Effective risk assessment and control of environmental antibiotic resistance depend on comprehensive information about antibiotic resistance genes (ARGs) and their microbial hosts. Advances in sequencing technologies and bioinformatics have enabled the identification of ARG hosts using metagenome-assembled contigs and genomes. However, these approaches often suffer from information loss and require extensive computational resources. Here we introduce a bioinformatic strategy that identifies ARG hosts by prescreening ARG-like reads (ALRs) directly from total metagenomic datasets. This ALR-based method offers several advantages: (1) it enables the detection of low-abundance ARG hosts with higher accuracy in complex environments; (2) it establishes a direct relationship between the abundance of ARGs and their hosts; and (3) it reduces computation time by approximately 44–96% compared to strategies relying on assembled contigs and genomes. We applied our ALR-based strategy alongside two traditional methods to investigate a typical human-impacted environment. The results were consistent across all methods, revealing that ARGs are predominantly carried by Gammaproteobacteria and Bacilli, and their distribution patterns may indicate the impact of wastewater discharge on coastal resistome. Our strategy provides rapid and accurate identification of antibiotic-resistant bacteria, offering valuable insights for the high-throughput surveillance of environmental antibiotic resistance. This study further expands our knowledge of ARG-related risk management in future.
Fluid–rock interactions involving chemical dissolution, mechanical erosion, and multiphase flow are central to a wide range of geological and engineering processes, yet they remain poorly understood due to the lack of integrated in situ observation tools. Existing methods often compromise between spatial resolution and temporal dynamics. Here, we develop a real-rock microfluidic platform that enables simultaneous visualization and quantification of erosion dynamics in multiphase reactive systems. The platform integrates fluorescence microscopy, micro-particle image velocimetry, and ion chromatography to monitor the coupled evolution of solid–liquid–gas interfaces and flow velocity fields at micrometer-scale resolution. Microfluidic chips fabricated directly from limestone preserve natural mineral heterogeneity, and the platform enables direct observation of rock surface evolution and multiphase flow behavior. This facilitates decoupled analysis of chemical dissolution and mechanical erosion—two processes often difficult to isolate in traditional systems. Using this system, we investigate erosion during acid–rock interactions and identify a transition between two regimes—transport-limited and reaction-limited—controlled by CO2 bubble mobility. In the transport-limited regime, immobile bubbles confine flow to thin films, enhancing dissolution and particle detachment. In the reaction-limited regime, surface-adhered bubbles shield reactive areas and reduce shear stress, suppressing erosion. We derive scaling laws that distinguish chemical and mechanical erosion rates and validate a theoretical model for the critical Péclet number marking the regime transition. This study advances understanding of erosion under multiphase flow and introduces a versatile experimental framework for probing pore-scale reactive transport. The platform can be extended to other rock types and fluids, offering a powerful tool for studying geochemical, physical, and biological processes in complex subsurface environments.
Salt crystallization within micro-fractures poses a significant challenge in shale gas production by impeding gas diffusion. This study investigates the real-time behavior of gas flow-induced salt crystallization within a visualized micro-fracture network. Observations reveal that salt crystals initially propagate along the fracture surface before exhibiting perpendicular growth. Crystal nucleation during the saturation stage occurs within a few seconds, while subsequent growth in the supersaturated stage takes approximately 15–20 s. Gas flow drives the evaporation of immobile water, leading to salt precipitation. Furthermore, increasing gas flow rate and decreasing solution salinity are found to accelerate crystal growth. To mitigate plugging damage caused by salt crystallization, controlling pressure differences and solution salinity is crucial.
Fe(II)-catalyzed ferrihydrite (Fh) transformation is a critical process in biogeochemical cycling and contributes to paleoenvironmental reconstruction, yet the underlying mechanisms by which organic matter modulates these transformations remain poorly understood. This study elucidates how four common carboxylic ligands (acetate, oxalate, malonate and citrate), representing mono-, di- and tri-carboxylic types, regulate each step of Fe(II)-catalyzed Fh transformation, ultimately shaping transformation kinetics, and product phases. Batch transformation experiments under anoxic conditions at pH 7.0 were conducted to monitor Fe(II) speciation and intermediate labile Fe(III) (Fe(III)labile) accumulation over time, and the temporal evolution of mineral phases, morphologies, and particle sizes was investigated using powder X-ray diffraction, Fourier transform infrared spectroscopy, and transmission electron microscopy. By decoupling individual reaction step, we revealed the distinct effects of these ligands on Fe(II) adsorption on Fh, Fe(II)-Fh interfacial electron transfer (IET), and the repolymerization of Fe(III)labile into secondary minerals. The mono-carboxylic ligand acetate exhibits minimal influence on these reaction steps within the studied concentration range (0.4–2 mM). Di-carboxylic ligands (malonate and oxalate, 0.2–1 mM) reduce Fe(II) adsorption, with stronger inhibition at higher concentrations, while citrate uniquely enhances Fe(II) adsorption by forming ternary surface complexes. These results indicate that the multi-carboxylic ligands, in contrast to mono-carboxylic acetate with negligible effect, exhibit dual, concentration-dependent effects on Fe(II)-catalyzed Fh transformation: at low concentrations, they primarily enhance the electron-donating capacity of surface-associated Fe(II), thereby accelerating Fe(III)labile accumulation through promoted Fe(II)-Fh IET. As ligand concentration increases, their inhibition of Fe(III)labile repolymerization becomes dominant, markedly suppressing the consumption and nucleation of Fe(III)labile. Moreover, these inhibitory effects are more pronounced for ligands with more carboxyl groups. Notably, the strong linear correlation between effective (uncomplexed) Fe(III)labile concentrations and secondary mineral formation rates demonstrates that carboxylic ligands primarily regulate Fh transformation by modulating the availability of Fe(III)labile for nucleation, with the concept of “effective” Fe(III)labile, as refined in this study, offering a more precise mechanistic and quantitative descriptor of the reactive Fe(III) pool that remains available for nucleation despite partial complexation by carboxylic ligands. Although both are dicarboxylic ligands, malonate and oxalate differentially direct Fh transformation by altering the surface free energy and nucleation barriers of lepidocrocite and goethite through distinct adsorption structures, thus shaping their morphologies, particle sizes, and relative proportions. This study offers new mechanistic insight into how carboxylic ligands regulate Fe(II)-catalyzed Fh transformation, enhancing understanding of iron mineral-organic matter interactions and their implications for iron cycling and mineral evolution in natural environments.
Despite its critical role in regulating the global climate and carbon cycle, the evolution of deep Pacific circulation has not been fully deciphered during the last glacial cycle. The effect of deep Pacific hydrographic change (e.g. oxygenation and circulation) on atmospheric CO2 variation is still uncertain. Here, we study redox-sensitive elements including V-U-Mn and benthic foraminiferal δ13C at the HYIV2015-B9 site in the southern South China Sea (SCS) to reconstruct the oxygenation and δ13C signals of water masses during the last glacial cycle. The intra-basin benthic foraminiferal δ13C gradient suggests enhanced stratification of the deep Pacific during the glacial compared to the interglacial, implying sluggish abyssal Pacific overturning. This is consistent with weak Pacific Deep Water (PDW) ventilation, as indicated by high contents of authigenic V and U, and low authigenic Mn. The inferred sluggish abyssal Pacific overturning is probably associated with less transport of Lower Circumpolar Deep Water, facilitating the expansion of respired carbon storage in the glacial deep Pacific. Meanwhile, the atmospheric CO2 rise is closely related to active abyssal Pacific overturning since late MIS 5, particularly when considering the impact of Southern Ocean upwelling modulated by Earth's obliquity. Overall, our data indicate the critical role of abyssal Pacific overturning in the carbon cycle, revealing the potential pathway for deep carbon dioxide outgassing in the North Pacific.
OBJECTIVES: Patients with polypoidal choroidal vasculopathy (PCV) exhibit variability in response to anti-VEGF therapy. This study aimed to analyse the aqueous humour proteomic profiles of PCV patients and provide preliminary insights for the identification of biomarkers associated with anti-VEGF drug responsiveness. METHODS: PCV patients who were treatment-naïve or untreated for more than 3 months were prospectively recruited from two hospitals in Beijing and Tianjin. Based on the relative changes in central macular thickness (ΔCMT/baseline-CMT) before and after anti-VEGF treatment, the PCV patients were divided into a good response (GR) group (≤-25%) and a poor response (PR) group (>-25%). Aqueous humour proteomics was performed by the Data-independent Acquisition-Mass Spectrometry (DIA-MS) method, and differentially expressed proteins (DEPs) analysis between the different PCV groups and the control group was conducted. Key DEPs were selected for preliminary validation in the aqueous humour using the Luminex method retrospectively. RESULTS: A total of 31 PCV patients (31 eyes) were included, 13 in the GR group and 18 in the PR group. A total of 414 DEPs were identified, including 36 significantly upregulated proteins, such as G protein regulatory factor 10 (RGS10), podocin (PODN) and epidermal growth factor (EGF), and 32 downregulated proteins, including RAB11FIP4 (Rab11 family-interacting protein 4), α-synuclein (SNCA), haemoglobin subunit δ (HBD) and interleukin 6 (IL6). Compared to the cataract control group (10 eyes), 134 proteins were significantly upregulated, and 72 were downregulated. KEGG pathway enrichment analysis revealed that the GR and PR groups differ in terms of cell communication, and cell signal transduction. Protein-protein interaction analysis revealed interactions between EGF and various DEPs. Validation of aqueous humour proteins using the Luminex method revealed that changes in the levels of EGF were associated with the anti-VEGF treatment response in PCV patients. CONCLUSIONS: PCV patients with good or poor anti-VEGF responses exhibit distinct aqueous humour proteomic profiles. Aqueous EGF may serve as a biomarker for the 'precise treatment' of PCV.
Iron (oxyhydr)oxide nanoparticles (IONPs) are formed in many aquatic and soil systems through nucleation and growth in solution (homogeneous precipitation), and at soil-water interfaces (heterogeneous precipitation). This review summarizes the roles of metal ions, organics, and microbes in the nucleation and growth of IONPs in natural settings. Metal ions can adsorb onto mineral surfaces that act as substrates to modify heterogeneous precipitation processes at soil (mineral/organic)–water interfaces. Further, metal ions could also affect homogeneous precipitation through lattice substitution or surface adsorption onto IONPs. Similarly, organic matter can interfere with heterogeneous IONP formation through adsorbing onto mineral surfaces, and can affect homogeneous IONP formation by complexing with iron ions and adsorbing onto IONP surfaces. Indeed, the physicochemical diversity of mineral surfaces and organic matter properties, especially regarding organic functional groups which have varied complexation and (de)protonation capabilities, can profoundly affect these processes. Microbial influences arise through the production of extracellular polymeric substances (EPS) and the redox modulation of the surrounding environment, which alter electron transfer dynamics and surface reactivity to affect the formation of IONPs. This review provides an integrated view of the roles of metals, organics and microbes in IONP formation, which can not only help in the understanding of the iron cycle, but also the biogeochemical fate of contaminants.
Iron (oxyhydr)oxide nanoparticles (IONPs), which are ubiquitous in many natural aquatic and soil systems, can strongly interact with nutrient and contaminant species in the environment through their large specific surface areas and redox reactivity, thus controlling the transport and fate of these elements. Following their formation, IONPs often undergo aggregation and phase transformation processes that collectively determine their long-term environmental stability. The aggregation of IONPs reduces colloidal stability and can lead to deposition and immobilization, whereas stable dispersed colloids can remain mobile and transport associated elements over long distances. The phase transformations of metastable, poorly crystalline IONPs (e.g., ferrihydrite) into more crystalline iron (oxhydr)oxides (e.g., goethite, hematite, and magnetite) profoundly alter particle properties and influence the retention or release of sorbed or structurally incorporated species. This review focuses on IONP aggregation and phase transformation as key processes controlling long-term IONP stability and critically examines how they are influenced by three common environmental factors: metal ions, organic matter (OM), and microbial activity. Metal ions can adsorb to IONP surfaces to modify surface charges or be structurally incorporated to affect IONP crystallography, thereby modulating inter-particle forces and transformation rates. OM can adsorb to IONP surfaces, and, depending on its concentration and molecular characteristics, it can either stabilize particles via electrostatic and/or steric repulsion, or promote aggregation through charge neutralization and bridging effects. Further, organic ligands can also often inhibit IONP transformation or alter transformation pathways by binding to reactive surface sites. Microbial activity influences IONP stability through extracellular polymeric substances (EPS) that coat or bridge particles, and through redox processes that generate or consume Fe(II), thereby either dispersing IONPs or accelerating their transformation into more stable mineral phases. This review summarizes present research on the effects of IONP interactions with metals, organics, and microbes on IONP aggregation and transformation. Such an understanding is crucial for predicting IONP stability and transport in the environment and the long-term cycling of associated organic and inorganic contaminants and nutrients.
Cyanobacteria are promising platforms for light-driven carbon fixation and carbohydrate biosynthesis. However, optimization strategies that focus solely on carbon allocation are insufficient to achieve substantial improvements in yield and sustainability. Here, Synechococcuselongatus PCC 7942 was engineered to enhance sucrose production by simultaneously increasing total carbon input and reinforcing the artificial sink. The engineered strain secreted 5.821 g L−1 sucrose, which was 27.4 times higher than the wild-type. Transcriptomic analysis revealed upregulation of abundant genes involved in carbon fixation, sucrose biosynthesis, and electron transport chains. Furthermore, a synthetic light-driven consortium was established to directly convert CO2 into value-added compounds. This system produced 323.5 mg L−1 polyhydroxybutyrate, reducing CO2 emissions by 12.4 g per g of polyhydroxybutyrate compared to conventional heterotrophic processes. These findings highlight the potential of cyanobacteria-based systems for carbon-negative biomanufacturing, demonstrating their role in advancing sustainable carbohydrate and biochemical production while exemplifying circular bioeconomy principles.