Fungal Nanophase Particles Catalyze Iron Transformation for Oxidative Stress Removal and Iron Acquisition

Simultaneous removal of hardness and organic matter from oilfield-produced water by microbially induced calcite precipitation

Oilfield-produced water (PW), the largest by-product of petroleum extraction, presents significant treatment challenges due to high concentrations of total dissolved solids, heavy metals, and organic compounds. In this study, a ureolytic bacterium Staphylococcus succinus J3, with efficient petroleum degradation and microbially induced calcite precipitation (MICP) capabilities, was screened for simultaneous removal of hardness ions and organic pollutants from PW. Strain J3 showed excellent removal of Ca2+ (95 %), organic contaminants (62 %), and heavy metals (100 % for As and Mn, 94 % for Cu, 71 % for Ba) in high salinity PW under low nutrient conditions. Mechanistic analysis revealed that the bacteria removed organic pollutants through biodegradation, and the biominerals generated by MICP further accelerated the removal of organic contaminants through adsorption. Meanwhile, molecular characterization via FT-ICR MS demonstrated the conversion of large organic molecules into smaller, less toxic compounds, facilitating the downstream treatment of PW. Furthermore, the ammonium by-product (NH4-N) from urea hydrolysis was efficiently recovered (83.73 %) as ammonium sulfate for agricultural production through Donnan dialysis (DD). This research presents a promising new approach for the pre-treatment of high-hardness organic wastewater and provides molecular-level insights into the mechanisms of organic matter removal, thus supporting the advancement and optimization of PW recycling technology.

Sulfur-mediated transformation, export and mineral complexation of organic and inorganic C, N, P and Si in dryland soils

The transformation characteristics of mineral-associated soil components have profound impacts on their physical, biological, and chemical properties in drying-affected soils, whereas their mechanisms of sequestration and transformation remain elusive. To elucidate these phenomena, the solid-phase, water extracts (labile state, LS) and alkali-extracts (complexed state, CS) of four drying-affected soil types were examined. On average, the contents of soil organic carbon (SOC), soil total nitrogen (STN), and soil total hydrogen (STH) decreased in the order: forest > grassland > agriculture > desert. The extracted dissolved organic matter (DOM)LS, DOMCS and nutrients varied greatly among soil types, which indicated the occurrence of mineralization, sequestration, neoformation, and either export or emission. In particular, the relatively high levels of dissolved inorganic carbon (DIC)LS and relatively low levels of DICCS in agricultural soils could be ascribed to the impact of human activities, i.e., tilling and cultivation, on mineral-bound DIC, leading to its export in LS forms. The stable isotopes of δ13C-SOC and their significant relationships with DICLS and SO42‒LS+CS suggest the occurrence of carbon and sulfur sequestration through the uptake of CO2, DIC, or carbonyl sulfide (COS) following their generation from SOC or DOM mineralization. In forested and agricultural soils, the humic substances (HS) components in LS forms were subjected to a substantial degradation, whereas HSCS components remained mostly unaffected, implying their occurrence in organo-mineral protection. Overall, low soil total sulfur (STS) and sulfate (SO42‒)LS+CS contents were correlated with high amounts of soil components in both the solid and liquid phases, and vice versa. These findings suggest that microbial SO42‒ might operate in the dissolution and mineralization of HS-bound organo-minerals, which would potentially generate soil inorganic carbon (SIC) or DIC, leading to either their subsequent sequestration as carbonate minerals or their exports and emissions as DIC and CO2.

A Novel Perspective on the Role of Hydroxyl Radicals in Soil Organic Carbon Mineralization within the Detritusphere: Stimulating C-Degrading Enzyme Activities

Detritusphere is a hotspot of carbon cycling in terrestrial ecosystems, yet the mineralization of soil organic carbon (SOC) within this microregion associated with reactive oxygen species (ROS) remains unclear. Herein, we investigated ROS production and distribution in the detritusphere of six representative soils and evaluated their contributions to SOC mineralization. We found that ROS production was significantly correlated with several soil chemical and biological factors, including pH, water-soluble phenols, water-extractable organic carbon, phenol oxidase activity, surface-bound or complexed Fe(II) and Fe(II) in low-crystalline minerals, highly crystalline Fe(II)-bearing minerals, and SOC. These factors collectively contributed to 99.6% of the variation in ROS production, as revealed by redundancy analyses. Among ROS, hydroxyl radicals (•OH) were key contributors to SOC mineralization, responsible for 10.4%-38.7% of CO2 emissions in ROS quenching experiments. Inhibiting •OH production decreased C-degrading enzyme activities, indicating that •OH stimulates CO2 emissions by increasing enzyme activity. Structural equation modeling further demonstrated that •OH promotes C-degrading enzyme activities by degrading water-soluble phenols to unlock the "enzyme latch" and by increasing SOC availability to upregulate C-degrading gene expression. These pathways contributed equally to SOC mineralization and exceeded its direct effect. These findings provide detailed insight into the mechanistic pathways of •OH-mediated carbon dynamics within the detritusphere.

Nanozymes and Their Potential Roles in the Origin of Life

The origin of life has long been a central scientific challenge, with various hypotheses proposed. The chemical evolution, which supposes that inorganic molecules can transform into organic molecules and subsequent primitive cells, laid the foundation for modern theories. Inorganic minerals are believed to play crucial catalytic roles in the process. However, the harsh reaction conditions of inorganic minerals hinder the accumulation of organic molecules, preventing the efficient transition from inorganic molecules to biomacromolecules. Given the inherent physicochemical properties and enzyme-like activities, this study proposes that nanozymes, nanomaterials with enzyme-like activities, act as efficient prebiotic catalysts in the origin of life. This hypothesis is based on the following: First, unlike traditional minerals, nanominerals can catalyze organic synthesis under milder conditions. Second, nanominerals can not only protect biomolecules from radiation damage but also catalyze polymerization reactions to form functional biomacromolecules and further lipid vesicles. More importantly, nanominerals are abundant in terrestrial and extraterrestrial environments. This perspective will systematically discuss the potential roles of nanozymes in the emergence of life based on the functions of minerals and the characteristics of nanozymes. We hope the research on nanozymes and the origin of life will bridge the gap between inorganic precursors and biomolecules under primitive environments.

Mineral states and sequestration processes involving soil biogenic components in various soils and desert sands of Inner Mongolia

Soil biogenic components are subject to continuous sequestration, and export from soils into the surrounding air and water environments. However, the processes involving the stability or lability of their mineral states remain still unclear. To assess these issues, we have measured various biogenic components in a number of agricultural, forest, grassland, and deep soils, as well as desert sands from Inner Mongolia, both in the solid state and liquid extracts. The contents of soil organic carbon (SOC) and soil total nitrogen (STN) were higher in soils than in sands, whilst those of soil total sulfur (STS) and inorganic carbon were higher in sands and deeper soils. The significant positive correlations found between STS and SOC, and STN, and their significant negative correlations with pH and δ13C-SOC in all soils suggest a pH-dependent sequestration of C, N, and S. The decreased stability of organo-mineral complexes at acidic pH, resulting from the acidification of humic substance (HS) functionalities, leads to a higher availability of nutrients that facilitates the sequestration of soil organic matter (SOM). Conversely, an increase in pH enhances the stability of organo-mineral complexes by promoting negatively charged HS functionalities, which reduces the availability of nutrients and the sequestration of SOM. The δ13C-SOC enrichment in desert sands (-17.63 to -7.10‰) and its depleted values in soils (-24.9 to -18.8‰) suggest the occurrence of C sequestration in desert, via uptake of enriched atmospheric CO2 (-8.4‰). The fluorescence spectra of humic substance components and their molecular weights in sands were typically different from those of soils. The predominant relatively low molecular weight (MW) (< 15-25 kDa) of alkali-extracted (complexed state: CS) components and the relatively high MW (> 25 - 15 kDa) of water-extracted (labile state: LS) components of all soils suggest, respectively, their involvement in organo-mineral complexes and for export into the surrounding environment. The quantities of LS and CS soil components differ significantly on dependence of soil characteristics, implying their corresponding lability or stability in soils. These findings will provide useful input for the management of the corresponding soil/sand ecosystems.

Reactions between ferric oxyhydroxide mineral coatings and a dimethoxyhydroquinone: A source of hydroxyl radicals

Quinones are organic molecules that facilitate electron-transfer reactions in terrestrial environments. The reduced forms, hydroquinones, are powerful reductants that can trigger non-enzymatic radical-based decomposition of organic matter and contaminants by simultaneous reduction of iron and oxygen. Iron oxides often occur as coatings on other minerals, thus our study investigated the reactions between the ferric oxyhydroxide (FeO(OH)) surface coatings on gibbsite (Al(OH)3) and 2,6-dimethoxy-1,4-hydroquinone (2,6-DMHQ). The main aim was to investigate the oxidation of 2,6-DMHQ and the generation ∙OH in the presence of O2 at low Fe concentrations in a novel setup that allows local structural characterization. The heterogeneous redox reactions between 2,6-DMHQ and the FeO(OH) coatings were studied at pH 5.0 as a function of the amount of Fe present on the gibbsite surfaces, including the effect of aging of the FeO(OH) coatings. The results showed that reactions between 2,6-DMHQ and FeO(OH) coated gibbsite under ambient conditions can generate substantial amounts of ·OH, comparable with amounts generated on pure ferrihydrite surfaces. The ·OH is the product of two sequential reactions: hydroquinone oxidation by O2 and degradation of the formed H2O2. The calculated rate constant of the former reaction is the same regardless of amount of FeO(OH) coating suggesting a surface catalytic process where 2,6-DMHQ is oxidized by O2 resulting in formation of H2O2. Subsequently, the observed induction period, the low Fe2+ (aq) concentrations in solution and the dependency of FeO(OH) coating amount influencing ·OH formation suggest that the pathway for ∙OH is through H2O2 decomposition by the surface sites on the FeO(OH) coating. Overall, this study shows that co-existence of oxygen, FeO(OH) and organic reductants, possibly secreted by soil microorganisms, creates favorable conditions for generation of ·OH contributing to decomposition of organic matter and organic pollutants in soil environments.

Molecular mechanisms of iron nanominerals formation in fungal extracellular polymeric substances (EPS) layers during fungus-mineral interactions

Extracellular polymeric substances (EPS), which envelop on fungal hyphae surface, interact strongly with minerals and play a crucial role in the formation of nanoscale minerals during biomineralization in nature environments. However, it remains poorly understood about the molecular mechanisms of nanominerals (i.e., iron nanominerals) formation in fungal EPS halos during fungus-mineral interactions. This process is vital because fungi typically grow attached to various mineral surfaces in nature. According to the changes of thickness of the fungal cell and EPS layers during the Trichoderma guizhouense NJAU 4742 and hematite cultivation experiments, we found that fungal biomineralization could trigger the formation of EPS layers. Fe-dominated nanominerals, aromatic C (283-286.1 eV), alkyl C (287.6-288.3 eV), and carboxylic C (288.4-289.1 eV) were the dominant chemical groups on the EPS layers, as determined by nanoscale secondary ion mass spectrometry (NanoSIMS), high-resolution transmission electron microscope (HRTEM), and carbon 1s near-edge X-ray absorption fine structure (NEXAFS) spectroscopy. Further, evidence from Fe K-edge X-ray absorption near-edge structure (XANES) and X-ray photoelectron spectroscopy (XPS) spectra indicated that oxygen vacancy (OV) was formed on the Fe-dominated nanomineral surface during fungus-mineral interactions, which played an important role in catalyzing H2O2 decomposition and HO∗ production. Taken together, the intrinsic peroxidase-like activity by reactive oxygen species (ROS) could modulate the Fe-dominated nanominerals formation in EPS layers to newly form a physical barrier between the cell and the external environments around hyphae, providing novel insights into the effects of ROS-mediated fungal-mineral interactions on fungal nutrient recycling, attenuation of contaminants, and biological control in nature environments.

Isolation of a methyl-reducing methanogen outside the Euryarchaeota

Methanogenic archaea are main contributors to methane emissions, and have a crucial role in carbon cycling and global warming. Until recently, methanogens were confined to Euryarchaeota, but metagenomic studies revealed the presence of genes encoding the methyl coenzyme M reductase complex in other archaeal clades1-4, thereby opening up the premise that methanogenesis is taxonomically more widespread. Nevertheless, laboratory cultivation of these non-euryarchaeal methanogens was lacking to corroborate their potential methanogenic ability and physiology. Here we report the isolation of a thermophilic archaeon LWZ-6 from an oil field. This archaeon belongs to the class Methanosuratincolia (originally affiliated with 'Candidatus Verstraetearchaeota') in the phylum Thermoproteota. Methanosuratincola petrocarbonis LWZ-6 is a strict hydrogen-dependent methylotrophic methanogen. Although previous metagenomic studies speculated on the fermentative potential of Methanosuratincolia members, strain LWZ-6 does not ferment sugars, peptides or amino acids. Its energy metabolism is linked only to methanogenesis, with methanol and monomethylamine as electron acceptors and hydrogen as an electron donor. Comparative (meta)genome analysis confirmed that hydrogen-dependent methylotrophic methanogenesis is a widespread trait among Methanosuratincolia. Our findings confirm that the diversity of methanogens expands beyond the classical Euryarchaeota and imply the importance of hydrogen-dependent methylotrophic methanogenesis in global methane emissions and carbon cycle.

Fungal biomineralization of toxic metals accelerates organic pollutant removal

Fungal biomineralization plays an important role in the biogeochemical cycling of metals in the environment and has been extensively explored for bioremediation and element biorecovery. However, the cellular and metabolic responses of fungi in the presence of toxic metals during biomineralization and their impact on organic matter transformations are unclear. This is an important question because co-contamination by toxic metals and organic pollutants is a common phenomenon in the natural environment. In this research, the biomineralization process and oxidative stress response of the geoactive soil fungus Aspergillus niger were investigated in the presence of toxic metals (Co, Cu, Mn, and Fe) and the azo dye orange II (AO II). We have found that the co-existence of toxic metals and AO II not only enhanced the fungal biomineralization of toxic metals but also accelerated the removal of AO II. We hypothesize that the fungus and in situ mycogenic biominerals (toxic metal oxalates) constituted a quasi-bioreactor, where the biominerals removed organic pollutants by catalyzing reactive oxygen species (ROS) generation resulting from oxidative stress. We have therefore demonstrated that a fungal/biomineral system can successfully achieve the goal of toxic metal immobilization and organic pollutant decomposition. Such findings inform the potential development of fungal-biomineral hybrid systems for mixed pollutant bioremediation as well as provide further understanding of fungal organic-inorganic pollutant transformations in the environment and their importance in biogeochemical cycles.

Unveiling the role of inorganic nanoparticles in Earth's biochemical evolution through electron transfer dynamics

This article explores the intricate interplay between inorganic nanoparticles and Earth's biochemical history, with a focus on their electron transfer properties. It reveals how iron oxide and sulfide nanoparticles, as examples of inorganic nanoparticles, exhibit oxidoreductase activity similar to proteins. Termed "life fossil oxidoreductases," these inorganic enzymes influence redox reactions, detoxification processes, and nutrient cycling in early Earth environments. By emphasizing the structural configuration of nanoparticles and their electron conformation, including oxygen defects and metal vacancies, especially electron hopping, the article provides a foundation for understanding inorganic enzyme mechanisms. This approach, rooted in physics, underscores that life's origin and evolution are governed by electron transfer principles within the framework of chemical equilibrium. Today, these nanoparticles serve as vital biocatalysts in natural ecosystems, participating in critical reactions for ecosystem health. The research highlights their enduring impact on Earth's history, shaping ecosystems and interacting with protein metal centers through shared electron transfer dynamics, offering insights into early life processes and adaptations.

Biological control of predatory fungi inhabiting activated sludge in wastewater treatment

The unfavorable phenomenon of activated sludge bulking that occurs in sewage treatment plants (WWTPs) is caused by the over-proliferation of filamentous bacteria that should be limited by the Lecane rotifers that feed on them; however, predatory, rotiferovorous fungi that often inhabit WWTPs pose a real threat to these organisms. To solve this problem, we investigated the interaction of the fungus Clonostachys rosea, which is a known Biological Control Agent (BCA) and the predacious Zoophagus sp. in simplified laboratory culture conditions. The presence of C. rosea in the cultures reduced the number of active traps, thus translating into a much smaller number of rotifers being caught. The mycelium of C. rosea was labeled with a red fluorescent protein (RFP). The life cycle of C. rosea that were attacking Zoophagus sp. (hunting for rotifers) is described. C. rosea spores germinate into single-celled forms and penetrate the interior of the Zoophagus mycelium where they feed on the cytoplasm. Then is the mycelium produced abundantly and forms conidiophores. This type of life strategy has not been known before. The obtained results demonstrated the potential of C. rosea as a BCA that can be used to protect rotifers in the event of an infection of activated sludge by the predatory fungi that threaten the rotifer population.

Nano-based theranostic approaches for infection control: current status and perspectives

Nano-based theranostic platforms constructed from various nanomaterials possess unique advantages in tackling bacterial and fungal infections while detecting pathogenic cells, making them a potential modality for addressing global healthcare burdens.

Mycorrhizae enhance reactive minerals but reduce mineral-associated carbon

Soil organic carbon (C) is the largest active C pool of Earth's surface and is thus vital in sustaining terrestrial productivity and climate stability. Arbuscular mycorrhizal fungi (AMF) form symbioses with most terrestrial plants and critically modulate soil C dynamics. Yet, it remains unclear whether and how AMF-root associations (i.e., mycorrhizae) interact with soil minerals to affect soil C cycling. Here we showed that the presence of both roots and AMF increased soil dissolved organic C and reactive Fe minerals, as well as litter decomposition and soil CO2 emissions. However, it reduced mineral-associated C. Also, high-resolution nanoscale secondary ion mass spectrometry images showed the existence of a thin coating (0.5-1.0 μm thick) of 56 Fe16 O- (Fe minerals) on the surface of 12 C14 N- (fungal biomass), illustrating the close physical association between fungal hyphae and soil Fe minerals. In addition, AMF genera were divergently related to reactive Fe minerals, with Glomus being positively but Paraglomus and Acaulospora negatively correlated with reactive Fe minerals. Moreover, the presence of roots and AMF, particularly when combined with litter addition, enhanced the abundances of several critical soil bacterial genera that are associated with the formation of reactive minerals in soils. A conceptual framework was further proposed to illustrate how AMF-root associations impact soil C cycling in the rhizosphere. Briefly, root exudates and the inoculated AMF not only stimulated the decomposition of litter and SOC and promoted the production of CO2 emission, but also drove soil C persistence by unlocking mineral elements and promoting the formation of reactive minerals. Together, these findings provide new insights into the mechanisms that underlie the formation of reactive minerals and have significant implications for understanding and managing soil C persistence.

The IV International Symposium on Fungal Stress and the XIII International Fungal Biology Conference

For the first time, the International Symposium on Fungal Stress was joined by the XIII International Fungal Biology Conference. The International Symposium on Fungal Stress (ISFUS), always held in Brazil, is now in its fourth edition, as an event of recognized quality in the international community of mycological research. The event held in São José dos Campos, SP, Brazil, in September 2022, featured 33 renowned speakers from 12 countries, including: Austria, Brazil, France, Germany, Ghana, Hungary, México, Pakistan, Spain, Slovenia, USA, and UK. In addition to the scientific contribution of the event in bringing together national and international researchers and their work in a strategic area, it helps maintain and strengthen international cooperation for scientific development in Brazil.

Organic carbon preservation in wetlands: Iron oxide protection vs. thermodynamic limitation

The sequestration of organic carbon (OC) in wetland sediments is influenced by the presence of oxygen or lack thereof. The mechanisms of OC sequestration under redox fluctuations, particularly by the co-mediation of reactive iron (Fe) protection and thermodynamic limitation by the energetics of the OC itself, remain unclear. Over the past 26 years, a combination of field surveys and remote sensing images had revealed a strong decline in both natural and constructed wetland areas in Tianjin. This decline could be attributed to anthropogenic landfill practices and agricultural reclamation efforts, which may have significant impacts on the oxidation-reduction conditions for sedimentary OC. The Fe-bound OC (CBD extraction) decreased by 2 to 10-fold (from 8.3 to 10% to 0.7-4.5%) with increasing sediment depth at three sites with varying water depths (WD). The high-resolution spectro-microscopy analysis demonstrated that Fe (oxyhydr)oxides were colocalized with sedimentary OC. Corresponding to lower redox potential, the nominal oxidation state of C (NOSC), which corresponds to the energy content in OC, became more negative (energy content increased) with increasing sediment depth. Taken together, the preservation of sedimentary OC is contingent on the prevailing redox conditions: In environments where oxygen availability is high, reactive Fe provides protection for OC, while in anoxic environments, thermodynamic constraints (i.e., energetic constraints) limit the oxidation of OC.

Biogenic metallic nanoparticles as enzyme mimicking agents

The use of biological systems such as plants, bacteria, and fungi for the synthesis of nanomaterials has emerged to fill the gap in the development of sustainable methods that are non-toxic, pollution-free, environmentally friendly, and economical for synthesizing nanomaterials with potential in biomedicine, biotechnology, environmental science, and engineering. Current research focuses on understanding the characteristics of biogenic nanoparticles as these will form the basis for the biosynthesis of nanoparticles with multiple functions due to the physicochemical properties they possess. This review briefly describes the intrinsic enzymatic mimetic activity of biogenic metallic nanoparticles, the cytotoxic effects of nanoparticles due to their physicochemical properties and the use of capping agents, molecules acting as reducing and stability agents and which aid to alleviate toxicity. The review also summarizes recent green synthetic strategies for metallic nanoparticles.

Electron microscopic imaging and NanoSIMS investigation on physiological responses of Aspergillus niger under Pb(II) and Cd(II) stress

In the bioremediation process, coexistence of lead (Pb) and cadmium causes complex toxicity, resulting in the difficulty of bioremediation. This study investigated the physiological responses and bioaccumulation mechanisms of the typical filamentous fungus Aspergillus niger under the coexistence of Pb and Cd. Four treatments were set up, i.e., control, sole Pb, sole Cd, and coexistence of Pb and Cd. The morphology of A. niger were observed by scanning electron microscopy (SEM) and transmission electron microscopy (TEM), respectively. Then, nano-scale secondary ion mass spectrometry (NanoSIMS) was applied to accurately investigate the distribution of heavy metals in the fungal cells under the coexistence of Pb and Cd. Finally, the metallogenic process and mineral types were simulated by Geochemist's Workbench (GWB). The electron microscopic and NanoSIMS imaging showed that Pb and Cd were accumulated in both the extracellular and intracellular regions of the A. niger cells. In particular, the accumulated Pb content was ten times higher than that of Cd. However, Cd showed stronger toxicity than Pb to A. niger. Compared with the control treatment, Cd stress resulted in a two-fold increase of cell diameter and more extracellular substances, whereas the cell diameter increased nearly four times in the coexistence treatment. Moreover, the bioaccumulation of Pb was more intense than that of Cd during competitive sorption. The GWB simulation confirmed that Pb2+ can form multiple minerals (e.g., PbC2O4, PbHPO4, and Pb3(PO4)2, etc.), which significantly weakened its toxicity on the cell surface. This study elucidated the morphological characteristics of A. niger and competitive bioaccumulation under the coexistence of Pb and Cd, which would facilitate the application of microorganisms to the bioremediation of coexisted metals.

Insights into phenanthrene attenuation by hydroxyl radicals from reduced iron-bearing mineral oxygenation

The oxygenation of Fe(II)-bearing minerals for hydroxyl radicals (HO^•) formation and contaminant attenuation receive increasing attention, while the mechanisms for specific Fe(II) species in manipulating HO^• formation and contaminant attenuation are unclear. Herein, a total of four Fe(III)-bearing minerals were applied in the reduction-oxygenation processes to produce HO^•. Results showed that the total HO^• generated from the Fe-(oxyhydr)oxides were significantly higher than those from the Fe-silicates, with the order of goethite and hematite (~1500 μmol kg^-1) > Fe-montmorillonite (~550 μmol kg^-1) > chlorite (~120 μmol kg^-1). The HO^• formation was largely hinged on the reactive Fe(II) species, i.e., the surface-adsorbed/low-crystalline Fe(II) in the Fe-bearing minerals. For the co-incubation of minerals and phenanthrene, the concentrations of phenanthrene decreased from the initial 3.0 mg L^-1 to 0.7 mg L^-1 and 1.9 mg L^-1 for Fe-montmorillonite and goethite, respectively, suggesting the HO^• mediated by the Fe-montmorillonite was more conducive for phenanthrene attenuation. The goethite tended to promote the formation of free HO^•, while the Fe-montmorillonite with interlayer structure can provide attachment sites for the surface-adsorbed/low-crystalline Fe(II), resulting in high potential for surface-bound HO^• formation and phenanthrene attenuation. This study highlights the importance of Fe-bearing minerals in manipulating HO^• formation, providing new insight into the removal of contaminants in ecosystems.

Nanoscale chemical mapping of exometabolites at fungal-mineral interfaces

Mineral-associated organic matter is an integral part of soil carbon pool. Biological processes contribute to the formation of such organo-mineral complexes when soil microbes, and in particular soil fungi, deposit a suite of extracellular metabolic compounds and their necromass on the mineral surfaces. While studied in bulk, micro- to nanoscale fungal-mineral interactions remain elusive. Of particular interest are the mutual effects at the interface between the fungal exometabolites and proximal mineral particles. In this work, we have grown saprotrophic and symbiotic fungi in contact with two soil minerals with contrasting properties: quartz and goethite, on top of X-ray transparent silicon nitride membrane windows and analyzed fungal hyphae by synchrotron-based scanning transmission X-ray microscopy in combination with near edge X-ray fine structure spectroscopy at C(K) and Fe(L) absorption edges. In the resultant chemical maps, we were able to visualize and differentiate organic compounds constituting the fungal cells, their extracellular metabolites, and the exometabolites adsorbing on the minerals. We found that the composition of the exometabolites differed between the fungal functional guilds, particularly, in their sugar to protein ratio and potassium concentration. In samples with quartz and goethite, we observed adsorption of the exometabolic compounds on the mineral surfaces with variations in their chemical composition around the particles. Although we did not observe clear alteration in the exometabolite chemistry upon mineral encounters, we show that fungal-mineral interaction result in reduction of Fe(III) in goethite. This process has been demonstrated for bulk systems, but, to our knowledge, this is the first observation on a single hypha scale offering insight into its underlying biological mechanisms. This demonstrates the link between processes initiated at the single-cell level to macroscale phenomena. Thus, spatially resolved chemical characterization of the microbial-mineral interfaces is crucial for an increased understanding of overall carbon cycling in soil.

Microbial community mediates hydroxyl radical production in soil slurries by iron redox transformation

The generation of reactive oxygen species (ROS) mediated by minerals and/or microorganisms plays a vital but underappreciated role in affecting carbon and nutrient cycles at soil-water interfaces. It is currently unknown which interactions between microbial communities and iron (Fe) minerals produce hydroxyl radical (HO^•), which is the strongest oxidant among ROS. Using a series of well-controlled anoxic incubations of soil slurries, we demonstrated that interactions between microbial communities and Fe minerals synergistically drove HO^• production (up to ∼100 nM after 21-day incubation). Microorganisms drove HO^• generation in anoxic environments predominantly by modulating iron redox transformation that was more prominent than direct production of ROS by microorganisms. Among the microbial communities, Geobacter, Paucimonas, Rhodocyclaceae_K82, and Desulfotomaculum were the key genera strongly affecting HO^• production. In manured soils, the former two species had higher abundances and were crucial for HO^• production. In contrast, the latter two species were mainly abundant and important in soils with mineral fertilizers. Our study suggests that abundant highly reactive oxidant HO^• can be generated in anoxic environments and the microbial community-mediated redox transformations of iron (oxyhydr)oxides may be responsible for the HO^• production. These findings shed light on the microbial generation of HO^• in fluctuating redox environments and on consequences for global C and nutrient cycling.

Single-cell stable isotope probing in microbial ecology

Environmental and host-associated microbiomes are typically diverse assemblages of organisms performing myriad activities and engaging in a network of interactions that play out in spatially structured contexts. As the sum of these activities and interactions give rise to overall microbiome function, with important consequences for environmental processes and human health, elucidating specific microbial activities within complex communities is a pressing challenge. Single-cell stable isotope probing (SC-SIP) encompasses multiple techniques that typically utilize Raman microspectroscopy or nanoscale secondary ion mass spectrometry (NanoSIMS) to enable spatially resolved tracking of isotope tracers in cells, cellular components, and metabolites. SC-SIP techniques are uniquely suited for illuminating single-cell activities in microbial communities and for testing hypotheses about cellular functions generated for example from meta-omics datasets. Here, we illustrate the insights enabled by SC-SIP techniques by reviewing selected applications in microbiology and offer a perspective on their potential for future research.

Molecular Trade-Offs between Lattice Oxygen and Oxygen Vacancy Drive Organic Pollutant Degradation in Fungal Biomineralized Exoskeletons

Fungal-mineral interactions can effectively alleviate cellular stress from organic pollutants, the production of which are expected to rapidly increase owing to the Earth moving into an unprecedented geological epoch, the Anthropocene. The underlying mechanisms that may enable fungi to combat organic pollution during fungal-mineral interactions remain unclear. Inspired by the natural fungal sporulation process, we demonstrate for the first time that fungal biomineralization triggers the formation of an ultrathin (hundreds of nanometers thick) exoskeleton, enriched in nanosized iron (oxyhydr)oxides and biomolecules, on the hyphae. Mapped biochemical composition of this coating at a subcellular scale via high spatial resolution (down to 50 nm) synchrotron radiation-based techniques confirmed aromatic C, C-N bonds, amide carbonyl, and iron (oxyhydr)oxides as the major components of the coatings. This nanobiohybrid system appeared to impart a strong (×2) biofunctionality for fungal degradation of bisphenol A through altering molecular-level trade-offs between lattice oxygen and oxygen vacancy. Together, fungal coatings could act as "artificial spores", which enable fungi to combat physical and chemical stresses in natural environments, providing crucial insights into fungal biomineralization and coevolution of the Earth's lithosphere and biosphere.

Non-host plants: Are they mycorrhizal networks players?

Common mycorrhizal networks (CMNs) that connect individual plants of the same or different species together play important roles in nutrient and signal transportation, and plant community organization. However, about 10% of land plants are non-mycorrhizal species with roots that do not form any well-recognized types of mycorrhizas; and each mycorrhizal fungus can only colonize a limited number of plant species, resulting in numerous non-host plants that could not establish typical mycorrhizal symbiosis with a specific mycorrhizal fungus. If and how non-mycorrhizal or non-host plants are able to involve in CMNs remains unclear. Here we summarize studies focusing on mycorrhizal-mediated host and non-host plant interaction. Evidence has showed that some host-supported both arbuscular mycorrhizal (AM) and ectomycorrhizal (EM) hyphae can access to non-host plant roots without forming typical mycorrhizal structures, while such non-typical mycorrhizal colonization often inhibits the growth but enhances the induced system resistance of non-host plants. Meanwhile, the host growth is also differentially affected, depending on plant and fungi species. Molecular analyses suggested that the AMF colonization to non-hosts is different from pathogenic and endophytic fungi colonization, and the hyphae in non-host roots may be alive and have some unknown functions. Thus we propose that non-host plants are also important CMNs players. Using non-mycorrhizal model species Arabidopsis, tripartite culture system and new technologies such as nanoscale secondary ion mass spectrometry and multi-omics, to study nutrient and signal transportation between host and non-host plants via CMNs may provide new insights into the mechanisms underlying benefits of intercropping and agro-forestry systems, as well as plant community establishment and stability.

Fungal-Mineral Interactions Modulating Intrinsic Peroxidase-like Activity of Iron Nanoparticles: Implications for the Biogeochemical Cycles of Nutrient Elements and Attenuation of Contaminants

Fungal-mediated extracellular reactive oxygen species (ROS) are essential for biogeochemical cycles of carbon, nitrogen, and contaminants in terrestrial environments. These ROS levels may be modulated by iron nanoparticles that possess intrinsic peroxidase (POD)-like activity (nanozymes). However, it remains largely undescribed how fungi modulate the POD-like activity of the iron nanoparticles with various crystallinities and crystal facets. Using well-controlled fungal-mineral cultivation experiments, here, we showed that fungi possessed a robust defect engineering strategy to modulate the POD-like activity of the attached iron minerals by decreasing the catalytic activity of poorly ordered ferrihydrite but enhancing that of well-crystallized hematite. The dynamics of POD-like activity were found to reside in molecular trade-offs between lattice oxygen and oxygen vacancies in the iron nanoparticles, which may be located in a cytoprotective fungal exoskeleton. Together, our findings unveil coupled POD-like activity and oxygen redox dynamics during fungal-mineral interactions, which increase the understanding of the catalytic mechanisms of POD-like nanozymes and microbial-mediated biogeochemical cycles of nutrient elements as well as the attenuation of contaminants in terrestrial environments.

What are the inorganic nanozymes? Artificial or inorganic enzymes!

The research on inorganic nanozymes remains very active since the first paper on the “intrinsic peroxidase-like properties of ferromagnetic nanoparticles” was published in Nature Nanotechnology in 2007. However, there is...

Fungal biomineralization

Fungi are key organisms of the biosphere with major roles in organic-matter decomposition, element cycling, plant pathogenicity, and symbioses in aquatic and terrestrial habitats. The vast majority exhibit a filamentous, branching growth form and are aerobic chemoorganotrophs that derive carbon and energy from organic substances, and are particularly associated with soil, the plant-root zone, and rock surfaces. It is now known that some fungi are lithotrophs, deriving energy from the oxidation of inorganic materials, whereas others are photoheterotrophs, deriving additional energy from light for organic matter utilization when oxygen is limited. This means that fungi are of much wider environmental significance than previously thought and explains their ubiquity in locations previously thought to be inimical to fungal existence, such as the deep subsurface and other anaerobic locations. In addition to such free-living species, fungi associated with photosynthetic partners are also of profound biosphere importance. For example, lichens, which are composed of a symbiotic association between a fungus and a phototrophic alga and/or cyanobacterium, are pioneer colonizers and bioweathering agents of rocks and minerals. Mycorrhizas are symbiotic, plant-root-associated fungi found to colonize the majority of plant genera, where they improve plant nutrition through solubilization of essential metals and phosphate from soil minerals. Biomineralization in the soil can also immobilize toxic metals in the vicinity of plant roots, thereby benefiting plant colonization and facilitating revegetation of contaminated habitats. Wherever fungi are found, transformation of metals and minerals is a key aspect of their activity, with biomineralization an important feature. Fungal biomineralization is an important facet of geomycology - namely the roles of fungi in geochemical and geophysical processes. This article seeks to highlight the concept of biomineralization as applied to fungi, the occurrence and significance of important fungal biominerals in natural and synthetic environments, and the applied potential of fungal biomineralization in nanobiotechnology.

Molybdenum Bioavailability and Asymbiotic Nitrogen Fixation in Soils are Raised by Iron (Oxyhydr)oxide-Mediated Free Radical Production

Nitrogen (N) fixation in soils is closely linked to microbially mediated molybdenum (Mo) cycling. Therefore, elucidating the mechanisms and factors that affect Mo bioavailability is crucial for understanding N fixation. Here, we demonstrate that long-term (26 years) manure fertilization increased microbial diversity and content of short-range ordered iron (oxyhydr)oxides that raised Mo bioavailability (by 2.8 times) and storage (by ∼30%) and increased the abundance of nifH genes (by ∼14%) and nitrogenase activity (by ∼60%). Nanosized iron (oxyhydr)oxides (ferrihydrite, goethite, and hematite nanoparticles) play a dual role in soil Mo cycling: (i) in concert with microorganisms, they raise Mo bioavailability by catalyzing hydroxyl radical (HO^•) production via the Fenton reactions and (ii) they increase Mo retention by association with the nanosized iron (oxyhydr)oxides. In summary, long-term manure fertilization raised the stock and bioavailability of Mo (and probably also of other micronutrients) by increasing iron (oxyhydr)oxide reactivity and intensified asymbiotic N fixation through an increased abundance of nifH genes and nitrogenase activity. This work provides a strategy for increasing biological N fixation in agricultural ecosystems.

Formation and mechanisms of hydroxyl radicals during the oxygenation of sediments in Lake Poyang, China

Seasonal flooding-drought transformation process of lake sediments lead to changes of dissolved oxygen and redox conditions and the resultant generation of hydroxyl radical (HO^•). To date, information on HO^• formation and its regulators in seasonal lake sediments is largely unexplored. In this study, a total of nineteen sediments were collected from Lake Poyang, China, with the formation and mechanisms of HO^• during the oxygenation process exploring via the incubation experiments, Fe K-edge X-ray adsorption spectroscopy, ultrafiltration, and fluorescent spectroscopy. Results showed that the concentrations of HO^• generated ranged from 3.75 ± 1.13 to 271.8 ± 22.81 μmol kg^-1, demonstrating high formation potential and obvious spatial heterogeneity. The yield of HO^• formed was positively correlated with the contents of Fe(II), sedimentary organic carbon, and dissolved organic carbon, showing a general contribution of these reduced substances to HO^• formation. Furthermore, application of Fe K-edge X-ray adsorption spectroscopy revealed the key species of sedimentary Fe-smectite for HO^• formation due to its high peroxidase-like activity. Besides inorganic Fe(II), the sedimentary dissolved organic matters (DOMs) represented an important regulator for HO^• formation, which contributed about 2-11% of the total HO^• generation. Moreover, the DOM-induced formation potential was found to be highly related to the molecular weight distribution that the low molecular weight- (LMW, <1 kDa) fraction exhibited higher HO^• formation potential than the bulk and high molecular weight- (HMW, 1 kDa-0.45 μm) counterparts. In addition, the omnipresent mineral Fe(II)-DOM interaction in sediment matrix exhibited another 2-6% of contribution to the total HO^• production. This study highlighted the importance of contents and species of Fe(II) and DOM in manipulating the HO^• yield, providing new insight into understanding the formation mechanisms of HO^• in the seasonal lake sediment.

Burst of hydroxyl radicals in sediments derived by flooding/drought transformation process in Lake Poyang, China

Oxygenation of the reduced species has been regarded as the major source for hydroxyl radical (HO) generation in aquatic environments. Yet, the O₂-induced formation of HO in lake sediments during the flooding/drought transformation process remained largely unexplored. In this study, two types of sediments from Wucheng (WC) and Nanji (NJ) area in Lake Poyang, China, were collected, respectively, with the burst of HO derived by flooding/drought transformation process exploring via the incubation experiments. Results showed that no obvious HO can be detected for the two sediments during the flooding period, while the concentrations of HO increased rapidly for the flooding/drought transformation process due to the enhanced dissolved oxygen contents. The highest concentrations of HO in the surface sediment were 2.45 ± 0.19 μmol kg^-1 for WC sediment and 0.69 ± 0.25 μmol kg^-1 for NJ sediment, showing higher burst potential of HO for the former. The contents of Fe(II) in the surface sediments for WC area (589.3 ± 37.29 mg kg^-1) were about two times higher than those for NJ area (308.4 ± 94.01 mg kg^-1) during the flooding period. Oxygenation of the surface Fe(II) contributed significantly to the burst of HO in the flooding/drought transformation process. Moreover, the higher percentage of humic-like substances in WC sediment indicated that the dissolved humic fraction exhibited also important role in the HO formation due to electrons transfer under redox conditions. This study highlighted the importance of reactive reduced species in manipulating the burst of HO in lake sediment, which is essential for understanding the geochemical cycling of several major and trace elements as well as the behavior and fate of the contaminants in aquatic ecosystems.

Coupling thermophilic composting and vermicomposting processes to remove Cr from biogas residues and produce high value-added biofertilizers

Removing pollutants and producing high value-added products are essential steps for sustainable disposal and utilization of biogas residues. Here, a coupled thermophilic composting and vermicomposting process was used to remove Cr from biogas residues, and the composting products were co-fermented with the plant growth-promoting fungus Trichoderma to produce high value-added biofertilizers. The results showed that thermophilic composting for 37 d markedly increased the total content of Cr but decreased the percentage of available Cr fractions. Synchrotron-radiation-based observations further provided direct evidence of the binding sites to support the results from traditional sequential extraction. At a density of 60 g earthworm/kg biogas residues, vermicomposting removed 23-31% of Cr from biogas residues. After vermicomposting, co-fermentation of biogas residues and Trichoderma was optimized, in which Trichoderma spores were 2-5 × 10⁸ cfu/g substrates. Together, coupling thermophilic composting and vermicomposting processes is a promising technique to remove a portion of heavy metals from biogas residues.

Mycology: Protein Control of Fungal Nanoparticle Formation

The ability of fungi to immobilize metals is an extraordinary phenomenon. Now, a protein involved in the formation of copper carbonate nanoparticles has been identified, and suggests that the process is under the control of the fungus, opening new avenues for the synthesis of nanomaterials.