HyGAnno: hybrid graph neural network-based cell type annotation for single-cell ATAC sequencing data.

Reliable cell type annotations are crucial for investigating cellular heterogeneity in single-cell omics data. Although various computational approaches have been proposed for single-cell RNA sequencing (scRNA-seq) annotation, high-quality cell labels are still lacking in single-cell sequencing assay for transposase-accessible chromatin (scATAC-seq) data, because of extreme sparsity and inconsistent chromatin accessibility between datasets. Here, we present a novel automated cell annotation method that transfers cell type information from a well-labeled scRNA-seq reference to an unlabeled scATAC-seq target, via a parallel graph neural network, in a semi-supervised manner. Unlike existing methods that utilize only gene expression or gene activity features, HyGAnno leverages genome-wide accessibility peak features to facilitate the training process. In addition, HyGAnno reconstructs a reference-target cell graph to detect cells with low prediction reliability, according to their specific graph connectivity patterns. HyGAnno was assessed across various datasets, showcasing its strengths in precise cell annotation, generating interpretable cell embeddings, robustness to noisy reference data and adaptability to tumor tissues.

Light-wave dynamic control of magnetism.

The enigmatic interplay between electronic and magnetic phenomena observed in many early experiments and outlined in Maxwell's equations propelled the development of modern electromagnetism1. Today, the fully controlled evolution of the electric field of ultrashort laser pulses enables the direct and ultrafast tuning of the electronic properties of matter, which is the cornerstone of light-wave electronics2-7. By contrast, owing to the lack of first-order interaction between light and spin, the magnetic properties of matter can only be affected indirectly and on much longer timescales, through a sequence of optical excitations and subsequent rearrangement of the spin structure8-16. Here we introduce the regime of ultrafast coherent magnetism and show how the magnetic properties of a ferromagnetic layer stack can be manipulated directly by the electric-field oscillations of light, reducing the magnetic response time to an external stimulus by two orders of magnitude. To track the unfolding dynamics in real time, we develop an attosecond time-resolved magnetic circular dichroism detection scheme, revealing optically induced spin and orbital momentum transfer in synchrony with light-field-driven coherent charge relocation17. In tandem with ab initio quantum dynamical modelling, we show how this mechanism enables the simultaneous control of electronic and magnetic properties that are essential for spintronic functionality. Our study unveils light-field coherent control of spin dynamics and macroscopic magnetic moments in the initial non-dissipative temporal regime and establishes optical frequencies as the speed limit of future coherent spintronic applications, spin transistors and data storage media.

Construction of Hydration Layer for Proton Transport by Implanting the Hydrophilic Center Ag0 in Nickel Metal-Organic Frameworks.

The directional arrangement of H2O molecules can effectively regulate the ordered protons transfer to improve transport efficiency, which can be controlled by the interaction between materials and H2O. Herein, a strategy to build a stable hydration layer in metal-organic framework (MOF) platforms, in which hydrophilic centers that can manipulate H2O molecules are implanted into MOF cavities is presented. The rigid grid-Ni-MOF is selected as the supporting material due to the uniformly distributed cavities and rigid structures. The Ag0 possesses potential combination ability with the hydrophilic substances, so it is introduced into the MOF as hydration layer centers. Relying on the strong interaction between Ag0 and H2O, the H2O molecules can rearrange around Ag0 in the cavity, which is intuitively verified by DFT calculation and molecular dynamics simulation. The establishment of a hydration layer in Ag@Ni-MOF regulates the chemical properties of the material and gives the material excellent proton conduction performance, with a proton conductivity of 4.86 × 10-2 S cm-1.

Species pool, local assembly processes: Disentangling the mechanisms determining bacterial α- and ß-diversity during forest secondary succession.

Across ecology, and particularly within microbial ecology, there is limited understanding how the generation and maintenance of diversity. Although recent work has shown that both local assembly processes and species pools are important in structuring microbial communities, the relative contributions of these mechanisms remain an important question. Moreover, the roles of local assembly processes and species pools are drastically different when explicitly considering the potential for saturation or unsaturation, yet this issue is rarely addressed. Thus, we established a conceptual model that incorporated saturation theory into the microbiological domain to advance the understanding of mechanisms controlling soil bacterial diversity during forest secondary succession. Conceptual model hypotheses were tested by coupling soil bacterial diversity, local assembly processes and species pools using six different forest successional chronosequences distributed across multiple climate zones. Consistent with the unsaturated case proposed in our conceptual framework, we found that species pool consistently affected α-diversity, even while local assembly processes on local richness operate. In contrast, the effects of species pool on ß-diversity disappeared once local assembly processes were taken into account, and changes in environmental conditions during secondary succession led to shifts in ß-diversity through mediation of the strength of heterogeneous selection. Overall, this study represents one of the first to demonstrate that most local bacterial communities might be unsaturated, where the effect of species pool on α-diversity is robust to the consideration of multiple environmental influences, but ß-diversity is constrained by environmental selection.

HEAT SHOCK PROTEIN 90.6 interacts with carbon and nitrogen metabolism components during seed development.

Carbon and nitrogen are the two main nutrients in maize (Zea mays L.) kernels, and kernel filling and metabolism determine seed formation and germination. However, the molecular mechanisms underlying the relationship between kernel filling and corresponding carbon and nitrogen metabolism remain largely unknown. Here, we found that HEAT SHOCK PROTEIN 90.6 (HSP90.6) is involved in both seed filling and the metabolism processes of carbon and nitrogen. A single-amino acid mutation within the HATPase_c domain of HSP90.6 led to small kernels. Transcriptome profiling showed that the expression of amino acid biosynthesis- and carbon metabolism-related genes was significantly downregulated in the hsp90.6 mutant. Further molecular evidence showed strong interactions between HSP90.6 and the 26S proteasome subunits REGULATORY PARTICLE NON-ATPASE6 (RPN6) and PROTEASOME BETA SUBUNITD2 (PBD2). The mutation of hsp90.6 significantly reduced the activity of the 26S proteasome, resulting in the accumulation of ubiquitinated proteins and defects in nitrogen recycling. Moreover, we verified that HSP90.6 is involved in carbon metabolism through interacting with the 14-3-3 protein GENERAL REGULATORY FACTOR14-4 (GF14-4). Collectively, our findings revealed that HSP90.6 is involved in seed filling and development by interacting with the components controlling carbon and nitrogen metabolism.

Inhibition of UHRF1 Improves Motor Function in Mice with Spinal Cord Injury.

Spinal-cord injury (SCI) is a severe condition that can lead to limb paralysis and motor dysfunction, and its pathogenesis is not fully understood. The objective of this study was to characterize the differential gene expression and molecular mechanisms in the spinal cord of mice three days after spinal cord injury. By analyzing RNA sequencing data, we identified differentially expressed genes and discovered that the immune system and various metabolic processes play crucial roles in SCI. Additionally, we identified UHRF1 as a key gene that plays a significant role in SCI and found that SCI can be improved by suppressing UHRF1. These findings provide important insights into the molecular mechanisms of SCI and identify potential therapeutic targets that could greatly contribute to the development of new treatment strategies for SCI.

Neutrophil Extracellular Traps Regulate Surgical Brain Injury by Activating the cGAS-STING Pathway.

Surgical brain injury (SBI), induced by neurosurgical procedures or instruments, has not attracted adequate attention. The pathophysiological process of SBI remains sparse compared to that of other central nervous system diseases thus far. Therefore, novel and effective therapies for SBI are urgently needed. In this study, we found that neutrophil extracellular traps (NETs) were present in the circulation and brain tissues of rats after SBI, which promoted neuroinflammation, cerebral edema, neuronal cell death, and aggravated neurological dysfunction. Inhibition of NETs formation by peptidylarginine deiminase (PAD) inhibitor or disruption of NETs with deoxyribonuclease I (DNase I) attenuated SBI-induced damages and improved the recovery of neurological function. We show that SBI triggered the activation of cyclic guanosine monophosphate-adenosine monophosphate synthase stimulator of interferon genes (cGAS-STING), and that inhibition of the cGAS-STING pathway could be beneficial. It is worth noting that DNase I markedly suppressed the activation of cGAS-STING, which was reversed by the cGAS product cyclic guanosine monophosphate-adenosine monophosphate (cGMP-AMP, cGAMP). Furthermore, the neuroprotective effect of DNase I in SBI was also abolished by cGAMP. NETs may participate in the pathophysiological regulation of SBI by acting through the cGAS-STING pathway. We also found that high-dose vitamin C administration could effectively inhibit the formation of NETs post-SBI. Thus, targeting NETs may provide a novel therapeutic strategy for SBI treatment, and high-dose vitamin C intervention may be a promising translational therapy with an excellent safety profile and low cost.

Exploring the role of gut microbiota in migraine risk: a two-sample Mendelian randomization study.

OBJECTIVES: The presence of intestinal flora in the gut has been linked to migraines in recent studies, but whether the association is causal or due to bias remains to be clarified. We aimed to explore whether there is a potential causal relationship between gut microbiota and migraine risk with this study. MATERIALS AND METHODS: We conducted a two-sample Mendelian randomized analysis study to explore whether gut microbiota has a causal relationship with migraine using publicly available data from large-scale genome-wide association studies. The inverse variance weighting was used as the main method, and weighted median and MR-Egger were used as supplementary methods for causal inference. Sensitivity analyses, including leave-one-out analysis, Cochran Q test, and MR-Egger intercept test, were used to verify the robustness of the results. RESULTS: After rigorous quality control of the results, we identified that genetic predisposition towards a higher abundance of genus.Lactobacillus was causally associated with higher of migraine (IVW OR = 1.10, 95% CI = 1.03 - 1.18, p = .004), whereas the higher abundance of family.Prvotellaceae predicted a decreased risk of migraine (IVW OR = 0.89, 95% CI = 0.80 - 0.98, p = .02). Sensitivity analyses indicated the results were not biased by pleiotropy. CONCLUSION: According to our research, there is evidence showing that gut microbiota may be involved in migraine development, which suggested that a stool examination might be helpful to recognize those with a higher risk of migraine. Further mechanisms remained to be elucidated in future studies.

Ingenious Modulation of Third-Order Nonlinear Optical Response of Zr-MOFs through Defect Engineering Based on a Mixed-Linker Strategy.

Defect engineering plays a pivotal role in regulating electronic structure and facilitating charge transfer, yielding captivating effects on third-order nonlinear optical (NLO) properties. In this work, we utilized a mixed-linker strategy to intentionally disrupt the initial periodic arrangement of UiO-66 and construct defects. Specifically, we incorporated tetrakis(4-carboxyphenyl)porphyrin (TCPP) with an exceptionally electron-rich delocalization system into the framework of UiO-66 using a one-pot solvothermal method, ingeniously occupying the partial distribution sites of the Zr6 clusters. Compared to UiO-66, the NLO absorption and refraction performance of TCPP/UiO-66 were significantly improved. Additionally, due to the presence of nitrogen-rich sites that can accommodate metal ions in the porphyrin ring of TCPP, Co(II), Ni(II), Cu(II), and Zn(II) are introduced into TCPP/UiO-66, extending the d-π conjugation effect to further regulate the defects. The NLO absorption behavior transforms saturation absorption (SA) to reverse saturation absorption (RSA), while the refraction behavior shifts from self-defocusing to self-focusing. This work shows that defects can effectively regulate the electronic structure, while TCPP plays a crucial role in significantly enhancing electron delocalization.

Third-Order Nonlinear Optical Modulation Behavior of Photoresponsive Bimetallic MOFs.

Bimetallic metal-organic frameworks (MOFs) capable of sensing external stimuli will provide more possibilities for further regulating third-order nonlinear optical (NLO) properties. In this work, we synthesized bimetallic MOFs (ZnCu-MOF and ZnCd-MOF) through central metal exchange using a photoresponsive Zn-MOF as a precursor. Compared with Zn-MOF, both ZnCu-MOF and ZnCd-MOF exhibit significantly enhanced third-order NLO absorption properties. This is mainly attributed to the introduction of metal ions with different electron configurations that can adjust the bandgap of MOFs and enhance electron delocalization, thus promoting electron transfer. Interestingly, the bimetallic MOFs show a transition from reverse saturation absorption (RSA) to saturation absorption (SA) after exposure to ultraviolet irradiation, as they retain the properties of directional photogenerated electron transfer. Photoresponsive bimetallic MOFs not only have the effect of bimetallic modulation of electronic structures but also have the characteristics of photoinduced electron transfer, exhibiting diversified optical properties. These findings provide a novel method for the development of multifunctional NLO materials.

Co-Doped Porous Carbon/Carbon Nanotube Heterostructures Derived from ZIF-L@ZIF-67 for Efficient Microwave Absorption.

Carbon-based magnetic metal composites derived from metal-organic frameworks (MOFs) are promising materials for the preparation of broadband microwave absorbers. In this work, the leaf-like co-doped porous carbon/carbon nanotube heterostructure was obtained using ZIF-L@ZIF-67 as precursor. The number of carbon nanotubes can be controlled by varying the amount of ZIF-67, thus regulating the dielectric constant of the sample. An optimum reflection loss of -42.2 dB is attained when ZIF-67 is added at 2 mmol. An effective absorption bandwidth (EAB) of 4.8 GHz is achieved with a thickness of 2.2 mm and a filler weight of 12%. The excellent microwave absorption (MA) ability is generated from the mesopore structure, uniform heterogeneous interfaces, and high conduction loss. The work offers useful guidelines to devise and prepare such nanostructured materials for MA materials.

VgrG Spike Dictates PAAR Requirement for the Assembly of the Type VI Secretion System.

Widely employed by Gram-negative pathogens for competition and pathogenesis, the type six protein secretion system (T6SS) can inject toxic effectors into neighboring cells through the penetration of a spear-like structure comprising a long Hcp tube and a VgrG-PAAR spike complex. The cone-shaped PAAR is believed to sharpen the T6SS spear for penetration but it remains unclear why PAAR is required for T6SS functions in some bacteria but dispensable in others. Here, we report the conditional requirement of PAAR for T6SS functions in Aeromonas dhakensis, an emerging human pathogen that may cause severe bacteremia. By deleting the two PAAR paralogs, we show that PAAR is not required for T6SS secretion, bacterial killing, or specific effector delivery in A. dhakensis. By constructing combinatorial PAAR and vgrG deletions, we demonstrate that deletion of individual PAAR moderately reduced T6SS functions but double or triple deletions of PAAR in the vgrG deletion mutants severely impaired T6SS functions. Notably, the auxiliary-cluster-encoded PAAR2 and VgrG3 are less critical than the main-cluster-encoded PAAR1 and VgrG1&2 proteins to T6SS functions. In addition, PAAR1 but not PAAR2 contributes to antieukaryotic virulence in amoeba. Our data suggest that, for a multi-PAAR T6SS, the variable role of PAAR paralogs correlates with the VgrG-spike composition that collectively dictates T6SS assembly. IMPORTANCE Gram-negative bacteria often encode multiple paralogs of the cone-shaped PAAR that sits atop the VgrG-spike and is thought to sharpen the spear-like T6SS puncturing device. However, it is unclear why PAAR is required for the assembly of some but not all T6SSs and why there are multiple PAARs if they are not required. Our data delineate a VgrG-mediated conditional requirement for PAAR and suggest a core-auxiliary relationship among different PAAR-VgrG modules that may have been acquired sequentially by the T6SS during evolution.

Guest-Induced Multilevel Charge Transport Strategy for Developing Metal-Organic Frameworks to Boost Photocatalytic CO2 Reduction.

Encapsulating photogenerated charge-hopping nodes and space transport bridges within metal-organic frameworks (MOFs) is a promising method of boosting the photocatalytic performance. Herein, this work embeds electron transfer media (9,10-bis(4-pyridyl)anthracene (BPAN)) in MOF cavities to build multi-level electron transfer paths. The MOF cavities are accurately regulated to investigate the significance of the multi-level electron transfer paths in the process of CO2 photoreduction by evaluating the difference in the number of guest media. The prepared MOFs, {[Co(BPAN)(1,4-dicarboxybenzene)(H2 O)2 ]·BPAN·2H2 O} and {[Co(BPAN)2 (4,4'-biphenyldicarboxylic acid)2 (H2 O)2 ]·2BPAN·2H2 O} (denoted as BPAN-Co-1 and BPAN-Co-2), exhibit efficient visible-light-driven CO2 conversion properties. The CO photoreduction efficacy of BPAN-Co-2 (5598 µmol g-1  h-1 ) is superior to that of most reported MOF-based catalysts. In addition, the enhanced CO2 photoreduction ability is supported by density functional theory (DFT). This work illustrates the feasibility of realizing charge separation characteristics in MOF catalysts at the molecular level, and provides new insight for designing high-performance MOFs for artificial photosynthesis.

Drivers of nematode diversity in forest soils across climatic zones.

Nematodes are the most abundant multi-cellular animals in soil, influencing key processes and functions in terrestrial ecosystems. Yet, little is known about the drivers of nematode abundance and diversity in forest soils across climatic zones. This is despite forests covering approximately 30% of the Earth's land surface, providing many crucial ecosystem services but strongly varying in climatic conditions and associated ecosystem properties across biogeographic zones. Here, we collected nematode samples from 13 forests across a latitudinal gradient. We divided this gradient into temperate, warm-temperate and tropical climatic zones and found that, across the gradient, nematode abundance and diversity were mainly influenced by soil organic carbon content. However, mean annual temperature and total soil phosphorus content in temperate zones, soil pH in warm-temperate zones, and mean annual precipitation in tropical zones were more important in driving nematode alpha-diversity, biomass and abundance. Additionally, nematode beta-diversity was higher in temperate than in warm-temperate and tropical zones. Together, our findings demonstrate that the drivers of nematode diversity in forested ecosystems are affected by the spatial scale and climatic conditions considered. This implies that high resolution studies are needed to accurately predict how soil functions respond if climate conditions move beyond the coping range of soil organisms.

VgrG-dependent effectors and chaperones modulate the assembly of the type VI secretion system.

The type VI secretion system (T6SS) is a spear-like nanomachine found in gram-negative pathogens for delivery of toxic effectors to neighboring bacterial and host cells. Its assembly requires a tip spike complex consisting of a VgrG-trimer, a PAAR protein, and the interacting effectors. However, how the spike controls T6SS assembly remains elusive. Here we investigated the role of three VgrG-effector pairs in Aeromonas dhakensis strain SSU, a clinical isolate with a constitutively active T6SS. By swapping VgrG tail sequences, we demonstrate that the C-terminal ~30 amino-acid tail dictates effector specificity. Double deletion of vgrG1&2 genes (VgrG3+) abolished T6SS secretion, which can be rescued by ectopically expressing chimeric VgrG3 with a VgrG1/2-tail but not the wild type VgrG3. In addition, deletion of effector-specific chaperones also severely impaired T6SS secretion, despite the presence of intact VgrG and effector proteins, in both SSU and Vibrio cholerae V52. We further show that SSU could deliver a V. cholerae effector VasX when expressing a plasmid-borne chimeric VgrG with VasX-specific VgrG tail and chaperone sequences. Pull-down analyses show that two SSU effectors, TseP and TseC, could interact with their cognate VgrGs, the baseplate protein TssK, and the key assembly chaperone TssA. Effectors TseL and VasX could interact with TssF, TssK and TssA in V. cholerae. Collectively, we demonstrate that chimeric VgrG-effector pairs could bypass the requirement of heterologous VgrG complex and propose that effector-stuffing inside the baseplate complex, facilitated by chaperones and the interaction with structural proteins, serves as a crucial structural determinant for T6SS assembly.

Aging-induced pseudouridine synthase 10 impairs hematopoietic stem cells.

Aged hematopoietic stem cells (HSC) exhibit compromised reconstitution capacity and differentiation-bias towards myeloid lineage, however, the molecular mechanism behind it remains not fully understood. In this study, we observed that the expression of pseudouridine (Ψ) synthase 10 is increased in aged hematopoietic stem and progenitor cells (HSPC) and enforced protein of Ψ synthase 10 (PUS10) recapitulates the phenotype of aged HSC, which is not achieved by its Ψ synthase activity. Consistently, we observed no difference of transcribed RNA pseudouridylation profile between young and aged HSPC. No significant alteration of hematopoietic homeostasis and HSC function is observed in young Pus10-/- mice, while aged Pus10-/- mice exhibit mild alteration of hematopoietic homeostasis and HSC function. Moreover, we observed that PUS10 is ubiquitinated by E3 ubiquitin ligase CRL4DCAF1 complex and the increase of PUS10 in aged HSPC is due to aging-declined CRL4DCAF1- mediated ubiquitination degradation signaling. Taken together, this study for the first time evaluated the role of PUS10 in HSC aging and function, and provided a novel insight into HSC rejuvenation and its clinical application.

DNA methylation-regulated LINC02587 inhibits ferroptosis and promotes the progression of glioma cells through the CoQ-FSP1 pathway.

BACKGROUND: Long noncoding RNAs (lncRNAs) are considered key players in the formation and development of tumors. Herein, Gene Expression Profiling Interactive Analysis (GEPIA) was employed as a bioinformatics technology. LINC02587 is differentially expressed in bladder urothelial cancer, glioblastoma, lung adenocarcinoma, lung SCC, melanoma, and other tumor tissue and cells. However, its impact on the emergence of glioma and its mechanism is remaining elusive. METHODS: Some of the in vitro assays employed in this study were the CCK-8 / Annexin-V / Transwell assays, colony formation, and wound healing, together with Western blot (WB) evaluation. MSP / BSP assays were employed for assessing the CpG island's methylation status in the LINC02587 promoter. Through transcriptome, ferroptosis-related experiments, and WB evaluation, it was confirmed that LINC02587 is correlated with the regulation of ferroptosis in tumor cells, and CoQ-Fsp1 is one of its regulatory pathways. Moreover, the underlined in-vitro results were further validated by in-vivo studies. RESULTS: The current study shows that the promoter sequence of LINC02587 is regulated by methylation. The silencing of LINC02587 can inhibit cellular proliferative, migrative, and invasive properties, and induce ferroptosis within gliomas through the CoQ-FSP1 pathway. CONCLUSIONS: LINC02587 is likely to be a novel drug target in treating glioma.

Utilizing Linear Polymers to Optimize Remanent Polarization and Construct Multilayer Interfaces to Obtain High-Efficient Poly(vinylidene fluoride)-Based Energy-Storage Composites.

Polyvinylidene fluoride (PVDF) has been widely studied as a ferroelectric polymer for energy dielectric applications. However, high-polarization PVDF has a low-efficiency issue, owing to high residual polarization. This study introduces highly insulating, low-loss linear polycarbonate (PC) into PVDF-based dielectrics. The PC layer optimizes the remanent polarization (Dr) of PVDF and maintains it within a small range, thus achieving a high charge-discharge efficiency. The multilayer structural design of PVDF-based dielectrics adjusts the interlayer electric field distribution. We have thoroughly studied the influence of the number and proportion of PC layers on the polarization and breakdown of the multilayer films as well as achieved collaborative regulation of dual parameters. Our results indicate that three layers of PC-PVDF-PC (CPC) films containing a large proportion of PC can polarize under high electric fields and maintain excellent charge-discharge efficiency, achieving an energy density and efficiency of 11.48 J/cm3 and 92.4%, respectively, under 610 kV/mm. The PVDF-based dielectrics prepared in this work are all organic films, and their flexibility and foldability are conducive to the preparation of flexible devices.

Rational Construction of Metal Organic Framework Hybrid Assemblies for Visible Light-Driven CO2 Conversion.

Photocatalytic reduction of CO2 to value-added chemicals is known to be a promising approach for CO2 conversion. The design and preparation of ideal photocatalysts for CO2 conversion are of pivotal significance for the sustainable development of the whole society. In this work, we integrated two functional organic linkers to prepare a novel metal organic framework (MOF) photocatalyst {[Co(9,10-bis(4-pyridyl)anthracene)0.5(bpda)]·4DMF} (Co-MOF). The existence of anthryl and amino groups leads to a wide range of visible light absorption and efficient separation of photogenerated electrons. To extend the lifetime of photogenerated electrons in the photocatalytic system, we modified Co-MOF particles onto g-C3N4. As expected, Co-MOF/g-C3N4 composites exhibited an ultrahigh selectivity (more than 97%) in the photocatalytic process, and the highest CO production rate (1824 µmol/g/h) was 7.1 and 27.2 times of Co-MOFs and g-C3N4, respectively. What's more, we also discussed the reaction mechanism of the Co-MOF/g-C3N4 photocatalytic CO2 reduction, and this work paves the pathway for designing photocatalysts with ideal CO2 reduction performance.

Spatiotemporal response of water quality in fragmented mangroves to anthropogenic activities and recommendations for restoration.

Mangroves have received substantial attention for their pivotal role as ecological barriers between land and sea, owing to their capacity to effectively capture considerable quantities of terrestrial pollutants. Mangrove fragmentation has been a widespread global trend. There is limited information on the water quality status of these small scattered mangrove patches in coastal sub-developed areas, coupled with a paucity of efficient and intuitive assessment methodologies. To address this gap, the Water Quality Index (WQI) was introduced to evaluate the spatiotemporal characteristics of mangrove water quality. The major sources of pollution and anthropogenic activities that affect mangrove water quality were identified. The results revealed an average WQI value of 44.1 ± 13.3 for mangrove patches, consistently indicating a "low" water quality classification throughout all seasons. Both the size and natural conditions impact the water quality of mangroves. The large artificial patch (WQI: 56.4 ± 7.61) and the natural patch (WQI: 46.6 ± 13.6) exhibited relatively superior water quality, while the WQI value of a size-equivalent artificial patch compared with the natural patch is 38.6 ± 11.8. Aquaculture was the primary human activity that adversely affected the water quality of mangroves, and the potential sources of pollution were rainfall runoff and river discharge. These findings elucidate the unfavorable water quality characteristics and dominant pollution of fragmented mangroves, and validate the applicability of the WQI method for long-term evaluation of the water quality in mangrove patches. This study provides a basis for decision-making in water quality assessment and management of coastal wetlands and marine ecosystems. Scientific guidance to the management for mangrove protection and restoration was offered, such as regulating aquaculture activities, controlling non-point source pollution, implementing mangrove reforestation by using native species in historical mangrove sites.