A critical review of mineral-microbe interaction and coevolution: mechanisms and applications

Antibacterial and therapeutic potential of historic deposits of silesian healing clay - terra sigillataSilesiaca

ETHNOPHARMACOLOGICAL RELEVANCE

The increasing evolution of pathogen resistance is a global problem that requires novel solutions. Recently, an increased interest in ethnomedicinal sources can be observed in the derivation of new medicines. The return to traditional medicinal formulations handed down for generations is being followed, but it is necessary to revise them again, taking into account the generally accepted research protocol.

AIM OF THE STUDY

We aimed to evaluate the antimicrobial potential of historical deposits of Silesian healing clay (SHC), used in ethnomedicine against Gram-positive bacteria and to assess their biological activity using a primary dermal fibroblast line (NHDF) and a model monocyte line (THP1).

MATERIALS AND METHODS

Information on medicinal clay deposits that occur in Silesia and are traditionally used in ethnomedicine or ancient medicine and known as terra sigillata Silesiaca or SHC, was selected on available source materials and old prints and maps from the archives of the Polish Geological Institute (Wrocław, Poland). Subsequently, their places of occurrence were identified and traced in the field by taking three deposits from the Silesia territory: Upper Silesia (D1), Opole Silesia (D2), and Lower Silesian (D3) Voivodeships for analysis. Their basic parameters and antimicrobial efficacy against pathogenic bacteria, Gram-positive streptococci and staphylococci, including methicillin-resistant strains, were examined. The study evaluated the effects of clays on growth and vitality using a primary dermal fibroblast line (NHDF) and a monocytic line (THP1). Studies were performed on a cell culture model to determine the effects on tissue regeneration (fibroblasts) and anti-inflammatory effects (monocytes). The study attempted to identify the mechanism of antimicrobial action, especially the textural characteristics and geochemical composition, as well as the environmental reaction (pH).

RESULTS

SHCs were classified into the following textural classes: clay loam (D1), clay (D2), and sand (D3). The tested deposits have antimicrobial properties that reduce the bacterial population (104 CFU) compared to the control (108 CFU). The antimicrobial effect depends on the type of clay and the species or strain of bacteria used. In-house studies clearly showed that Staphylococcus aureus Pcm 2054 and Staphylococcus epidermidis MRSE ATCC 2538 cells were completely adsorbed by clay minerals from clay D3.13. Furthermore, 10% leachates also showed an antimicrobial effect, as a reduction in bacterial populations was observed ranging from 91 to 100%. The results showed stimulation of fibroblast culture proliferation and inhibition of the growth of inflammatory cells (monocytes).

CONCLUSION

SHCs tested have antimicrobial potential, in particular D2.7, D2.11, and D3.13. The D3.13 deposit had a bactericidal effect against the staphylococci tested. Aqueous solutions of clays also showed bacteriostatic effect. The results obtained in cell culture model tests indicate properties that modulate the healing process - stimulation of fibroblast growth (NHDF line) and inhibition of monocyte growth (THP1 line).

Nano-micro materials regulated biocatalytic metabolism for efficient environmental remediation: Fine engineering the mass and electron transfer in multicellular environments

The escalating energy and environmental crises have spurred significant research interest into developing efficient biological remediation technologies for sustainable contaminant and resource conversion. Integrating engineered nano-micro materials (NMMs) with these biocatalytic processes offers a promising approach to improve the microbial performance for environmental remediation. Core to such material-enhanced hybrid biocatalysis systems (MHBSs) is the rational regulation of metabolic processes with the assistance of NMMs, where a fine engineered mass and electron transfer is beneficial for the improved biocatalytic activity. However, the specific mechanisms of those NMMs-enhanced microbial metabolisms are normally overlooked. Here, we review the recent progress in MHBSs, focusing primarily on the mass/electron transfer regulation strategies for an enhanced microbial behavior. Specifically, the NMMs-regulated mass and electron transfer in extracellular, interfacial, and intracellular environment are summarized, where the patterns of diverse microbiological response are discussed thoroughly. Notably, fine modifications of cell interfaces and intracellular compartments by NMMs could even endow the biohybrids with new metabolic functions beyond their natural capabilities. Further, we also emphasize the importance of matching the various metabolic demands of biosystems with the diverse properties of NMMs to achieve efficient environmental remediation through a coordinated regulation strategy. Finally, major challenges and opportunities for the future development and practical implementation of MHBSs for environment remediation practices are given, aiming to provide future system design guidelines for attaining desirable biological behaviors.

Zn2+ adsorption in ferric-silicates microstructures in sulfidic tailings mediated through mineral weathering by Acidithiobacillus species

Heavy metals released from metallic sulfidic tailings pose significant environmental threats by contaminating surface and groundwater in mining areas. Sustainable rehabilitation methods are essential to remove or stabilize these metals, improving the quality of acid mine drainage and minimizing pollution. This study examines the adsorption capacity of zinc ions (Zn2+) by different iron-silicate mineral groups under natural weathering and bacteria-regulated weathered conditions. Batch experiments revealed that all tested mineral groups exhibit limited adsorption Zn2+ on iron-silicate surfaces, with adsorption behavior aligning with Langmuir and Freundlich isotherm models. Among the mineral groups, pristine iron-muscovite (2.58 mg/g) and iron-chlorite (4.52 mg/g) demonstrated the highest Zn2+adsorption capacity, primarily due to favorable ion exchange properties and surface characteristics. Acidic conditions induced by pyrite oxidation and the experimental growth medium slightly reduced Zn2+ adsorption in samples without microbial inoculation. In contrast, the addition of Acidithiobacillus species modestly enhanced Zn2+ adsorption, likely through microbial alteration of silicate surface properties and the formation of secondary iron-silicate aggregates with high adsorption potential. The dominant adsorption mechanisms included electrostatic attractions, surface complexation and coprecipitation. It is recommended to elevate pH levels and thus enhance metal ion adsorption through the incorporation of alkaline additives such as zeolites or bauxite residue to optimize Zn2+ immobilization in sulfidic tailings. This study highlights the importance of both microbial and clay mineral selection in designing effective strategies for stabilizing Zn2+ in metallic sulfidic tailings.

Effects of EDTA and Bicarbonate on U(VI) Reduction by Reduced Nontronite

Widespread Fe-bearing clay minerals are potential materials capable of reducing and immobilizing U(VI). However, the kinetics of this process and the impact of environmental factors remain unclear. Herein, we investigated U(VI) reduction by chemically reduced nontronite (rNAu-2) in the presence of EDTA and bicarbonate. U(VI) was completely reduced within 192 h by rNAu-2 alone, and higher Fe(II) in rNAu-2 resulted in a higher U(VI) reduction rate. However, the presence of EDTA and NaHCO3 initially inhibited U(VI) reduction by forming stable U(VI)-EDTA/carbonato complexes and thus preventing U(VI) from adsorbing onto the rNAu-2 surface. However, over time, EDTA facilitated the dissolution of rNAu-2, releasing Fe(II) into solution. Released Fe(II) competed with U(VI) to form Fe(II)-EDTA complexes, thus freeing U(VI) from negatively charged U(VI)-EDTA complexes to form positively charged U(VI)-OH complexes, which ultimately promoted U(VI) adsorption and triggered its reduction. In the NaHCO3 system, U(VI) complexed with carbonate to form U(VI)-carbonato complexes, which partially inhibited adsorption to the rNAu-2 surface and subsequent reduction. The reduced U(IV) largely formed uraninite nanoparticles, with a fraction present in the rNAu-2 interlayer. Our results demonstrate the important impacts of clay minerals, organic matter, and bicarbonate on U(VI) reduction, providing crucial insights into the uranium biogeochemistry in the subsurface environment and remediation strategies for uranium-contaminated environments.

Synergized Effects of Amino Acids and NaCl to Enhance Silicate Mineral Dissolution in Aqueous Environments for Efficient Atmospheric CO2 Removal

Enhanced weathering of silicate minerals is a promising approach for reducing atmospheric CO2 levels by increasing the aquatic pH and facilitating CO2 dissolution. However, the slow and unsustainable dissolution of silicate minerals in natural environments remains a challenge. This study proposed a new CO2 capture system that uses the combined effect of amino acids and NaCl to promote mineral dissolution, and its characteristics were investigated experimentally. The results showed that amino acids are promising for enhancing the near-congruent dissolution of silicate minerals, specifically at weakly alkaline pHs (i.e., 8), implying the long-term effectiveness of the system. Comprehensive findings revealed a 13-fold increase in the level of Ca extraction from wollastonite (CaSiO3) in the presence of 0.1 mol/L glutamic acid (Glu) over 72 h at 35 °C and a 22-fold increase in the level of CO2 capture efficiency. However, Fe-bearing minerals, such as olivine ((Mg,Fe)2SiO4), are unsuitable for application, because the enhanced Fe extraction results in the generation of Fe hydroxide, which lowers pH and consequently reduces CO2 capture efficiency. Moreover, NaCl facilitates the release of the Ca-Glu complex from mineral surfaces into the solution, synergizing amino acids to promote mineral dissolution. A semiclosed application system is proposed, with future studies needed to assess ecological impacts and ensure long-term sustainability.

Contrasting Effects of Catecholate and Hydroxamate Siderophores on Molybdenite Dissolution

Molybdenum (Mo) is essential for many enzymes but is often sequestered within minerals, rendering it not readily bioavailable. Metallophores, metabolites secreted by microorganisms and plants, promote mineral dissolution to increase the metal bioavailability. However, interactions between metallophores and Mo-bearing minerals remain unclear. In this study, catecholate protochelin and hydroxamate desferrioxamine B (DFOB) were utilized to examine their effects on dissolution of the common Mo-bearing mineral, molybdenite (MoS2), under both oxic and anoxic conditions. Protochelin promoted molybdenite dissolution under oxic conditions, with the formation of MoO3 on the surface and Mo-siderophore complexes in solution. This was attributed to air-oxidation of both molybdenite and protochelin, as evidenced by lack of dissolution under anoxic conditions but enhanced dissolution by either preoxidized protochelin or preoxidized molybdenite. Liquid chromatography-mass spectroscopy, X-ray photoelectron spectroscopy, and time-of-flight secondary ion mass spectrometry analyses revealed degradation of protochelin and adsorptions of its byproducts on molybdenite surface to promote dissolution. Conversely, DFOB inhibited molybdenite dissolution under both oxic and anoxic conditions, likely attributed to surface adsorption of DFOB and its weak complexation with Mo(VI) at the circumneutral pH. This work highlights the need to consider the balance between promoting and inhibitory effects of different metallophores on Mo-mineral dissolution.

The trigger mechanisms and the gene regulatory pathways of organic acid secretion during the vanadium-titanium magnetite tailing bioleaching

The long-term mining of vanadium-titanium (V-Ti) magnetite has generated a large accumulation of tailings, which can lead to metal pollution via microbial bioleaching. Current research has focused on the bioleaching of minerals, and a few studies have explored microbial responses to metals only through limited metabolite concentrations. However, the trigger mechanisms of metal release during the V-Ti magnetite tailing bioleaching and key gene regulatory pathways for organic acid metabolism are still unclear. This study screened a bioleaching fungus from the V-Ti magnetite tailing pond groundwater. The fungus promoted tailing dissolution by secreting more organic acids (808.99 mg L-1) than without tailings (671.11 mg L-1). The released metals were responsible for the difference in organic acid metabolism. The tailing-released Fe, Zn, and V were the triggers for the organic acid secretion via up-regulating the functional genes of citric, formic, and succinic acids in the TCA cycle, Methane metabolism, and D-arginine and D-ornithine metabolisms. Fe and V also led to the accumulation of malic acid through up-regulating functional genes during the conversion of phenylalanine, tyrosine, and glycine. Ni and Cu were the inhibitors by up-regulating related functional genes and promoting the conversion of acetyl-CoA to acetoacetyl-CoA, resulting in a decrease in organic acid concentrations. This study demonstrated the triggering metals of bioleaching and fungal gene regulation pathways, which provide a novel strategy for fungi domestication by considering the up-regulating metals to improve the bioleaching efficiency.

Alkane degradation coupled to Fe(III) reduction mediated by Gram-positive bacteria

Petroleum hydrocarbon contamination, such as n-alkanes, poses a significant global threat to ecosystems and human health. Microbial remediation emerges as a promising strategy for addressing this issue through both aerobic and anaerobic processes. Notably, the majority of anaerobic hydrocarbon degraders identified to date are Gram-negative bacteria. In this study, two electroactive Gram-positive strains, Lysinibacillus spp. strains SL-6A and SL-12A, were isolated from oil-contaminated soils in the Shengli Oilfield, China. Our experiments demonstrated that these strains effectively degraded n-hexadecane (n-C16) through extracellular Fe(III) reduction. When ferric citrate was used as the electron acceptor, strains SL-6A and SL-12A degraded 94.2 % and 87.4 % of n-C16, respectively, within 72 hours. This process was further confirmed using Fe(III)-containing minerals. Surface-enhanced Raman spectroscopy, UV-vis spectroscopy, and cyclic voltammetry data collectively indicated that surface-associated c-type cytochromes (c-Cyts) were crucial for extracellular electron transfer (EET), facilitating Fe(III) reduction. In addition, our strains were capable of producing flavin mononucleotide (FMN), a well-known redox-active organic molecule involved in EET processes, particularly in the presence of Fe(III). Whole-genome sequencing confirmed the pathways for n-alkane degradation and the synthesis of c-Cyts and FMN in our strains. This research highlights the potential of electroactive Gram-positive bacteria in hydrocarbon degradation in contaminated soils.

Human milk metals and metalloids shape infant microbiota

Background: The profile of metal(loid)s in human milk is essential for infant growth and development, yet its impact on the development of the infant microbiota remains unclear. Elements, such as manganese, zinc, iron or copper, play crucial roles in influencing infant health. Aim: To investigate the metal(loid) content within human milk and its influence on the infant's gut microbiota within the first 2 months after birth. Methods: Human milk samples and infant stool samples from 77 mother-infant dyads in the MAMI cohort were collected at two time points: the early transitional stage and the mature stage. Metallomic profiling of human milk was conducted using inductively coupled plasma-mass spectrometry (ICP-MS). The infant gut microbiota was profiled through 16S rRNA amplicon sequencing and maternal-infant clinical data were available. Spearman's rank correlation coefficientsprovided insights into metal(loid)-microbiota relationships. Results: Independent cross-sectional analyses of mother-infant pairs at two time points, significant variations in metal concentrations and differences in microbial abundances and diversities were observed. Notably, Bifidobacterium genus abundance was higher during the mature lactation stage. During early lactation, we found a significant positive correlation between infant gut Corynebacterium and human milk nickel concentrations, and negative correlations between Veillonella spp. and antimony, and Enterobacter spp. and copper. Additionally, Simpson's diversity was negatively correlated with iron. In the mature lactation stage, we identified eleven significant correlations between metals and microbiota. Notably, Klebsiella genus showed multiple negative correlations with iron, antimony, and vanadium. Conclusion: Our study highlights the significance of metal(loid)-microbiota interactions in early infant development, indicating that infant gut Klebsiella genus may be particularly vulnerable to fluctuations in metal(loid) levels present in human milk, when compared to other genera. Future research should explore these interactions at a strain level and the implications on infant health and development. This trial was registered as NCT03552939.

Photocatalytic material-microorganism hybrid systems in water decontamination

Biological processes are widely used technologies for water decontamination, but they are often limited by insufficient bioavailable carbon sources or biorecalcitrant contaminants. The recently developed photocatalytic material-microorganism hybrid (PMH) system combines the light-harvesting capacities of photocatalytic materials with specific enzymatic activities of whole cells, efficiently achieving solar-to-chemical conversion. By integrating the benefits of both photocatalysis and biological processes, the PMH system shows great potential for water decontamination. While recent reviews have focused primarily on its application in green energy development, this review emphasizes the latest advancements in PMH systems for water decontamination, covering various applications, key considerations, and synergistic mechanisms. This review aims to provide a fundamental understanding of the PMH system and explore its broader potential in environmental remediation.

Deciphering the biodegradation of thiamethoxam by Phanerochaete chrysosporium with natural siderite: Synergistic mechanisms, transcriptomics characterization, and molecular simulation

Fungi play vital roles in the fate of organic pollutants, particularly when interacting with minerals in aquatic and soil environments. Mechanisms by which fungi may mitigate pollutions in fungus-mineral interactions are still unclear. Inspired by biogeochemical cycling, we constructed a range of co-culture systems to investigate synergistic effects of the white-rot fungus Phanerochaete chrysosporium and the iron-bearing mineral siderite on thiamethoxam (THX) transformation, a common neonicotinoid pesticide. Co-culturing with siderite significantly enhanced THX transformation during the initial 10 days with a dose effect, achieving 86 % removal within 25 days. Fungi could affect siderite's dissolution, transformation, and precipitation through their biological activities. These interactions triggered physiological adaptation and resilience in fungi. Siderite could enhance the activity of fungal ligninolytic enzymes and cytochrome P450, facilitating biotransformation. Genes expression related to growth, energy metabolism, and oxidative stress response upregulated, enhancing fungal resilience to THX. The primary THX degradation pathways included nitro-reduction, C-N cleavage, and de-chlorination. Molecular dynamics simulations provided insights into catalytic mechanisms of enzyme-THX interactions. Together, siderite could act as natural enhancers that endowed fungi to resist physical and chemical stresses in environments, providing insights into contaminants attenuation, fungal biomineralization, and the coevolution of the Earth's lithosphere and biosphere.

In Silico Prediction of Alkaline Phosphatase Interaction with the Natural Inhibitory 5-Azaindoles Guitarrin C and D

The natural 5-azaindoles, marine sponge guitarrin C and D, were observed to exert inhibitory activity against a highly active alkaline phosphatase (ALP) CmAP of the PhoA family from the marine bacterium Cobetia amphilecti, with IC50 values of 8.5 and 110 µM, respectively. The superimposition of CmAP complexes with p-nitrophenyl phosphate (pNPP), a commonly used chromogenic aryl substrate for ALP, and the inhibitory guitarrins C, D, and the non-inhibitory guitarrins A, B, and E revealed that the presence of a carboxyl group at C6 together with a hydroxyl group at C8 is a prerequisite for the inhibitory effect of 5-azaindoles on ALP activity. The 10-fold more active guitarrin C could compete with pNPP for binding sites in the ALP active site due to similarities in size, three-dimensional structure, and the orientation of the COOH group along the phosphate group. However, the inhibition of CmAP and calf intestinal ALP (CIAP) by guitarrin C was observed to occur via a non-competitive mode of action, as evidenced by a twofold decrease in Vmax and an unchanged Km. In contrast, the kinetic model with guitarrin D, with an additional OH group at C7, reflected a mixed type of inhibition, with a decrease in both values. The sensitivity of CIAP to guitarrins C and D was shown to be slightly lower than that of CmAP, with IC50 values of 195 and 230 µM, respectively. Nevertheless, these findings prompted the prediction of complexes of human ALP isoenzymes with guitarrins C and D.

Clay minerals and clay-based materials for heavy metals pollution control

Heavy metal contamination is a huge hazard to the environment and human health, and research into removing heavy metals from their primary sources (industrial and agricultural wastes) has increased significantly. Adsorption has received interest due to its distinct benefits over other treatment approaches. The distinctive qualities of clay minerals, such as their high specific surface area, strong cation exchange capacity, and varied structures, make them particularly ideal for use in the manufacture of adsorbents. The customizable structure and performance of clay minerals allow for unprecedented diversity in adsorbent creation, opening up new possibilities for the development of high-efficiency and functional adsorption technologies. In this review, various approaches for developing optimal adsorbents from raw materials are presented. Then, the correlation between functionalization and performance is investigated, focusing on the effects of structural features and surface properties on adsorption performance. The research progress on the synthesis of adsorbents using clay minerals and other functional materials is systematically reported. Finally, the challenges and opportunities in designing and utilizing innovative clay mineral adsorbents are discussed.

Magnesium polypeptide combined with microbially induced calcite precipitation for remediation of lead contamination in phosphate mining wasteland soil

Soil Pb contamination is inevitable, as a result of phosphate mining. It is essential to explore more effective Pb remediation approaches in phosphate mining wasteland soil to ensure their viability for a gradual return of soil quality for cultivation. In this study, a Pb-resistant urease-producing bacterium, Serratia marcescens W1Z1, was screened for remediation using microbially induced carbonate precipitation (MICP). Magnesium polypeptide (MP) was prepared from soybean meal residue, and the combined remediation of Pb contamination with MP and MICP in phosphate mining wasteland soil was studied. Remediation of Pb using a combination of MP with MICP strain W1Z1 (WM treatment) was the most effective, with the least exchangeable Pb at 30.37% and the most carbonate-bound Pb at 40.82%, compared to the other treatments, with a pH increase of 8.38. According to the community analysis, MP moderated the damage to microbial abundance and diversity caused by MICP. Total nitrogen (TN) was positively correlated with Firmicutes, pH, and carbonate-bound Pb. Serratia inoculated with strain W1Z1 were positively correlated with bacteria belonging to the Firmicutes phylum and negatively correlated with bacteria belonging to Proteobacteria. The available phosphate (AP) in the phosphate mining wasteland soil could encapsulate the precipitated Pb by ion exchange with carbonate, making it more stable. Combined MP-MICP remediation of Pb contamination in phosphate mining wasteland soil was effective and improved the soil microenvironment.

Advanced bacteria-based biomaterials for environmental applications

A large amount of anthropogenic CO2 emissions are derived from Portland cement production, contributing to global warming, which threatens human health and exposes flora and fauna to ecological imbalance. With concerns about the high maintenance and repair costs of concrete, the development of microbially induced calcium carbonate precipitation (MICP)-based self-healing concrete has been extensively examined. Bacterial carriers for microcrack healing could enhance the concrete's self-healing capacity by maintaining bacterial activity and viability. To reduce cement consumption, the development of sustainable engineered living materials (ELMs) based on MICP has become a promising new research topic that combines synthetic biology and material science, and they can potentially serve as alternatives to traditional construction materials. This review aims to describe bacterial carriers and the ongoing development of advanced ELMs based on MICP. We also highlight the emerging issues linked to applying MICP technology at the commercial scale, including economic challenges and environmental concerns.

Dynamics of plastic debris and its density change between river compartments in the Tuul River system, Mongolia

Plastic pollution in river environments has become an emerging global concern. However, the migration of plastic and changes in its properties between river compartments are less understood. This study demonstrates the plastic debris aging and the dynamics between floodplain, surface water, and sediment compartments of the Tuul River, Mongolia. Plastic occurrence is evaluated in terms of their abundance, size, shape, polymer type, and photodegradation in each compartment. Photodegradation stages were calculated using the carbonyl index (CI). Plastic abundance was 5.46 ± 3.53 items m-2 in the floodplain, 155 ± 100.7 items m-3 in the surface water, and 128.4 ± 76.3 items kg-1 in the sediment. Microplastics dominated in the size category in all compartments, while macro- and megaplastics were found only in the floodplain. Polyethylene and polypropylene dominated the surface water and sediment, while polystyrene was the predominant plastic in the floodplain. A positive correlation was found between the distributed polymer types in the surface water and sediment compartments. The similar composition in size and polymer type suggests vertical plastic migration from water to sediment. Although CI values showed that the plastic aging was significantly different between water and sediment (water, 0.61 ± 0.26, and sediment, 0.90 ± 0.68), the dominance of low-density plastics with high CI in the sediment suggests that the aged plastic density changed during the vertical transport in the river system.

Biogeochemical cycles of iron: Processes, mechanisms, and environmental implications

The iron (Fe) biogeochemical cycle is critical for abiotic and biological environmental processes that overlap spatially and may compete with each other. The development of modern molecular biology technologies promoted the understanding of the electron transport mechanisms of Fe-cycling-related microorganisms. Recent studies have revealed a novel pathway for microaerophilic ferrous iron (Fe(II))-oxidizers in extracellular Fe(II) oxidation. In addition, OmcS, OmcZ, and OmcE nanowires on the cell surface have been shown to promote electron transfer between microorganisms and their environment. These processes affect the fate of pollutants in directly or indirectly ways, such as greenhouse gas emissions. In this review, these advances and the environmental implications of the Fe cycle process were discussed, with a particular focus on the mechanisms of intracellular or extracellular electron transport in microorganisms.

Lithological Controls on Soil Aggregates and Minerals Regulate Microbial Carbon Use Efficiency and Necromass Stability

Microbial carbon (C) use efficiency (CUE) drives soil C formation, while physical-chemical protection stabilizes subsequent microbial necromass, both shaped by soil aggregates and minerals. Soils inherit many properties from the parent material, yet the influence of lithology and associated soil geochemistry on microbial CUE and necromass stabilization remains unknow. Here, we quantified microbial CUE in well-aggregated bulk soils and crushed aggregates, as well as microbial necromass in bulk soils and the mineral-associated organic matter fraction, originating from carbonate-containing (karst) and carbonate-free (clastic rock, nonkarst) parent materials along a broad climatic gradient. We found that aggregate crushing significantly increased microbial CUE in both karst and nonkarst soils. Additionally, compared to nonkarst soils, calcium-rich karst soils increased macroaggregate stability and decreased the ratio of oligotrophic to copiotrophic microbial taxa, leading to a reduction in microbial CUE. Moreover, microbial CUE was negatively associated with iron (hydr)oxides in karst soils, attributed to the greater abundance of iron (hydr)oxides and higher soil pH. Despite the negative effects of soil aggregation and minerals on microbial CUE, particularly in karst soils, these soils concurrently showed greater microbial necromass stability through organo-mineral associations compared to nonkarst soils. Consequently, (i) bedrock lithology mediates the effects of aggregates and minerals on microbial CUE and necromass stability; and (ii) balancing minerals' dual roles in diminishing microbial CUE and enhancing microbial necromass stability is vital for optimizing soil C preservation.

Enhanced Rock Weathering as a Source of Metals to Promote Methanogenesis and Counteract CO2 Sequestration

Enhanced weathering of (ultra)mafic rocks has been proposed as a promising approach to sequester atmospheric CO2 and mitigate climate change. However, these silicate rocks contain varying amounts of trace metals, which are essential cofactors of metallaenzymes in methanogens. We found that weathering of crushed peridotite and basalt significantly promoted the growth and methanogenesis of a model methanogen─Methanosarcina acetivorans C2A under the condition of excess substrate. The released trace metals from peridotite and basalt, especially Fe, Ni, and Co, accounted for the promotion effect. Observation at different spatial scales showed a close association between the rocks and cells. Proteomic analysis revealed that rock amendment significantly enhanced the expression of core metalloenzymes in the methylotrophic methanogenesis pathway. Our study uncovers a previously unrecognized but important negative effect of enhanced rock weathering on methane production, which may counteract the carbon sequestration effort.

The Influence of Exogenous CdS Nanoparticles on the Growth and Carbon Assimilation Efficiency of Escherichia coli

This study investigated the impact of CdS nanoparticles (NPs) on Escherichia coli growth and metabolism under varying conditions. Under illumination, CdS NPs significantly enhanced bacterial growth, glucose assimilation, and biomass accumulation. Key metabolic and stress response genes showed increased expression, indicating improved ATP synthesis and oxidative stress resistance. Additionally, CdS NPs enhanced the electrochemical properties of E. coli, promoting efficient electron transfer. No significant changes were observed in the dark. These findings suggest that light-activated CdS NPs promote E. coli growth and metabolic efficiency by upregulating crucial genes involved in growth and oxidative stress management.

Chromium(VI) Adsorption and Reduction in Soils under Anoxic Conditions: The Relative Roles of Iron (oxyhr)oxides, Iron(II), Organic Matters, and Microbes

Chromium (Cr) transformation in soils mediated by iron (Fe) (oxyhr)oxides, Fe(II), organic matter (OM), and microbes is largely unexplored. Here, their coupling processes and mechanisms were investigated during anoxic incubation experiments of four Cr(VI) spiked soil samples with distinct physicochemical properties from the tropical and subtropical regions of China. It demonstrates that easily oxidizable organic carbon (EOC, 55-84%) and microbes (16-48%) drive Cr(VI) reduction in soils enriched with goethite and/or hematite, among which in dryland soils microbial sulfate reduction may also be involved. In contrast, EOC (38 ± 1%), microbes (33 ± 1%), and exchangeable and poorly crystalline Fe (oxyhr)oxide-associated Fe(II) (29 ± 3%) contribute to Cr(VI) reduction in paddy soils enriched with ferrihydrite. Additionally, exogenous Fe(II) and microbes significantly enhance Cr(VI) reduction in ferrihydrite- and goethite-rich soils, and Fe(II) greatly promotes but microbes slightly inhibit Cr passivation. Both Fe(II) and microbes, especially the latter, promote OM mineralization and result in the most substantial OM loss in ferrihydrite-rich paddy soils. During the incubation, part of the ferrihydrite converts to goethite but microbes may hinder the transformation. These results provide deep insights into the geochemical fates of redox-sensitive heavy metals mediated by the complicated effects of Fe, OM, and microbes in natural and engineered environments.

A combination of physiology, metabolomics, and genetics reveals the two-component system ResS/ResR-mediated Fe and Al release from biotite by Pseudomonas pergaminensis F77

Understanding of the mechanisms on bacteria-regulated mineral dissolution functions is important for further insight into mineral-microbe interactions. The functions of the two-component system have been studied. However, the molecular mechanisms involved in bacterial two-component system-mediated mineral dissolution are poorly understood. Here, the two-component regulatory system ResS/ResR in the mineral-solubilizing bacterium Pseudomonas pergaminensis F77 was characterized for its involvement in biotite dissolution. Strain F77 and the F77ΔresS, F77ΔresR, and F77ΔresS/R mutants were constructed and compared for the ResS/ResR system-mediated Fe and Al release from biotite in the medium and the mechanisms involved. After 3 days of incubation, the F77ΔresS, F77ΔresR, and F77ΔresS/R mutants significantly decreased the Fe and Al concentrations in the medium compared with F77. The F77ΔresS/R mutant had a greater impact on Fe and Al release from biotite than did the F77ΔresS or F77ΔresR mutant. The F77∆resS/R mutant exhibited significantly reduced Fe and Al concentrations by 21-61 % between 12 h and 48 h of incubation compared with F77. Significantly increased pH values and decreased cell counts on the mineral surfaces were found in the presence of the F77∆resS/R mutant compared with those in the presence of F77 between 12 h and 48 h of incubation. Metabolomic analysis revealed that the extracellular metabolites associated with biotite dissolution were downregulated in the F77ΔresS/R mutant. These downregulated metabolites included GDP-fucose, 20-carboxyleukotriene B4, PGP (16:1(9Z)/16:0), 3',5'-cyclic AMP, and a variety of acidic metabolites involved in carbohydrate, amino acid, and lipid metabolisms, glycan biosynthesis, and cellular community function. Furthermore, the expression levels of the genes involved in the production of these metabolites were downregulated in the F77ΔresS/R mutant compared with those in F77. Our findings suggested that the ResS/ResR system in F77 contributed to mineral dissolution by mediating the production of mineral-solubilizing related extracellular metabolites and bacterial adsorption on mineral surface.

Distribution and drivers of co-hosts of antibiotic and metal(loid) resistance genes in the fresh-brackish-saline groundwater

Groundwater is an essential source of drinking water and agricultural irrigation water, and its protection has become a global goal for public health. However, knowledge about heavy metal(loid) resistance genes (MRGs) in groundwater and the potential co-selection of antibiotic resistance genes (ARGs) have seldom been developed. Here, during the wet and dry seasons, we collected 66 groundwater samples (total dissolved solids = 93.9-9530 mg/L) adjacent to Baiyangdian Lake in Northern China, which presented the few metal(loid) and antibiotic contamination. We identified 160 MRGs whose composition exhibited significant seasonal variation, and dissolved metal(loid)s (particularly Ba) played a determinative role in promoting the MRGs proliferation though with relatively low concentrations, suggesting the relatively vulnerable groundwater ecosystems. Moreover, 27.4% of MRG-carrying metagenome-assembled genomes (MAGs) simultaneously carried ARGs, with the most frequently detected MRG types of Cu, Hg, and As, and ARG types of multidrug and bacitracin. Physicochemical variables, variables related to total dissolved solids, metal(loid)s, and antibiotics synthetically shaped the variation of MRG-ARG hosts in groundwater. We found that the increase of MRG-ARG hosts was critically responsible for the spread of MRGs and ARGs in groundwater. Our findings revealed the widespread co-occurrence of MRGs and ARGs in few-contaminated groundwater and highlighted the crucial roles of salinity in their propagation and transmission.

Use of corncob and pineapple peel as associated substrates for biosurfactant production

Biosurfactants are amphiphilic biomolecules with promising tensoative and emulsifying properties that find application in the most varied industrial sectors: environment, food, agriculture, petroleum, cosmetics, and hygiene. In the current work, a 23 full-factorial design was performed to evaluate the effect and interactions of pineapple peel and corncob as substrates for biosurfactant production by Bacillus subtilis LMA-ICF-PC 001. In a previous stage, an alkaline pretreatment was applied to corncob samples to extract the xylose-rich hydrolysate. The results indicated that pineapple peel extract and xylose-rich hydrolysate acted as partial glucose substitutes, minimizing production costs with exogenous substrates. Biosurfactant I (obtained at 8.11% pineapple peel extract, 8.11% xylose-rich hydrolysate from corncob, and 2.8109 g/L glucose) exhibited a significant surface tension reduction (52.37%) and a promising bioremediation potential (87.36%). On the other hand, biosurfactant III (obtained at 8.11% pineapple peel extract, 31.89% xylose-rich hydrolysate from corncob, and 2.8109 g/L glucose) exhibited the maximum emulsification index in engine oil (69.60%), the lowest critical micellar concentration (68 mg/L), and the highest biosurfactant production (5.59 g/L). These findings demonstrated that using pineapple peel extract and xylose-rich hydrolysate from corncob effectively supports biosurfactant synthesis by B. subtilis, reinforcing how agro-industrial wastes can substitute traditional carbon sources, contributing to cost reduction and environmental sustainability.

Nutrient removal efficacy and microbial dynamics in constructed wetlands using Fe(III)-mineral substrates for low carbon-nitrogen ratio sewage treatment

This study evaluated the roles of two common sources of Fe(III)-minerals-volcanic rock (VR) and synthetic banded iron formations from waste iron tailings (BIF-W)-in vertical flow-constructed wetlands (VFCWs). The evaluation was conducted in the absence of critical environmental factors, including Fe(II), Fe(III), and soil organic matter (SOM), using metagenomic analysis and integrated correlation networks to predict nitrogen removal pathways. Our findings revealed that Fe(III)-minerals enhanced metabolic activities and cellular processes related to carbohydrate decomposition, thereby increasing the average COD removal rates by 10.7% for VR and 5.90% for BIF-W. Notably, VR improved nitrogen removal by 1.70% and 5.40% compared to BIF-W and the control, respectively. Fe(III)-mineral amendment in bioreactors also improved the retention of denitrification and nitrification bacteria (phylum Proteobacteria) and anammox bacteria (phylum Planctomycetes), with increases of 3.60% and 3.20% using VR compared to BIF-W. Metagenomic functional prediction indicated that the nitrogen removal mechanisms in VFCWs with low C/N ratios involve simultaneous partial nitrification, ANAMMOX, and denitrification (SNAD). Network-based analyses and correlation pathways further suggest that the advantages of Fe(III)-minerals are manifested in the enhancement of denitrification microorganisms. Microbial communities may be activated by the functional dissolution of Fe(III)-minerals, which improves the stability of SOM or the conversion of Fe(III)/Fe(II). This study provides new insights into the functional roles of Fe(III)-minerals in VFCWs at the microbial community level, and provides a foundation for developing Fe-based SNAD enhancement technologies.

Acidithiobacillus species mediated mineral weathering promotes lead immobilization in ferric-silica microstructures at sulfidic tailings

Immobilization and stabilization of heavy metals (HMs) in sulfidic and metallic tailings are critical to long-term pollution control and sustainable ecological rehabilitation. This study aims to unravel immobilization mechanisms of Pb (Ⅱ) in the neoformed hardpan structure resulting from Acidithiobacillus spp. accelerated bioweathering of sulfides in the presence of silicates. It was found that the bioweathered mineral composite exhibited an elevated Pb (Ⅱ) adsorption capacity compared to that of natural weathered mineral composite. A suit of microspectroscopic techniques such as synchrotron-based X-ray Absorption Spectroscopy (XAS), X-ray Photoelectron Spectroscopy (XPS), Fourier Transform Infrared Spectroscopy (FTIR) and Field-Emission Scanning Electron Microscope (FE-SEM) indicated that secondary Fe-bearing minerals, functional groups, and surface properties in the neoformed hardpan were key factors contributing to Pb (Ⅱ) adsorption and immobilization in ferric-silica microstructures. The underlying mechanisms might involve surface adsorption-complexation, dissolution-precipitation, electrostatic attraction, and ion exchange. Microbial communities within the muscovite groups undergoing bioweathering processes demonstrated distinctive survival strategies and community composition under the prevailing geochemical conditions. This proof of concept regarding Pb (Ⅱ) immobilization in microbial transformed mineral composite would provide the basis for scaling up trials for developing field-feasible methodology to management HMs pollution in sulfidic and metallic tailings in near future.

Evaluating Natural Source Zone Depletion and Enhanced Source Zone Depletion in laboratory columns via soil redox continuous sensing and microbiome characterization

To optimally employ Natural Source Zone Depletion (NSZD) and Enhanced Source Zone Depletion (ESZD) at sites impacted by light non-aqueous phase liquids (LNAPL), monitoring strategies are required. Emerging use of subsurface oxidation-reduction potential (ORP) sensors shows promise for tracking redox evolution, which reflects ongoing biogeochemical processes. However, further understanding of how soil redox dynamics relate to subsurface microbial activity and LNAPL degradation pathways is needed. In this work, soil ORP sensors and DNA and RNA sequencing-based microbiome analysis were combined to elucidate NSZD and ESZD (biostimulation via periodic sulfate addition and biosparging) processes in columns containing LNAPL-impacted soils from a former petroleum refinery. Results show expected relationships between continuous soil redox and active microbial communities. Continuous data revealed spatial and temporal detail that informed interpretation of the hydrocarbon biodegradation data. Redox increases were transient for sulfate addition, and sequencing revealed how hydrocarbon concentration and composition impacted microbiome structure and naphthalene degradation. Periodic biosparging did not result in fully aerobic conditions suggesting observed biodegradation improvements could be explained by alternative anaerobic metabolisms (e.g., iron reduction due to air oxidizing reduced iron). Collectively, data suggest combining continuous redox sensing with microbiome analysis provides insights beyond those possible with either monitoring tool alone.

Molecular response to the influences of Cu(II) and Fe(III) on forming biogenic manganese oxides by Pseudomonas putida MnB1

The biogeochemical cycle of biogenic manganese oxides (BioMnOx) is closely associated with the environmental behavior and fate of various pollutants. It is significantly interfered by many metals, such as Cu and Fe. However, the bacterial molecular responses are not clear. Here, the effects of Cu(II) and Fe(III) on oxidation of manganese by Pseudomonas putida MnB1 and the bacterial molecular response mechanisms have been studied. The bacterial oxidation of manganese were promoted by both Fe(III) and Cu(II) and the final manganese oxidation rate of the Cu(II) group exceeded 16 % that of the Fe(III) group. The results of transcriptome indicated that Cu(II) promoted manganese oxidation by up-regulating the expression levels of multicopper oxidase (MCO) and peroxidase(POD), and by stimulating electron transfer, while Fe(III) promoted this process by accelerating the electron transfer and nitrogen cycling, and activating POD. The protein-protein interaction (PPI) network indicated that the MCO genes (mnxG and mcoA) were directly linked to the copper homeostasis proteins (cusA, cusB, czcC and cusF). Cytochrome c was closely related to the genes related to nitrogen cycling (glnA, glnL, and putA) and electrons transfer (cycO, cycD, nuoA, nuoK, and nuoL), which also promoted manganese oxidation. This study provides a molecular level insight into the oxidation of Mn(II) by Pseudomonas putida MnB1 with Cu(II) and/or Fe(III) ions.

Trace metal interaction with thermophilic phototrophic anaerobic bacterium Chloroflexus aurantiacus

Towards improving the knowledge of possible paleo-microorganisms interaction with trace metals (micro-nutrients and toxicants), we studied adsorption of Mn, Zn, Sr, Cd, and Pb onto modern Chloroflexus aurantiacus, thermophilic anoxygenic phototrophic bacterium which could be highly abundant in the Precambiran aquatic environments. Acid-base surface titrations allowed quantifying the number of proton-active surface groups, whereas non-electrostatic linear programming method (LPM) was used to assess the surface site concentrations and adsorption reaction constants between divalent cations (Zn, Mb, Sr, Cd, Pb) and bacterial surface, based on results of pH-dependent adsorption edge and constant-pH 'langmuirian' adsorption experiments. The total proton/hydroxyl binding site number of Chl. aurantiacus surfaces was sizably lower than that of other phototrophic anaerobic bacteria studied previously using similar experimental and modeling approach. Divalent metals exhibited a decreasing order of adsorption affinity (Pb > Cd ≥ Zn ≥ Mn > Sr), which reflected the order of cation hydrolysis and was similar to adsorption order on other phototrophic bacteria. At the same time, adsorption of Zn increased with increasing of temperature, from 4 °C to 60 °C and was stronger under light compared to the darkness. This suggested some active metabolic control involved in this metal interaction with bacterial surfaces. Overall, Chl. aurantiacus exhibited trace metal adsorption parameters (site number and binding constants) which were lower compared to other anoxygenic phototrophic bacteria (Rhodopseudomonas palustris; Rhodobacter blasticus) and cyanobacteria. This may reflect different bioavailability of trace metals in the paleo-ocean, given that thermophilic Chl. aurantiacus are among the oldest phototrophs on the planet.

Understanding Nanoscale Interactions between Minerals and Microbes: Opportunities for Green Remediation of Contaminated Sites

In situ contaminant degradation and detoxification mediated by microbes and minerals is an important element of green remediation. Improved understanding of microbe-mineral interactions on the nanoscale offers promising opportunities to further minimize the environmental and energy footprints of site remediation. In this Perspective, we describe new methodologies that take advantage of an array of multidisciplinary tools─including multiomics-based analysis, bioinformatics, machine learning, gene editing, real-time spectroscopic and microscopic analysis, and computational simulations─to identify the key microbial drivers in the real environments, and to characterize in situ the dynamic interplay between minerals and microbes with high spatiotemporal resolutions. We then reflect on how the knowledge gained can be exploited to modulate the binding, electron transfer, and metabolic activities at the microbe-mineral interfaces, to develop new in situ contaminant degradation and detoxication technologies with combined merits of high efficacy, material longevity, and low environmental impacts. Two main strategies are proposed to maximize the synergy between minerals and microbes, including using mineral nanoparticles to enhance the versatility of microorganisms (e.g., tolerance to environmental stresses, growth and metabolism, directed migration, selectivity, and electron transfer), and using microbes to synthesize and regenerate highly dispersed nanostructures with desired structural/surface properties and reactivity.

Exploring the influence of deposit mineral composition on biofilm communities in oil and gas systems

Introduction

Inside oil and gas pipelines, native microbial communities and different solid compounds typically coexist and form mixed deposits. However, interactions between these deposits (primarily consisting of mineral phases) and microorganisms in oil and gas systems remain poorly understood. Here, we investigated the influence of magnetite (Fe3O4), troilite (FeS), and silica (SiO2) on the microbial diversity, cell viability, biofilm formation, and EPS composition of an oil-recovered multispecies consortium.

Methods

An oilfield-recovered microbial consortium was grown for 2 weeks in separate bioreactors, each containing 10 g of commercially available magnetite (Fe3O4), troilite (FeS), or silica (SiO2) at 40°C ± 1°C under a gas atmosphere of 20% CO2/80% N2.

Results

The microbial population formed in troilite significantly differed from those in silica and magnetite, which exhibited significant similarities. The dominant taxa in troilite was the Dethiosulfovibrio genus, whereas Sulfurospirillum dominated in magnetite and silica. Nevertheless, biofilm formation was lowest on troilite and highest on silica, correlating with the observed cell viability.

Discussion

The dissolution of troilite followed by the liberation of HS- (H2S) and Fe2+ into the test solution, along with its larger particle size compared to silica, likely contributed to the observed results. Confocal laser scanning microscopy revealed that the EPS of the biofilm formed in silica was dominated by eDNA, while those in troilite and magnetite primarily contained polysaccharides. Although the mechanisms of this phenomenon could not be determined, these findings are anticipated to be particularly valuable for enhancing MIC mitigation strategies currently used in oil and gas systems.

Biological assessment and radiological impact in Keana, North Central Nigeria: environmental implication and metabolites production

The objective of the research was to examine microbial characteristics, metabolites produced, and the potential radiological risks present in mining soils located in Keana, North Central Nigeria. Soil samples were collected from various locations within Keana, Nasarawa State. Bacterial isolation was carried out, and molecular techniques were employed to characterize the bacteria found in the collected soil samples. Additionally, the susceptibility of these isolates to antibiotics was determined, and the bacteria screened for their ability to produce metabolites. The isolated bacteria were classified into three groups: Actinobacteria, Firmicutes, and Proteobacteria. The analysis of the spectra revealed that 1595 compounds were produced, including carboxylic acids, nitro compounds, aldehydes, anhydrides, esters, ketones, amides, phenols, alcohols, alkanes, alkenes, alkynes, and arenes. Some of the metabolites produced were oleic acid, 1,3-dioxolane, linoelaidic acid and oleic acid, 1-nonadecene, butylated hydroxytoluene, diisooctyl phthalate, bis(2-ethylhexyl) phthalate among others, and 1,2-benzenedicarboxylic acid (85.32%) as the most produced metabolite. Among the antibiotics tested, levofloxacin and ciprofloxacin exhibited the strongest antibacterial properties against the isolates. Airborne gamma-ray spectrometry analysis identified elevated levels of potassium, thorium, and uranium in the soils, indicating potential environmental hazards. However, no significant correlation was found between the presence of bacteria and radioactive elements. These findings emphasize the importance of comprehensive environmental monitoring in Keana to address potential health risks associated with microbial contamination and radioactive materials. Additionally, the study highlighted the role of microbial diversity in Keana soils in promoting the production of secondary metabolites with potential applications in pharmaceutical and industrial sectors..

Molecular and microbial insights towards anaerobic biodegradation of anionic polyacrylamide in oil sands tailings

Anionic polyacrylamide (A-PAM) is widely used as a flocculant in the management of oil sands tailings. Nevertheless, apprehensions arise regarding its potential biodegradation and environmental consequences within the context of oil sands tailings. Consequently, it is imperative to delve into the anaerobic biodegradation of A-PAM in oil sands tailings to gain a comprehensive understanding of its influence on tailings water quality. This work explored the dynamics of A-PAM biodegradation across concentrations: 50, 100, 250, 500, 1000, and 2000 mg/kg TS. The results showed a significant decrease in A-PAM concentration and molecular weight at lower concentrations (50 and 100 mg/kg TS) compared to higher ones, suggesting enhanced degradation efficiency. Likewise, the organic transformation and methane production exhibited dependency on A-PAM concentrations. The peak concentrations observed were 20.0 mg/L for volatile fatty acids (VFAs), 0.07 mg/L for acrylamide (AMD), and 8.9 mL for methane yield, with these maxima being recorded at 50 mg/kg TS. The biodegradation efficiency diminishes at higher concentrations of A-PAM, potentially due to the inhibitory effects of polyacrylic acid accumulation. A-PAM biodegradation under anaerobic condition did not contribute to acute toxicity or genotoxicity. SEM-EDS, FT-IR and XRD analyses further revealed that higher concentrations of A-PAM inhibited the biodegradation by altering floc structure and composition, thereby restricting the microbial activity. Major microorganisms, including Smithella, Candidatus_Cloacimonas, W5, XBB1006, and DMER64 were identified, highlighting A-PAM's dual role as a source of carbon and nitrogen under anaerobic conditions. The above findings from this research not only significantly advance understanding of A-PAM's environmental behavior but also contribute to the effective management practices in oil sands tailings.

Interfacial interactions between minerals and organic matter: Mechanisms and characterizations

Minerals and organic matter are essential components of soil, with minerals acting as the "bone" and organic matter as the "skin". The interfacial interactions between minerals and organic matter result in changes in their chemical composition, structure, functional groups, and physical properties, possessing a significant impact on soil properties, functions, and biogeochemical cycles. Understanding the interfacial interactions of minerals and organic matter is imperative to advance soil remediation technologies and carbon targets. Consequently, there is a growing interest in the physicochemical identification of the interfacial interactions between minerals and organic matter in the academic community. This review provides an overview of the mechanisms underlying these interactions, including adsorption, co-precipitation, occlusion, redox, catalysis and dissolution. Moreover, it surveys various methods and techniques employed to characterize the mineral-organic matter interactions. Specifically, the up-to-date spectroscopic techniques for chemical information and advanced microscopy techniques for physical information are highlighted. The advantages and limitations of each method are also discussed. Finally, we outline future research directions for interfacial interactions and suggests areas for improvement and development of characterization techniques to better understand the mechanisms of mineral-organic matter interactions.

Evaluating the low-rank coal degradation efficiency bioaugmented with activated sludge

Microbial bioaugmentation of coal is considered as a viable and ecologically sustainable approach for the utilization of low-rank coals (LRC). The search for novel techniques to derive high-value products from LRC is currently of great importance. In response to this demand, endeavors have been undertaken to develop microbially based coal solubilization and degradation techniques. The impact of supplementing activated sludge (AS) as a microbial augmentation to enhance LRC biodegradation was investigated in this study. The LRC and their biodegradation products were characterized using the following methods: excitation-emission Matrices detected fluorophores at specific wavelength positions (O, E, and K peaks), revealing the presence of organic complexes with humic properties. FTIR indicated the increased amount of carboxyl groups in the bioaugmented coals, likely due to aerobic oxidation of peripheral non-aromatic structural components of coal. The bacterial communities of LRC samples are primarily composed of Actinobacteria (up to 36.2%) and Proteobacteria (up to 25.8%), whereas the Firmicutes (63.04%) was the most abundant phylum for AS. The community-level physiological profile analysis showed that the microbial community AS had high metabolic activity of compared to those of coal. Overall, the results demonstrated successful stimulation of LRC transformation through supplementation of exogenous microflora in the form of AS.

The impact of microbial community structure changes on the migration and release of typical heavy metal (loid)s during the revegetation process of mercury-thallium mining waste slag

The effect of changes in microbial community structure on the migration and release of toxic heavy metal (loid)s is often ignored in ecological restoration. Here, we investigated a multi-metal (mercury and thallium, Tl) mine waste slag. With particular focus on its strong acidity, poor nutrition, and high toxicity pollution characteristics, we added fish manure and carbonate to the slag as environmental-friendly amendments. On this basis, ryegrass, which is suitable for the remediation of metal waste dumps, was then planted for ecological restoration. We finally explored the influence of changes in microbial community structure on the release of Tl and As in the waste slag during vegetation reconstruction. The results show that the combination of fish manure and carbonate temporarily halted the release of Tl, but subsequently promoted the release of Tl and arsenic (As), which was closely related to changes in the microbial community structure in the waste slag after fish manure and carbonate addition. The main reason for these patterns was that in the early stage of the experiment, Bacillaceae inhibited the release of Tl by secreting extracellular polymeric substances; with increasing time, Actinobacteriota became the dominant bacterium, which promoted the migration and release of Tl by mycelial disintegration of minerals. In addition, the exogenously added organic matter acted as an electron transport medium for reducing microorganisms and thus helped to reduce nitrate or As (Ⅴ) in the substrate, which reduced the redox potential of the waste slag and promoted As release. At the same time, the phylum Firmicutes, including specific dissimilatory As-reducing bacteria that are capable of converting As into a more soluble form, further promoted the release of As. Our findings provide a theoretical basis for guiding the ecological restoration of relevant heavy-metal (loid) mine waste dumps.

Driving mechanism of different nutrient conditions on microbial mediated nitrate reduction in magnetite-present river infiltration zone

Significant research is focused on the ability of riparian zones to reduce groundwater nitrate contamination. Owing to the extremely high redox activity of nitrate, naturally existing electron donors, such as organic matter and iron minerals, are crucial in facilitating nitrate reduction in the riparian zone. Here, we examined the coexistence of magnetite, an iron mineral, and nitrate, a frequently observed coexisting system in sediments, to investigate nitrate reduction features at various C/N ratios and evaluate the response of microbial communities to these settings. Additionally, we aimed to use this information as a foundation for examining the effect of nutritional conditions on the nitrate reduction process in magnetite-present environments. These results emphasise the significance of organic matter in enabling dissimilatory nitrate reduction to ammonium (DNRA) and enhancing the connection between nitrate reduction and iron in sedimentary environments. In the later phases of nitrate reduction, nitrogen fixation was the prevailing process in low-carbon environments, whereas high-carbon environments tended to facilitate the breakdown of organic nitrogen. High-throughput sequencing analysis revealed a robust association between C/N ratios and alterations in microbial community composition, providing insights into notable modifications in essential functioning microorganisms. The nitrogen-fixing bacterium Ralstonia is more abundant in ecosystems with scarce organic matter. In contrast, in settings rich in organic matter, microorganisms, such as Acinetobacter and Clostridia, which may produce ammonia, play crucial roles. Moreover, the population of iron bacteria grows in such an environment. Hence, this study proposes that C/N ratios can influence Fe(II)/Fe(III) conversions and simultaneously affect the process of nitrate reduction by shaping the composition of specific microbial communities.

Differential degradation of petroleum hydrocarbons by Shewanella putrefaciens under aerobic and anaerobic conditions

The complexity of crude oil composition, combined with the fluctuating oxygen level in contaminated environments, poses challenges for the bioremediation of oil pollutants, because of compound-specific microbial degradation of petroleum hydrocarbons under certain conditions. As a result, facultative bacteria capable of breaking down petroleum hydrocarbons under both aerobic and anaerobic conditions are presumably effective, however, this hypothesis has not been directly tested. In the current investigation, Shewanella putrefaciens CN32, a facultative anaerobic bacterium, was used to degrade petroleum hydrocarbons aerobically (using O2 as an electron acceptor) and anaerobically (using Fe(III) as an electron acceptor). Under aerobic conditions, CN32 degraded more saturates (65.65 ± 0.01%) than aromatics (43.86 ± 0.03%), with the following order of degradation: dibenzofurans > n-alkanes > biphenyls > fluorenes > naphthalenes > alkylcyclohexanes > dibenzothiophenes > phenanthrenes. In contrast, under anaerobic conditions, CN32 exhibited a higher degradation of aromatics (53.94 ± 0.02%) than saturates (23.36 ± 0.01%), with the following order of degradation: dibenzofurans > fluorenes > biphenyls > naphthalenes > dibenzothiophenes > phenanthrenes > n-alkanes > alkylcyclohexanes. The upregulation of 4-hydroxy-3-polyprenylbenzoate decarboxylase (ubiD), which plays a crucial role in breaking down resistant aromatic compounds, was correlated with the anaerobic degradation of aromatics. At the molecular level, CN32 exhibited a higher efficiency in degrading n-alkanes with low and high carbon numbers relative to those with medium carbon chain lengths. In addition, the degradation of polycyclic aromatic hydrocarbons (PAHs) under both aerobic and anaerobic conditions became increasingly difficult with increased numbers of benzene rings and methyl groups. This study offers a potential solution for the development of targeted remediation of pollutants under oscillating redox conditions.

Photosynthetic response of Chlamydomonas reinhardtii and Chlamydomonas sp. 1710 to zinc toxicity

Zinc (Zn) is an essential trace element but can lead to water contamination and ecological deterioration when present in excessive amounts. Therefore, investigating the photosynthetic response of microalgae to Zn stress is of great significance. In this study, we assessed the photosynthetic responses of neutrophilic Chlamydomonas reinhardtii and acidophilic Chlamydomonas sp. 1710 to Zn exposure for 96 h. The specific growth rate (μ), chlorophyll-a (Chl-a) content, and chlorophyll fluorescence parameters were determined. The results demonstrated that Chlamydomonas sp. 1710 was much more tolerant to Zn than C. reinhardtii, with the half-maximal inhibitory concentration (IC50) values of 225.4 mg/L and 23.4  mg/L, respectively. The μ and Chl-a content of C. reinhardtii decreased in the presence of 15  mg/L Zn, whereas those of Chlamydomonas sp. 1710 were unaffected by as high as 100  mg/L Zn. Chlorophyll fluorescence parameters indicated that the regulation of energy dissipation, including non-photochemical quenching, played a crucial role in Zn stress resistance for both Chlamydomonas strains. However, in the case of C. reinhardtii, non-photochemical quenching was inhibited by 5  mg/L Zn in the first 48 h, whereas for Chlamydomonas sp. 1710, it remained unaffected under 100  mg/L Zn. Chlamydomonas sp. 1710 also exhibited a 20 times stronger capacity for regulating the electron transfer rate than C. reinhardtii under Zn stress. The light energy utilization efficiency (α) of Chlamydomonas sp. 1710 had the most highly non-linear correlation with μ, indicating the energy utilization and regulation process of Chlamydomonas sp. 1710 was well protected under Zn stress. Collectively, our findings demonstrate that the photosystem of Chlamydomonas sp. 1710 is much more resilient and tolerant than that of C. reinhardtii under Zn stress.

Interaction of microorganisms with carbonates from the micro to the macro scales during sedimentation: Insights into the early stage of biodegradation

The assembly process of Organic Matter (OM) from single molecules to polymers and the formation process of Ca-CO3 ion-pairs are explored at the micro-scale, and then the relationship between OM and carbonate based on the results of microbially-induced carbonate precipitation (MICP) laboratory experiments is established at the macro-scale. Molecular dynamics (MD) is used to model the assembly of OM (a) in an aqueous solution, (b) on surfaces of calcite (10 1‾ 4) crystals and (c) on defective calcite (101‾ 4) crystal surfaces. From the MICP experiments, carbonate minerals containing abundant OM were precipitated and were characterized by Scanning Electron Microscopy (SEM), X-Ray Diffractometry (XRD) and Fourier Transform Infrared Spectroscopy (FTIR). The results of the MD show that OM is assembled into polymers in all three simulation systems. Although the Ca-CO3 ion-pairs and OM were briefly combined, the aggregation assembly of OM molecules and the precipitation of carbonate calcium are not related in the long run. The highly specific surface area of the defective calcite shows an increase in the adsorption of OM. The van der Waals forces, which are primarily responsible for controlling the assembly of OM molecules, increase with the degree of aggregation. According to the MICP experiments, OM is enriched on the mineral surfaces, and more OM is found at the steps of defective crystals with their larger surface areas. Through MD and MICP laboratory experiments, this work systematically describes the interaction of OM and carbonate minerals from the micro to the macro scales, and this provides insight into the interaction between OM and carbonates and biogeochemical processes related to the accumulation of OM in sediments.

Water masses influence the variation of microbial communities in the Yangtze River Estuary and its adjacent waters

The Yangtze River estuary (YRE) are strongly influenced by the Kuroshio and terrigenous input from rivers, leading to the formation of distinct water masses, however, there remains a limited understanding of the full extent of this influence. Here the variation of water masses and bacterial communities of 58 seawater samples from the YRE and its adjacent waters were investigated. Our findings suggested that there were 5 water masses in the studied area: Black stream (BS), coastal water in the East China Sea (CW), nearshore mixed water (NM), mixed water in the middle and deep layers of the East China Sea (MM), and deep water blocks in the middle of the East China Sea (DM). The CW mass harbors the highest alpha diversity across all layers, whereas the NM mass exhibits higher diversity in the surface layer but lower in the middle layers. Proteobacteria was the most abundant taxa in all water masses, apart from that, in the surface layer masses, Cyanobacterium, Bacteroidota, and Actinobacteriota were the highest proportion in CW, while Bacteroidota and Actinobacteriota were the highest proportion in NM and BS; in the middle layer, Bacteroidota and Actinobacteriota were dominant phylum in CW and BS masses, but Cyanobacterium was main phylum in NM mass; in the bottom layer, Bacteroidota and Actinobacteriota were the dominant phylum in CW, while Marininimicrobia was the dominated phylum in DM and MM masses. Network analysis suggests water masses have obvious influence on community topological characteristics, moreover, community assembly across masses also differ greatly. Taken together, these results emphasized the significant impact of water masses on the bacterial composition, topological characteristics and assembly process, which may provide a theoretical foundation for predicting alterations in microbial communities within estuarine ecosystems under the influence of water masses.

Iron coatings on carbonate rocks shape the attached bacterial aquifer community

Most studies of groundwater ecosystems target planktonic microbes, which are easily obtained via water samples. In contrast, little is known about the diversity and function of microbes adhering to rock surfaces, particularly to consolidated rocks. To investigate microbial attachment to rock surfaces, we incubated rock chips from fractured aquifers in limestone-mudstone alternations in bioreactors fed with groundwater from two wells representing oxic and anoxic conditions. Half of the chips were coated with iron oxides, representing common secondary mineralization in fractured rock. Our time-series analysis showed bacteria colonizing the chips within two days, reaching cell numbers up to 4.16 × 105 cells/mm2 after 44 days. Scanning electron microscopy analyses revealed extensive colonization but no multi-layered biofilms, with chips from oxic bioreactors more densely colonized than from anoxic ones. Estimated attached-to-planktonic cell ratios yielded values of up to 106: 1 and 103: 1, for oxic and anoxic aquifers, respectively. We identified distinct attached and planktonic communities with an overlap between 17 % and 42 %. Oxic bioreactors were dominated by proteobacterial genera Aquabacterium and Rhodoferax, while Rheinheimera and Simplicispira were the key players of anoxic bioreactors. Motility, attachment, and biofilm formation traits were predicted in major genera based on groundwater metagenome-assembled genomes and reference genomes. Early rock colonizers appeared to be facultative autotrophs, capable of fixing CO2 to synthesize biomass and a biofilm matrix. Late colonizers were predicted to possess biofilm degrading enzymes such as beta-glucosidase, beta-galactosidase, amylases. Fe-coated chips of both bioreactors featured more potential iron reducers and oxidizers than bare rock chips. As secondary minerals can also serve as energy source, they might favor primary production and thus contribute to subsurface ecosystem services like carbon fixation. Since most subsurface microbes seem to be attached, their contribution to ecosystem services should be considered in future studies.

Mineral-mediated stability of organic carbon in soil and relevant interaction mechanisms

Soil, the largest terrestrial carbon reservoir, is central to climate change and relevant feedback to environmental health. Minerals are the essential components that contribute to over 60% of soil carbon storage. However, how the interactions between minerals and organic carbon shape the carbon transformation and stability remains poorly understood. Herein, we critically review the primary interactions between organic carbon and soil minerals and the relevant mechanisms, including sorption, redox reaction, co-precipitation, dissolution, polymerization, and catalytic reaction. These interactions, highly complex with the combination of multiple processes, greatly affect the stability of organic carbon through the following processes: (1) formation or deconstruction of the mineral-organic carbon association; (2) oxidative transformation of the organic carbon with minerals; (3) catalytic polymerization of organic carbon with minerals; and (4) varying association stability of organic carbon according to the mineral transformation. Several pieces of evidence related to the carbon turnover and stability during the interaction with soil minerals in the real eco-environment are then demonstrated. We also highlight the current research gaps and outline research priorities, which may map future directions for a deeper mechanisms-based understanding of the soil carbon storage capacity considering its interactions with minerals.

Spatiotemporal successions of N, S, C, Fe, and As cycling genes in groundwater of a wetland ecosystem: Enhanced heterogeneity in wet season

Microorganisms in wetland groundwater play an essential role in driving global biogeochemical cycles. However, largely due to the dynamics of spatiotemporal surface water-groundwater interaction, the spatiotemporal successions of biogeochemical cycling in wetland groundwater remain poorly delineated. Herein, we investigated the seasonal coevolution of hydrogeochemical variables and microbial functional genes involved in nitrogen, carbon, sulfur, iron, and arsenic cycling in groundwater within a typical wetland, located in Poyang Lake Plain, China. During the dry season, the microbial potentials for dissimilatory nitrate reduction to ammonium and ammonification were dominant, whereas the higher potentials for nitrogen fixation, denitrification, methane metabolism, and carbon fixation were identified in the wet season. A likely biogeochemical hotspot was identified in the area located in the low permeable aquifer near the lake, characterized by reducing conditions and elevated levels of Fe2+ (6.65-17.1 mg/L), NH4+ (0.57-3.98 mg/L), total organic carbon (1.02-1.99 mg/L), and functional genes. In contrast to dry season, higher dissimilarities of functional gene distribution were observed in the wet season. Multivariable statistics further indicated that the connection between the functional gene compositions and hydrogeochemical variables becomes less pronounced as the seasons transition from dry to wet. Despite this transition, Fe2+ remained the dominant driving force on gene distribution during both seasons. Gene-based co-occurrence network displayed reduced interconnectivity among coupled C-N-Fe-S cycles from the dry to the wet season, underpinning a less complex and more destabilizing occurrence pattern. The rising groundwater level may have contributed to a reduction in the stability of functional microbial communities, consequently impacting ecological functions. Our findings shed light on microbial-driven seasonal biogeochemical cycling in wetland groundwater.

A review of organophosphonates, their natural and anthropogenic sources, environmental fate and impact on microbial greenhouse gases emissions - Identifying knowledge gaps

Organophosphonates (OPs) are a unique group of natural and synthetic compounds, characterised by the presence of a stable, hard-to-cleave bond between the carbon and phosphorus atoms. OPs exhibit high resistance to abiotic degradation, excellent chelating properties and high biological activity. Despite the huge and increasing scale of OP production and use worldwide, little is known about their transportation and fate in the environment. Available data are dominated by information concerning the most recognised organophosphonate - the herbicide glyphosate - while other OPs have received little attention. In this paper, a comprehensive review of the current state of knowledge about natural and artificial OPs is presented (including glyphosate). Based on the available literature, a number of knowledge gaps have been identified that need to be filled in order to understand the environmental effects of these abundant compounds. Special attention has been given to GHG-related processes, with a particular focus on CH4. This stems from the recent discovery of OP-dependent CH4 production in aqueous environments under aerobic conditions. The process has changed the perception of the biogeochemical cycle of CH4, since it was previously thought that biological methane formation was only possible under anaerobic conditions. However, there is a lack of knowledge on whether OP-associated methane is also formed in soils. Moreover, it remains unclear whether anthropogenic OPs affect the CH4 cycle, a concern of significant importance in the context of the increasing rate of global warming. The literature examined in this review also calls for additional research into the date of OPs in waste and sewage and in their impact on environmental microbiomes.

Enhancing La(III) biosorption and biomineralization with Micromonospora saelicesensis: Involvement of phosphorus and formation of monazite nano-minerals

The release of rare earth elements (REEs) from mining wastes and their applications has significant environmental implications, necessitating the development of effective prevention and reclamation strategies. The mobility of REEs in groundwater due to microorganisms has garnered considerable attention. In this study, a La(III) resistant actinobacterium, Micromonospora saelicesensis KLBMP 9669, was isolated from REE enrichment soil in GuiZhou, China, and evaluated for its ability to adsorb and biomineralize La(III). The findings demonstrated that M. saelicesensis KLBMP 9669 immobilized La(III) through the physical and chemical interactions, with immobilization being influenced by the initial La(III) concentration, biomass, and pH. The adsorption kinetics followed a pseudo-second-order rate model, and the adsorption isotherm conformed to the Langmuir model. La(III) adsorption capacity of this strain was 90 mg/g, and removal rate was 94 %. Scanning electron microscope (SEM) coupled with energy dispersive X-ray spectrometer (EDS) analysis revealed the coexistence of La(III) with C, N, O, and P. Fourier transform infrared spectroscopy (FTIR) and X-ray photoelectron spectroscopy (XPS) investigations further indicated that carboxyl, amino, carbonyl, and phosphate groups on the mycelial surface may participate in lanthanum adsorption. Transmission electron microscopy (TEM) revealed that La(III) accumulation throughout the M. saelicesensis KLBMP 9669, with some granular deposits on the mycelial surface. Selected area electron diffraction (SAED) confirmed the presence of LaPO4 crystals on the M. saelicesensis KLBMP 9669 biomass after a prolonged period of La(III) accumulation. This post-sorption nano-crystallization on the M. saelicesensis KLBMP 9669 mycelial surface is expected to play a crucial role in limiting the bioimmobilization of REEs in geological repositories.

Shewanella oneidensis MR-1 dissimilatory reduction of ferrihydrite to highly enhance mineral transformation and reactive oxygen species production in redox-fluctuating environments

Diverse paths generated by reactive oxygen species (ROS) can mediate contaminant transformation and fate in the soil/aquatic environments. However, the pathways for ROS production upon the oxygenation of redox-active ferrous iron minerals are underappreciated. Ferrihydrite (Fh) can be reduced to produce Fe(II) by Shewanella oneidensis MR-1, a representative strain of dissimilatory iron-reducing bacteria (DIRB). The microbial reaction formed a spent Fh product named mr-Fh that contained Fe(II). Material properties of mr-Fh were characterized with X-ray diffraction (XRD), scanning electron microscopy (SEM), and X-ray photoelectron spectroscopy (XPS). Magnetite could be observed in all mr-Fh samples produced over 1-day incubation, which might greatly favor the Fe(II) oxygenation process to produce hydroxyl radical (•OH). The maximum amount of dissolved Fe(II) can reach 1.1 mM derived from added 1 g/L Fh together with glucose as a carbon source, much higher than the 0.5 mM generated in the case of the Luria-Bertani carbon source. This may confirm that MR-1 can effectively reduce Fh and produce biogenetic Fe(II). Furthermore, the oxygenation of Fe(II) on the mr-Fh surface can produce abundant ROS, wherein the maximum cumulative •OH content is raised to about 120 μM within 48 h at pH 5, but it is decreased to about 100 μM at pH 7 for the case of MR-1/Fh system after a 7-day incubation. Thus, MR-1-mediated Fh reduction is a critical link to enhance ROS production, and the •OH species is among them the predominant form. XPS analysis proves that a conservable amount of Fe(II) species is subject to adsorption onto mr-Fh. Here, MR-1-mediated ROS production is highly dependent on the redox activity of the form Fe(II), which should be the counterpart presented as the adsorbed Fe(II) on surfaces. Hence, our study provides new insights into understanding the mechanisms that can significantly govern ROS generation in the redox-oscillation environment.

Unlocking the potential of biosurfactants: Production, applications, market challenges, and opportunities for agro-industrial waste valorization

Biosurfactants are eco-friendly compounds with unique properties and promising potential as sustainable alternatives to chemical surfactants. The current review explores the multifaceted nature of biosurfactant production and applications, highlighting key fermentative parameters and microorganisms able to convert carbon-containing sources into biosurfactants. A spotlight is given on biosurfactants' obstacles in the global market, focusing on production costs and the challenges of large-scale synthesis. Innovative approaches to valorizing agro-industrial waste were discussed, documenting the utilization of lignocellulosic waste, food waste, oily waste, and agro-industrial wastewater in the segment. This strategy strongly contributes to large-scale, cost-effective, and environmentally friendly biosurfactant production, while the recent advances in waste valorization pave the way for a sustainable society.

Acidithiobacillus species drive the formation of ferric-silica cemented microstructure: Insights into early hardpan development for mine site rehabilitation

Hardpan-based profiles naturally formed under semi-arid climatic conditions have substantial potential in rehabilitating sulfidic tailings, resulting from their aggregation microstructure regulated by Fe-Si cements. Nevertheless, eco-engineered approaches for accelerating the formation of complex cementation structure remain unclear. The present study aims to investigate the microbial functions of extremophiles on mineral dissolution, oxidation, and aggregation (cementation) through a microcosm experiment containing pyrites and polysilicates, of which are dominant components in typical sulfidic tailings. Microspectroscopic analysis revealed that pyrite was rapidly dissolved and massive microbial corrosion pits were displayed on pyrite surfaces. Synchrotron-based X-ray absorption spectroscopy demonstrated that approximately 30 % pyrites were oxidized to jarosite-like (ca. 14 %) and ferrihydrite-like minerals (ca. 16 %) in talc group, leading to the formation of secondary Fe precipitates. The Si ions co-dissolved from polysilicates may be embedded into secondary Fe precipitates, while these clustered Fe-Si precipitates displayed distinct morphology (e.g., "circular" shaped in the talc group, "fine-grained" shaped in the chlorite group, and "donut" shaped in the muscovite group). Moreover, the precipitates could join together and act as cementing agents aggregating mineral particles together, forming macroaggregates in talc and chlorite groups. The present findings revealed critical microbial functions on accelerating mineral dissolution, oxidation, and aggregation of pyrite and various silicates, which provided the eco-engineered feasibility of hardpan-based technology for mine site rehabilitation.