing standalone treatment methods. Optimally, the ICPB achieves complete removal of sulfamethoxazole, along with 87.7 % removal of DOC, and 81.8 % reduction in nitrate levels. Its ability to sustain pollutant removal and biological activity over multiple cycles can be attributed to the special formation of biofilm and mineralization of sulfamethoxazole, minimizing both photocatalytic damage and toxic inhibitory effects on microbes. The dominant microbial genera of ICPB system included Castellaniella, Acidovorax, Raoultella, Giesbergeria, and Alicycliphilus. Additionally, the study sheds light on a potential mechanism for the concurrent treatment of recalcitrant organics and nitrates by the ICPB system, presenting a novel and highly effective approach for addressing biologically resistant wastewater.