Lake ecological restoration of vegetation removal mitigates algal blooms and alters landscape patterns of water and sediment bacteria.

Elucidating the influences of ecological restoration measure of lakeshore vegetation removal on water quality and biological community is an important but underestimated subject. We adopted molecular and statistical tools to estimate ecological restoration performance in a plateau lake receiving vegetation removal and simultaneously investigated variabilities of bacterial communities in water and sediment. Significant decreases in lake trophic level and algal bloom degree followed notable decreases in water total nitrogen and total phosphorus after vegetation removal. Non-significant changes in sediment nutrients accompanied remarkable variabilities of abundance and composition of nutrient-cycling functional genes (NCFGs) of sediment bacteria. Taxonomic and phylogenetic α-diversities, functional redundancies, and dispersal potentials of bacteria in water and sediment decreased after vegetation removal, and community successions of water and sediment bacteria were separately significant and non-significant. There were opposite changes in ecological attributes of bacteria in water and sediment in response to vegetation removal, including niche breadth, species replacement, richness difference, community complexity, and community stability. Species replacement rather than richness difference affected more on taxonomic ß-diversities of bacteria in water and sediment before and after vegetation removal, and determinism rather than stochasticity dominated bacterial community assemblage. Our results highlighted vegetation removal mitigated algal bloom and affected differently on landscapes of water and sediment bacteria. These findings point to dominant ecological mechanisms underlying landscape shifts in water and sediment bacteria in a disturbed lake receiving vegetation removal and have the potential to guide lake ecological restoration.

Thoracic Radiotherapy Improves the Survival in Patients With EGFR-Mutated Oligo-Organ Metastatic Non-Small Cell Lung Cancer Treated With Epidermal Growth Factor Receptor-Tyrosine Kinase Inhibitors: A Multicenter, Randomized, Controlled, Phase III Trial.

PURPOSE: This multicenter, randomized, phase III clinical trial (Northern Radiation Oncology Group of China-002) focused on patients with oligo-organ metastatic non-small cell lung cancer (NSCLC) who have epidermal growth factor receptor (EGFR) mutations. We aimed to investigate whether first-line concurrent thoracic radiotherapy (TRT) and EGFR-tyrosine kinase inhibitors (TKIs), compared with TKIs alone, could achieve better survival. MATERIALS AND METHODS: The patients in the TKI plus TRT group received 60 Gy to primary lung tumor and positive regional lymph nodes. Radiotherapy for metastases to other sites was determined by clinicians. The primary end point was the progression-free survival (PFS). Secondary end points included overall survival (OS) and treatment-related adverse events (TRAEs). The first and second interim analyses were performed in March 2021 and March 2022. RESULTS: Between April 14, 2016, and February 25, 2022, a total of 118 patients were enrolled. Compared with the TKI alone group, the TKI plus TRT group achieved significantly better PFS (hazard ratio [HR], 0.57; P = .004) and OS (HR, 0.62; P = .029). The median PFS was 10.6 months in the TKI alone group and 17.1 months in the TKI plus TRT group. The median OS was 26.2 months and 34.4 months in the TKI alone group and TKI plus TRT group, respectively. The TKI plus TRT group showed better local control but was associated with a higher incidence of severe TRAEs (11.9% v 5.1%). CONCLUSION: For patients with EGFR-mutated oligo-organ metastatic NSCLC treated with first-line EGFR-TKIs, concurrent TRT improves the PFS and OS, and TRAEs are acceptable and tolerable.

Dissolved organic matter (DOM) rather than warming and eutrophication directly affects partial pressure of CO2 (pCO2) in mesocosm systems.

Environmental warming and eutrophication pose significant challenges to shallow lake systems, where dissolved organic matter (DOM) serves as a diverse and intricate mixture of organic macromolecules, playing a pivotal role in aquatic ecosystems. Despite its complexity, comprehending the interplay between environmental changes and DOM composition alterations and their subsequent impacts on aqueous CO2 partial pressure (pCO2) is essential for a better understanding of carbon cycling. Yet, our current understanding in this realm remains limited. To address this gap, mesocosm systems were established to investigate how elevated water temperature and eutrophication, alongside changes in DOM composition, influence pCO2 dynamics. Results indicate that while temperature and nutrient levels do not directly influence pCO2 fluctuations, they indirectly affect aqueous pCO2 through their modulation of DOM composition. Elevated temperature and nutrient concentrations notably enhance both the production and degradation of indigenous protein-like organic matter and increase the accumulation of humic-like organic compounds, with phosphorus released from sediment playing a particularly significant role. Furthermore, the degradation rate of protein-like organic matter significantly exceeds its accumulation rate. On the other hand, the impact of water eutrophication on DOM composition surpasses that of temporal temperature variations, with a 2∼4 °C temperature rise showing minimal effects on DOM composition. Notably, the degradation of protein-like organic matter markedly increases aqueous pCO2, while the rise in humic-like organic matter in water exerts minimal influence on pCO2 concentrations. A comprehensive understanding of carbon cycling processes under environmental changes will facilitate effective management of lake ecosystems and the advancement of carbon mitigation technologies.

Biochemical profiling of the protein encoded by grass carp reovirus genotype II.

In this study, we obtained the whole genome sequence of GCRV-DY197 and investigated the localization, post-translational modifications, and host interactions of the 11 viral proteins encoded by GCRV-DY197 in grass carp ovary (GCO) cells. The whole genome sequence is 24,704 kb and contains 11 segments (S1-S11). Subcellular localization showed that the VP1, VP2, VP3, VP5, VP56, and VP35 proteins were localized in both cytoplasm and nucleus, whereas the NS79, VP4, VP41, VP6, and NS38 proteins were localized in the cytoplasm. The NS79 and NS38 proteins were phosphorylated, and the ubiquitination modification sites were identified in VP41 and NS38. An interaction network containing 9 viral proteins and 140 host proteins was also constructed. These results offer a theoretical basis for an in-depth understanding of the biochemical characteristics and pathogenic mechanism of GCRV-II.

A droplet digital PCR assay to detect Chinese rice-field eels rhabdovirus.

Chinese rice-field eels rhabdovirus (CrERV) causes haemorrhagic disease in Chinese rice-field eels (Monopterus albus), leading to significant mortality and economic losses. Sensitive detection of CrERV nucleic acids is essential to control the spread of this pathogen and to treat infected individuals. Herein, we developed an efficient and sensitive droplet digital PCR (ddPCR) method to rapidly detect and quantify CrERV. The ddPCR assay optimal conditions were an annealing temperature of 53°C, and primer and probe concentrations of 0.5 and 0.25 µM, respectively. The assay had a diagnostic sensitivity of 0.23 copies/µL, and was highly specific, showing no cross reactivity with other viruses (infectious haematopoietic necrosis virus, grass carp reovirus, spring viremia of carp virus, largemouth bass ranavirus, carp edema virus, Chinese giant salamander iridovirus, and white spot syndrome virus). Real-time quantitative PCR testing of 30 Chinese rice-field eels samples detected CrERV in 7 samples (23.3%), whereas ddPCR detected CrERV in 12 samples (40%), demonstrating its higher sensitivity. Thus, ddPCR represents an advanced method to absolutely quantify CrERV in infected fish with low virus concentrations, providing a valuable tool to manage the spread and impact of CrERV.

Species pool and local assembly processes drive ß diversity of ammonia-oxidizing and denitrifying microbial communities in rivers along a latitudinal gradient.

Both regional species pool and local community assembly mechanism drive the microbial diversity patterns across geographical gradients. However, little has been done to separate their effects on the ß diversity patterns of microbial communities involved in nitrogen (N) cycling in river ecosystems. Here, we use high-throughput sequencing of the archaeal amoA, bacterial amoA, nirK, and nirS genes, null model, and neutral community model to distinguish the relative importance of species pool and local assembly processes for ammonia-oxidizing and denitrifying communities in river wetlands along a latitudinal gradient in eastern China. Results indicated that the ß diversity of the nirS-type denitrifying community co-varied with γ diversity and environmental heterogeneity, implying that regional species pool and heterogeneous selection explained variation in ß diversity. However, the ß diversity of ammonia-oxidizing and nirK-type denitrifying communities did not correlate with γ diversity and environmental heterogeneity. The continuous hump distribution of ß deviation along the latitudinal gradient and the lower species dispersal rate indicated that the dispersal limitation shaped the variation in ß diversity of ammonia-oxidizing and nirK-type denitrifying communities. Additionally, biotic interactions drove ammonia-oxidizing and nirS-type denitrifying communities by influencing species co-occurrence patterns. Our study highlights the importance of regional species pool and local community assembly processes in shaping geographical patterns of N-cycling microorganisms and extends knowledge of their adaptability to a continuously changing environment on a large scale.

Identification of Aeromonas veronii as the Pathogen Associated with Massive Mortality in Bronze Gudgeon (Coreius heterodon).

Aeromonas veronii, an opportunistic pathogen toward aquatic organisms, was identified as the causative pathogen (isolate WH10) in diseased bronze gudgeon via bacterial isolation, and morphological, physiological, biochemical, and molecular characterization. WH10 exerted its pathogenicity via five virulence genes, including those encoding cytotoxic enterotoxins (act and alt), lipase (lip), a quorum sensing-controlled virulence factor (LuxS), and a Type III secretion system inner membrane component (ascV). WH10 was shown to be sensitive to compound sulfamethoxazoles, cefothiophene, doxycycline, and sulfamethoxazole. Toward bronze gudgeon, WH10 had a median lethal dose (LD50) of 1.36 × 106 colony forming units/mL. Analysis of blood parameters of diseased fish revealed significant increases in monocytes and neutrophils, but decreased numbers of lymphocytes. Serum aspartate aminotransferase activity and triglyceride concentration were significantly higher in diseased fish than in healthy fish. The reverse was noted for alkaline phosphatase, total protein, albumin, total cholesterol, and glucose. Thus, Aeromonas veronii is implicated as the causative agent of the mass mortality observed in bronze gudgeon, warranting further investigations into the diagnosis, epidemiology, prevention, and treatment of this infectious disease.

Metagenomic insights into nitrogen-cycling microbial communities and their relationships with nitrogen removal potential in the Yangtze River.

Nitrogen (N) pollution is a major threat to river ecosystems worldwide. Elucidating the community structure of N-cycling microorganisms in rivers is essential to understanding how ecosystem processes and functions will respond to increasing N inputs. However, previous studies generally focus on limited functional genes through amplicon sequencing or quantitative PCR techniques and cannot cover all N-cycling microorganisms. Here, metagenomic sequencing and genome binning were used to determine N-cycling genes in water, channel sediments, and riparian soils of the Yangtze River, which has been heavily polluted by N. Additionally, the denitrification and anaerobic ammonium oxidation (anammox) rates that reflect N removal potential were measured using 15N isotope pairing technique. Results showed that functional genes involved in organic N metabolism (i.e., organic degradation and synthesis) and nitrate reduction pathways (i.e., dissimilatory and assimilatory nitrate reduction to ammonium and denitrification) were more abundant and diverse than other N-cycling genes. A total of 121 metagenome-assembled genomes (MAGs) were identified to be involved in N-cycling processes, and the key MAGs were mainly taxonomically classified as Alphaproteobacteria and Gammaproteobacteria. The abundance and diversity of most N-cycling genes were higher in soils and sediments than in water, as well as higher in downstream and midstream than in upstream sites. These spatial variations were explained not only by local environment and vegetation but also by geographical and climatic factors. N removal process (i.e., denitrification and anammox) rates were significantly related to the abundance or diversity of several N-cycling genes, and climate and edaphic factors could regulate denitrification and anammox rates directly and indirectly through their effects on functional genes. Overall, these results provide a new avenue for further understanding the biogeographic patterns and environmental drivers of N-cycling microorganisms in rivers from the metagenomic perspective.

Predicting Disease-Metabolite Associations Based on the Metapath Aggregation of Tripartite Heterogeneous Networks.

The exploration of the interactions between diseases and metabolites holds significant implications for the diagnosis and treatment of diseases. However, traditional experimental methods are time-consuming and costly, and current computational methods often overlook the influence of other biological entities on both. In light of these limitations, we proposed a novel deep learning model based on metapath aggregation of tripartite heterogeneous networks (MAHN) to explore disease-related metabolites. Specifically, we introduced microbes to construct a tripartite heterogeneous network and employed graph convolutional network and enhanced GraphSAGE to learn node features with metapath length 3. Additionally, we utilized node-level and semantic-level attention mechanisms, a more granular approach, to aggregate node features with metapath length 2. Finally, the reconstructed association probability is obtained by fusing features from different metapaths into the bilinear decoder. The experiments demonstrate that the proposed MAHN model achieved superior performance in five-fold cross-validation with Acc (91.85%), Pre (90.48%), Recall (93.53%), F1 (91.94%), AUC (97.39%), and AUPR (97.47%), outperforming four state-of-the-art algorithms. Case studies on two complex diseases, irritable bowel syndrome and obesity, further validate the predictive results, and the MAHN model is a trustworthy prediction tool for discovering potential metabolites. Moreover, deep learning models integrating multi-omics data represent the future mainstream direction for predicting disease-related biological entities.

Internal transformation and damming regulate the longitudinal variation of DOM bioavailability in a large river.

Understanding the spatial patterns of dissolved organic matter (DOM) and factors that influence them is crucial for maintaining river ecosystem functions and riverine health, considering the significant role of DOM in water quality and aquatic ecosystems. Nevertheless, there is limited knowledge regarding the spatial variation of DOM bioavailability and the factors driving them in large river systems. This study involved 39 sampling locations along the main stem of the Changjiang River, spanning its entire length (>5000 km) during a dry season. Spatial patterns of DOM were assessed by measurements of DOC concentrations and eight fluorescence DOM indices, namely fluorescence index (FI-A and FI-B), Trytophan/Tyrosine, Humic A, Humic C, humification indices (HIX-A and HIX-B), and Freshness index (ß/α). The results revealed that the water DOM in the main stem of the Changjiang River primarily originated from terrestrial sources. A decline in DOM bioavailability was observed from the upper to the lower basin, aligning with the carbon processing prediction rather than the river continuum concept (RCC). The pure effect of physicochemical factors (25.30%) was greater than that of geographic factors (9.40%). The internal transformation processes determined the significant longitudinal decreases of DOM bioavailability. While no significant difference in DOM bioavailability was observed between reaches before and after the dams, the construction of dams was found to improve DOM bioavailability at the subsection scale and reduce the spatial autocorrelation of DOM bioavailability across the entire basin.

Plant diversity is more important than soil microbial diversity in explaining soil multifunctionality in Qinghai-Tibetan plateau wetlands.

The Qinghai-Tibetan Plateau harbors rich and diverse wetlands that provide multiple ecological functions simultaneously. Although the relationships between biodiversity and wetland functioning have been well studied in recent decades, the links between the multiple features of plant and microbial communities and soil multifunctionality (SMF) remain unknown in the high-altitude wetlands that are extremely sensitive to human disturbance. Here, using the single function, averaging, weighted, and multiple-threshold methods, we calculated the SMF of Qinghai-Tibetan wetlands based on 15 variables associated with soil nutrient status, nutrient cycle, and greenhouse gas emission. We then related SMF to multidimensional (species, phylogenetic, and functional) diversity of plants and soil microorganisms and microbial network modules. The results showed that plant diversity explained more variance in SMF than soil microbial diversity, and plant species richness and phylogenetic distance were positive predictors of SMF. Bacterial network modules were more positively related to SMF than fungal network modules, and the alpha diversity of bacterial network modules contributed more to SMF than the diversity of the whole bacterial community. Pediococcus, Hirsutella, and Rhodotorula were biomarkers for SMF and had significant relationships with nitrogen mineralization and greenhouse gas emissions. Together, these results highlight the importance of plant diversity and bacterial network modules in determining the SMF, which are crucial to predicting the response of ecosystem functioning to biodiversity loss under intensifying anthropogenic activities.

In Vitro Toxicity and Modeling Reveal Nanoplastic Effects on Marine Bivalves.

Nanoplastics (NPs) represent a growing concern for global environmental health, particularly in marine ecosystems where they predominantly accumulate. The impact of NPs on marine benthic organisms, such as bivalves, raises critical questions regarding ecological integrity and food safety. Traditional methods for assessing NP toxicity are often limited by their time-intensive nature and ethical considerations. Herein, we explore the toxicological effects of NPs on the marine bivalve Ruditapes philippinarum, employing a combination of in vitro cellular assays and advanced modeling techniques. Results indicate a range of adverse effects at the organismal level, including growth inhibition (69.5-108%), oxidative stress, lipid peroxidation, and DNA damage in bivalves, following exposure to NPs at concentrations in the range of 1.6 × 109-1.6 × 1011 particles/mL (p/mL). Interestingly, the growth inhibition predicted by models (54.7-104%), based on in vitro cellular proliferation assays, shows strong agreement with the in vivo outcomes of NP exposure. Furthermore, we establish a clear correlation between cytotoxicity observed in vitro and the toxicological responses at the organismal level. Taken together, this work suggests that the integration of computational modeling with in vitro toxicity assays can predict the detrimental effects of NPs on bivalves, offering insightful references for assessing the environmental risk assessment of NPs in marine benthic ecosystems.

Polyphyllin I Sensitizes Cisplatin-Resistant Human Cervical Cancer Cells to Cisplatin Treatment.

Cervical cancer (CC) is a common gynecological malignancy, and improving cisplatin sensitivity has become a hot topic in CC chemotherapy research. Polyphyllin I (PPI), a potent bioactive compound found in Rhizoma Paridis, known for its anticancer properties, remains underexplored in CC resistance. In this study, we evaluated PPI's impact on cisplatin-resistant CC cells and elucidated its underlying mechanism. Our findings reveal that PPI enhances the sensitivity of cisplatin-resistant CC cells to the drug, promotes apoptosis, and inhibits cell migration. Mechanistically, PPI was found to regulate p53 expression and its target genes, and suppressing p53 expression reverses PPI's sensitizing effect in drug-resistant CC cells. In conclusion, PPI showed promise in sensitizing cisplatin-resistant human CC cells to cisplatin treatment, suggesting that it could serve as a potent adjunct therapy for cervical cancer, particularly for cases that have developed resistance to cisplatin, thereby providing a promising basis for further clinical investigation into PPI for enhancing the efficacy of existing chemotherapy regimens in resistant cervical cancer.

Differential responses of temperature sensitivity of greenhouse gases emission to seasonal variations in plateau riparian zones.

Riparian zones, regarded as hotspots for greenhouse gas (GHG) emissions, where the variation in temperature sensitivity (Q10) of GHG emissions is crucial for assessing GHG budgets under global warming. However, the seasonal Q10 of GHG emissions from high-elevation riparian zones and underlying microbial mechanisms are poorly documented. This study focuses on seasonal Q10 patterns of GHG emissions from riparian zones along the Lhasa River on the Tibetan Plateau. CO2 and CH4 emissions from riparian soils were more sensitive to temperature in spring than in summer. The opposite trend was observed for Q10 of N2O emissions. Soil organic carbon (SOC) had relatively large direct effects on the Q10-CO2 value in summer, whereas soil nitrate nitrogen (SNO3--N) was the determinant of Q10-CO2 value in spring. mcrA:pmoA and soil microbial biomass C (SMBC) had strong direct effects on the Q10 of CH4 emissions in summer; the Q10-CH4 value in spring was significantly affected by the mcrA abundance. SMBC and the nirK + nirS abundance were key factors affecting the Q10-N2O value. Q10-CO2 and Q10-CH4 values exhibited strong seasonalities in the lower reaches of riparian soils, mainly due to the seasonalities of SNO3--N and mcrA:pmoA, respectively. The Q10-N2O value in the middle and upper reaches of riparian soils presented seasonality, which was largely due to the seasonalities of soil ammonia nitrogen and microbial biomass carbon. During thawing, plant productivity increased, substrate carbon was sufficient, microbial biomass increased, and inorganic nitorgen and denitrifier abundance decreased, causing 29.67% and 37.47% decreases in the Q10-CO2 and Q10-CH4 values, respectively, and a 70.85% increase in the Q10-N2O value, indicating that the potential release of N2O from riparian zones along the plateau river was more susceptible to seasonal variations. Our findings are conducive to accurately evaluating the potential contribution of GHG emissions from high-elevation riparian zones to global warming.

Denitrification dominates dissimilatory nitrate reduction across global natural ecosystems.

Denitrification, anaerobic ammonium oxidation (anammox), and dissimilatory nitrate reduction to ammonium (DNRA) are three competing processes of microbial nitrate reduction that determine the degree of ecosystem nitrogen (N) loss versus recycling. However, the global patterns and drivers of relative contributions of these N cycling processes to soil or sediment nitrate reduction remain unknown, limiting our understanding of the global N balance and management. Here, we compiled a global dataset of 1570 observations from a wide range of terrestrial and aquatic ecosystems. We found that denitrification contributed up to 66.1% of total nitrate reduction globally, being significantly greater in estuarine and coastal ecosystems. Anammox and DNRA could account for 12.7% and 21.2% of total nitrate reduction, respectively. The contribution of denitrification to nitrate reduction increased with longitude, while the contribution of anammox and DNRA decreased. The local environmental factors controlling the relative contributions of the three N cycling processes to nitrate reduction included the concentrations of soil organic carbon, ammonium, nitrate, and ferrous iron. Our results underline the dominant role of denitrification over anammox and DNRA in ecosystem nitrate transformation, which is crucial to improving the current global soil N cycle model and achieving sustainable N management.

Linking ecosystem multifunctionality to microbial community features in rivers along a latitudinal gradient.

Microorganisms regulate numerous ecosystem functions and show considerable differences along a latitudinal gradient. Although studies have revealed the latitudinal patterns of microbial community structure and single ecosystem function, the latitudinal patterns of ecosystem multifunctionality (EMF) and how microbial communities affect EMF along a latitudinal gradient remain unclear. Here, we collected channel sediments, riparian rhizosphere soils, and riparian bulk soils from 30 rivers across China and calculated EMF using 18 variables related to nitrogen cycling, nutrient pool, plant productivity, and water quality. We also determined microbial diversity (taxonomic and functional) and microbial network complexity using metagenomic sequencing. The results showed that EMF significantly decreased with increasing latitude in riparian rhizosphere and bulk soils but not in channel sediments. Microbial taxonomic and functional richness (observed species) in channel sediments were significantly higher in the low-latitude group than in the high-latitude group. However, microbial co-occurrence networks were more complex in the high-latitude group compared with the low-latitude group. Abiotic factors, primarily geographic and climatic factors, contributed more to EMF than microbial diversity and network complexity parameters in which only betweenness centralization had a significant relationship with EMF. Together, this study provides insight into the latitudinal pattern of EMF in rivers and highlights the importance of large-scale factors in explaining such latitudinal patterns.IMPORTANCEEcosystem multifunctionality (EMF) is the capacity of an ecosystem to provide multiple functions simultaneously. Microorganisms, as dominant drivers of belowground processes, have a profound effect on ecosystem functions. Although studies have revealed the latitudinal patterns of microbial community structure and single ecosystem function, the latitudinal patterns of EMF and how microbial communities affect EMF along a latitudinal gradient remain unclear. We collected channel sediments, riparian rhizosphere soils, and riparian bulk soils from 30 rivers along a latitudinal gradient across China and calculated EMF using 18 variables related to nitrogen cycling, nutrient pool, plant productivity, and water quality. This study fills a critical knowledge gap regarding the latitudinal patterns and drivers of EMF in river ecosystems and gives new insights into how microbial diversity and network complexity affect EMF from a metagenomic perspective.

Investigating the Impact of Disrupting the Glutamine Metabolism Pathway on Ammonia Excretion in Crucian Carp (Carassius auratus) under Carbonate Alkaline Stress Using Metabolomics Techniques.

With the gradual decline in freshwater resources, the space available for freshwater aquaculture is diminishing and the need to maximize saline water for aquaculture is increasing. This study aimed to elucidate the impact mechanisms of the disruption of the glutamate pathway on serum metabolism and ammonia excretion in crucian carp (Carassius auratus) under carbonate alkaline stress. A freshwater control group (C group), a 20 mmol/L NaHCO3 stress group (L group), and a 40 mmol/L NaHCO3 stress group (H group) were established. After 30 days of exposure, methionine sulfoximine (MSO) was injected to block the glutamate pathway metabolism, and the groups post-blocking were labeled as MC, ML, and MH. Ultra-high-performance liquid chromatography coupled with the quadrupole time-of-flight mass spectrometry (UPLC-Q-TOF/MS) metabolomics technique was employed to detect changes in the composition and content of crucian carp serum metabolites. Significant differential metabolites were identified, and related metabolic pathways were analyzed. The results revealed that, following the glutamate pathway blockade, a total of 228 differential metabolites (DMs) were identified in the three treatment groups. An enrichment analysis indicated significant involvement in glycerophospholipid metabolism, arachidonic acid metabolism, sphingolipid metabolism, purine metabolism, arginine and proline biosynthesis, pantothenate and CoA biosynthesis, glutathione metabolism, and fatty acid degradation, among other metabolic pathways. The results showed that ROS imbalances and L-arginine accumulation in crucian carp after the glutamate pathway blockade led to an increase in oxidative stress and inflammatory responses in vivo, which may cause damage to the structure and function of cell membranes. Crucian carp improves the body's antioxidant capacity and regulates cellular homeostasis by activating glutathione metabolism and increasing the concentration of phosphatidylcholine (PC) analogs. Additionally, challenges such as aggravated ammonia excretion obstruction and disrupted energy metabolism were observed in crucian carp, with the upregulation of purine metabolism alleviating ammonia toxicity and maintaining energy homeostasis through pantothenate and CoA biosynthesis as well as fatty acid degradation. This study elucidated the metabolic changes in crucian carp under carbonate alkaline stress after a glutamate pathway blockade at the cellular metabolism level and screened out the key metabolic pathways, which provide a scientific basis for further in-depth studies on the ammonia excretion of freshwater scleractinian fishes under saline and alkaline habitats at a later stage.

Activity and community structure of nitrifiers and denitrifiers in nitrogen-polluted rivers along a latitudinal gradient.

Nitrogen (N) cycling in rivers is particularly active and dynamic due to excess nutrient inputs worldwide. However, the multidimensional spatial patterns of the activity and community structure of N-cycling microorganisms in rivers remain unclear, limiting our understanding of river ecological functions, especially N removal capacity. Here, we measured the nitrification and denitrification rates and identified nitrifying and denitrifying microorganisms using high-throughput sequencing of archaeal amoA, bacterial amoA, nirK, and nirS genes in channel sediments, riparian rhizosphere soils, and riparian bulk soils of 30 N-polluted rivers across China. Results showed that in the lateral dimension, nitrification rates in sediments did not differ significantly from those in rhizosphere and bulk soils, but denitrification rates were higher in sediments than in bulk soils. However, the archaeal amoA gene abundance in sediments was considerably lower than that in rhizosphere and bulk soils, and bacterial amoA gene abundance in sediments was greater than that in rhizosphere soils. In the vertical dimension, both nitrification and denitrification rates in riparian bulk soils decreased with soil depth, and topsoils harbored more nitrifying and denitrifying microbes than subsoils. Denitrification but not nitrification rates increased with latitude and altitude but decreased with increasing mean annual temperature and precipitation. Overall, these results provide new insights into the multidimensional spatial patterns of river N cycling at a large scale, which is crucial to evaluating the N removal function of global rivers.

Surface-Charge-Driven Ferroptosis and Mitochondrial Dysfunction Is Involved in Toxicity Diversity in the Marine Bivalve Exposed to Nanoplastics.

Nanoplastics (NPs) pervade daily life, posing serious threats to marine ecosystems. Despite the crucial role that surface charge plays in NP effects, there is a substantial gap in our understanding of how surface charge influences NP toxicity. Herein, by exposing Ruditapes philippinarum (R. philippinarum) to both positively charged NPs (p-NPs) and negatively charged NPs (n-NPs) at environmentally relevant particle number levels for a duration of 35 days, we unequivocally demonstrate that both types of NPs had discernible impacts on the clams depending on their surface charge. Through transcriptomic and proteomic analyses, we unveiled the primary mechanisms behind p-NP toxicity, which stem from induced mitochondrial dysfunction and ferroptosis. In contrast, n-NPs predominantly stimulated innate immune responses, influencing salivary secretion and modulating the complement and coagulation cascades. Furthermore, in vitro tests on clam immune cells confirmed that internalized p-NPs triggered alterations in mitochondrial morphology, a decrease in membrane potential, and the initiation of ferroptosis. Conversely, n-NPs, to a certain extent, moderated the expression of genes related to immune responses, thus mitigating their adverse effects. Taken together, these findings indicate that the differential surface-charge-driven ferroptosis and mitochondrial dysfunction in clams play a critical role in the toxicity profile of NPs, providing an insightful reference for assessing the ecological toxicity associated with NPs.

Type VI secretion system drives bacterial diversity and functions in multispecies biofilms.

Type VI secretion system (T6SS) plays an essential role in interspecies interactions and provides an advantage for a strain with T6SS in multispecies biofilms. However, how T6SS drives the bacterial community structure and functions in multispecies biofilms still needs to be determined. Using gene deletion and Illumina sequencing technique, we estimated bacterial community responses in multispecies biofilms to T6SS by introducing T6SS-containing Pseudomonas putida KT2440. Results showed that the niche structure shifts of multispecies biofilms were remarkably higher in the presence of T6SS than in the absence of T6SS. The presence of T6SS significantly drove the variation in microbial composition, reduced the alpha-diversity of bacterial communities in multispecies biofilms, and separately decreased and increased the relative abundance of Proteobacteria and Bacteroidota. Co-occurrence network analysis with inferred putative bacterial interactions indicated that P. putida KT2440 mainly displayed strong negative associations with the genera of Psychrobacter, Cellvibrio, Stenotrophomonas, and Brevundimonas. Moreover, the function redundancy index of the bacterial community was strikingly higher in the presence of T6SS than in the absence of T6SS, regardless of whether relative abundances of bacterial taxa were inhibited or promoted. Remarkably, the increased metabolic network similarity with T6SS-containing P. putida KT2440 could enhance the antibacterial activity of P. putida KT2440 on other bacterial taxa. Our findings extend knowledge of microbial adaptation strategies to potential bacterial weapons and could contribute to predicting biodiversity loss and change in ecological functions caused by T6SS.