Comparing the Potential of Silicon Nanoparticles and Conventional Silicon for Salinity Stress Alleviation in Soybean (Glycine max L.): Growth and Physiological Traits and Rhizosphere/Endophytic Bacterial Communities.

In this study, 20-day-old soybean plants were watered with 100 mL of 100 mM NaCl solution and sprayed with silica nanoparticles (SiO2 NPs) or potassium silicate every 3 days over 15 days, with a final dosage of 12 mg of SiO2 per plant. We assessed the alterations in the plant's growth and physiological traits, and the responses of bacterial microbiome within the leaf endosphere, rhizosphere, and root endosphere. The result showed that the type of silicon did not significantly impact most of the plant parameters. However, the bacterial communities within the leaf and root endospheres had a stronger response to SiO2 NPs treatment, showing enrichment of 24 and 13 microbial taxa, respectively, compared with the silicate treatment, which led to the enrichment of 9 and 8 taxonomic taxa, respectively. The rhizosphere bacterial communities were less sensitive to SiO2 NPs, enriching only 2 microbial clades, compared to the 8 clades enriched by silicate treatment. Furthermore, SiO2 NPs treatment enriched beneficial genera, such as Pseudomonas, Bacillus, and Variovorax in the leaf and root endosphere, likely enhancing plant growth and salinity stress resistance. These findings highlight the potential of SiO2 NPs for foliar application in sustainable farming by enhancing plant-microbe interactions to improve salinity tolerance.

Genome sequences of the first Autographiviridae phages infecting marine Roseobacter.

The ubiquitous and abundant marine phages play critical roles in shaping the composition and function of bacterial communities, impacting biogeochemical cycling in marine ecosystems. Autographiviridae is among the most abundant and ubiquitous phage families in the ocean. However, studies on the diversity and ecology of Autographiviridae phages in marine environments are restricted to isolates that infect SAR11 bacteria and cyanobacteria. In this study, ten new roseophages that infect marine Roseobacter strains were isolated from coastal waters. These new roseophages have a genome size ranging from 38 917 to 42 634 bp and G+C content of 44.6-50 %. Comparative genomics showed that they are similar to known Autographiviridae phages regarding gene content and architecture, thus representing the first Autographiviridae roseophages. Phylogenomic analysis based on concatenated conserved genes showed that the ten roseophages form three distinct subgroups within the Autographiviridae, and sequence analysis revealed that they belong to eight new genera. Finally, viromic read-mapping showed that these new Autographiviridae phages are widely distributed in global oceans, mostly inhabiting polar and estuarine locations. This study has expanded the current understanding of the genomic diversity, evolution and ecology of Autographiviridae phages and roseophages. We suggest that Autographiviridae phages play important roles in the mortality and community structure of roseobacters, and have broad ecological applications.

Acute pancreatitis associated with pleural effusion: MDCT manifestations and anatomical basis.

BACKGROUND: Acute pancreatitis (AP) is a severe condition with complications that can impact multiple organ systems throughout the body. Specifically, the diffusion of peripancreatic effusion to the pleural cavity is a significant phenomenon in AP. However, its pathways and implications for disease severity are not fully understood. OBJECTIVE: This study aims to investigate the anatomical routes of peripancreatic effusion diffusion into the pleural cavity in patients with AP and to analyze the correlation between the severity of pleural effusion (PE) and the computed tomography severity index (CTSI) and acute physiology and chronic health evaluation II (APACHE II) scoring system. METHODS: 119 patients with AP admitted to our institution were enrolled in this study (mean age 50 years, 74 male and 45 female). Abdominal CT was performed, and the CTSI and APACHE II index were used to evaluate the severity of the AP, Meanwhile, the prevalence and semiquantitative of PE were also mentioned. The anatomical pathways of peripancreatic effusion draining to pleural were analyzed. Finally, the correlation relationship between the severity of AP and the PE was analyzed. RESULTS: In 119 patients with AP, 74.8% of patients had PE on CT. The anatomic pathways of peripancreatic effusion draining to pleural included esophageal hiatus in 33.7% of patients, aortic hiatus in 6.7% of patients and inferior vena cava hiatus in 3.37% of patients. The rating of PE on CT was correlated with CTSI scores (r= 0.449, P= 0.000) and was slightly correlated with the APACHE II scores (r= 0.197, P= 0.016). CONCLUSION: PE is a common complication of AP, which can be caused by anatomic pathways such as diaphragmatic hiatus. Due to its correlation with the CTSI score, the PE may be a supplementary indicator in determining the severity of AP.

Source identification and risk assessment of trace metals in surface sediment of China Sea by combining APCA-MLR receptor model and lead isotope analysis.

This study aimed to investigate the distribution, pollution, risk and sources of trace metals in sediments along China Sea. Clear spatial variations were found for Cr, Mn, Co, Ni, Cu, Zn, Se, Mo, Ag, Cd, and Pb, whereas As did not show spatial variation. East China Sea (ECS) contained the highest concentrations of Mn, Co, Ni, Cu, Zn, South China Sea (SCS) shallow sea contained the highest concentrations of Zn, Se, Mo, Ag, Cd, and Pb, whereas coral reefs contained the lowest concentrations of trace metals. Spatial variations could be explained by economic development characteristics along China Sea. As, Se and Cd exhibited low to moderate pollution in China Sea sediment, yet pollution for Cu, Zn, Ni, and Ag appeared in some regions. Sediment in ECS had moderate ecological risks and other regions at low ecological risks. The absolute principle component score-multiple linear regression (APCS-MLR) and Pb stable isotope indicated that 43-74% of trace metals (Ni, Cu, Zn, As, Se, Cd, and Pb) were derived from anthropogenic sources like traffic emission, agricultural activities, industrial source. No pollution and ecological risk were observed in coral reefs, yet 39-71% (Pb) was derived from anthropogenic activities such as motor vessels.

Global, regional, and national burden of liver cancer due to non-alcoholic steatohepatitis, 1990-2019: a decomposition and age-period-cohort analysis.

BACKGROUND: Identifying past temporal trends in non-alcoholic steatohepatitis (NASH)-associated liver cancer (NALC) can increase public awareness of the disease and facilitate future policy development. METHODS: Annual deaths and age-standardized death rates (ASDR) for NALC from 1990 to 2019 were collected from the Global Burden of Disease (GBD) 2019 study. The long-term trend and the critical inflection of mortality of NALC were detected by Joinpoint analysis. Age-period-cohort analysis was employed to evaluate the effects of age, period, and cohort. Last, decomposition analysis was used to reveal the aging and population growth effects for NALC burden. RESULTS: Between 1990 and 2019, the ASDR of NALC witnessed an overall declining trend on a global scale, with a decrease in females and a stable trend in males. However, the global ASDR demonstrated a significant upward trend from 2010 to 2019. Southern sub-Saharan Africa and Southeast Asia have the highest NALC burdens, while high socio-demographic index (SDI) region experienced the fastest escalation of NALC burdens over 30 years. The decomposition analysis revealed that population growth and aging were the primary catalysts behind the increase in global NALC deaths. Age-period-cohort analyses showed that NALC mortality declined the fastest among females aged 40-45 years in high SDI region, accompanied by a deteriorating period effect trend during the period of 2010-2019. CONCLUSION: The global absolute deaths and ASDR of NALC have witnessed a rise in the past decade, with populations exhibiting considerable disparities based on sex, age, and region. Population growth, aging, and metabolism-related factors were the main factors behind the increase in global NALC deaths.

Porcine reproductive and respiratory syndrome virus upregulates SMPDL3B to promote viral replication by modulating lipid metabolism.

Porcine reproductive and respiratory syndrome virus (PRRSV) poses a severe threat to the health of pigs globally. Host factors play a critical role in PRRSV replication. Using PRRSV as a model for genome-scale CRISPR knockout (KO) screening, we identified a host factor critical to PRRSV infection: sphingomyelin phosphodiesterase acid-like 3B (SMPDL3B). Our findings show that SMPDL3B restricted PRRSV attachment, entry, replication, and secretion and that its depletion significantly inhibited PRRSV proliferation, indicating that SMPDL3B plays a positive role in PRRSV replication. Our data also show that SMPDL3B deficiency resulted in an accumulation of intracellular lipid droplets (LDs). The expression level of key genes (ACC, SCD-1, and FASN) involved in lipogenesis was increased, whereas the fundamental lipolysis gene, ATGL, was inhibited when SMPDL3B was knocked down. Overall, our findings suggest that SMPDL3B deficiency can effectively inhibit viral infection through the modulation of lipid metabolism.

Genomic diversity and biogeographic distributions of a novel lineage of bacteriophages that infect marine OM43 bacteria.

The marine methylotrophic OM43 clade is considered an important bacterial group in coastal microbial communities. OM43 bacteria, which are closely related to phytoplankton blooms, have small cell sizes and streamlined genomes. Bacteriophages profoundly shape the evolutionary trajectories, population dynamics, and physiology of microbes. The prevalence and diversity of several phages that infect OM43 bacteria have been reported. In this study, we isolated and sequenced two novel OM43 phages, MEP401 and MEP402. These phages share 90% of their open reading frames (ORFs) and are distinct from other known phage isolates. Furthermore, a total of 99 metagenomic viral genomes (MVGs) closely related to MEP401 and MEP402 were identified. Phylogenomic analyses suggest that MEP401, MEP402, and these identified MVGs belong to a novel subfamily in the family Zobellviridae and that they can be separated into two groups. Group I MVGs show conserved whole-genome synteny with MEP401, while group II MVGs possess the MEP401-type DNA replication module and a distinct type of morphogenesis and packaging module, suggesting that genomic recombination occurred between phages. Most members in these two groups were predicted to infect OM43 bacteria. Metagenomic read-mapping analysis revealed that the phages in these two groups are globally ubiquitous and display distinct biogeographic distributions, with some phages being predominant in cold regions, some exclusively detected in estuarine stations, and others displaying wider distributions. This study expands our knowledge of the diversity and ecology of a novel phage lineage that infects OM43 bacteria by describing their genomic diversity and global distribution patterns. IMPORTANCE OM43 phages that infect marine OM43 bacteria are important for host mortality, community structure, and physiological functions. In this study, two OM43 phages were isolated and characterized. Metagenomic viral genome (MVG) retrieval using these two OM43 phages as baits led to the identification of two phage groups of a new subfamily in the family Zobellviridae. We found that group I MVGs share similar genomic content and arrangement with MEP401 and MEP402, whereas group II MVGs only possess the MEP401-type DNA replication module. Metagenomic mapping analysis suggests that members in these two groups are globally ubiquitous with distinct distribution patterns. This study provides important insights into the genomic diversity and biogeography of the OM43 phages in the global ocean.

Identification and restoration of hydrological processes alteration during the fish spawning period.

The hydrological processes play an important role in stimulating fish spawning behavior. Changes in the natural hydrological processes will alter the populations and distribution of fish, which may have a negative impact on the native aquatic organisms. The aim of this study is to identify the alteration of the water rising process during the fish spawning period and to construct an ecological flow optimization model to restore the water rising conditions for fish reproduction. The Mann-Kendall test and the sliding t-test were used to detect the mutation year of the mean daily flow data sets in the fish spawning period in each monitoring year. Then the data sets can be divided into pre-altered and post-altered periods. The water rising process was characterized by the water rising processes count, the duration, the daily flow increase rate, the date of the water rising process, and the initial water rising flow. The changes in hydrological processes in the middle reaches of the Yangtze River were investigated by comparing the post-altered and pre-altered characteristic parameters. Furthermore, we integrated the statistical values of the five characteristic parameters in pre-altered into an ecological flow optimization model to simulate the natural water rising processes for the spawning of the Four Major Chinese Carps (FMCC) and Chinese Sturgeon (CS). The analysis showed that after the hydrological mutation year, the duration and the initial water rising flow in the FMCC spawning season were increased, with hydrological alteration degrees of 63.10% and 70.16%, respectively; however, the daily flow increase rate was significantly decreased, with hydrological alteration of 86.50%. During the CS spawning season, the water rising processes count and the initial water rising flow were dramatically altered parameters, with hydrological alteration degrees of 50.86% and 83.27%, respectively. The former parameter increased, but the latter decreased significantly in the post-altered period. To induce the spawning activity of FMCC and CS, appropriate ecological flows and hydrological parameters were proposed. These results showed that during the spawning seasons of FMCC and CS, the hydrological processes of the middle reaches of the Yangtze River changed significantly. Therefore, ecological flow must be ensured through ecological operation of upstream reservoirs to provide suitable spawning conditions in target fish spawning grounds.

Cytosolic distribution of copper in the gills of field-collected oysters with different copper bioaccumulation.

Oysters can hyper-accumulate copper (Cu) without apparent toxicity, but the mechanism of sequestering excessive cytosolic Cu in oysters remains unclear. We here investigated the Cu distribution in the cytosolic proteins (CPs) in the gills of oysters (Crassostrea hongkongensis) through size-exclusion chromatography coupled to inductively coupled plasma mass spectrometry (SEC-ICP-MS). Oysters collected from the southern coast of China contained a gradient of gill Cu concentrations ranging from 132 to 3540 µg g-1 (dry weight), with 7-41 % of Cu distributed in the CPs fraction. The CPs-Cu concentrations were 8.6 times higher in oysters with high Cu concentrations compared to low concentrations. In the CPs, Cu was dispersed with a broad range of molecular weight, suggesting the involvement of various cytosolic proteins in Cu binding. Among the 10 major Cu peaks, peaks 2 (>600 kDa) and peak 8 (18 kDa) contained substantial Cu and showed obvious differences in response to the variation of CPs-Cu levels. Peak 8 contained metallothionein-like proteins that decreased their role in Cu binding as CPs-Cu concentrations increased. LC-MS/MS analysis revealed that peak 2 contained macromolecular protein complexes (MPCs), which played a critical role in binding excess Cu. The comparison with other bivalve species further suggested that sequestering excess CPs-Cu in MPCs was a special strategy employed by oysters in response to high Cu accumulation. This study provides valuable insights into the mechanism of hyper-accumulation and sequestration of Cu in oysters and helps to better understand Cu biomonitoring by oysters.

Effects of Culinary Procedures on Concentrations and Bioaccessibility of Cu, Zn, and As in Different Food Ingredients.

Although cooked diets are the primary sources for humans to absorb trace elements, there is limited data available on the concentrations and bioaccessibility of trace elements in cooked food ingredients. This work aims to evaluate the effects of culinary procedures on the concentrations and bioaccessibility of trace elements in common food ingredients. Twelve food species from the local market were treated with four culinary procedures (boiling, steaming, baking, and frying), then the bioaccessibility of copper (Cu), zinc (Zn), and arsenic (As) were evaluated using the in vitro digestion method. The subcellular distribution of these elements was also determined using the sequential fractionation method. The results show that culinary procedures decreased the retention rate of As during cooking (100% for raw and 65-89% for cooked ingredients) and the bioaccessibility of Cu and Zn during digestion (nearly 75% for raw and 49-65% for cooked ingredients), resulting in a reduction of the total bioaccessible fraction (TBF) of Cu, Zn, and As in food ingredients. The TBF of Cu, Zn, and As in all tested food ingredients followed the order: raw (76-80%) > steaming and baking (50-62%) > boiling and frying (41-50%). The effects of culinary procedures were associated with the subcellular distribution of trace elements. As was dominantly distributed in heat-stable proteins (51-71%), which were more likely to be lost during cooking. In comparison, Cu and Zn were mainly bound to the insoluble fraction and heat-denatured proteins (60-89% and 61-94% for Cu and Zn, respectively), which become less digestible in cooked ingredients. In conclusion, these results suggest that culinary procedures reduce the absorption of Cu, Zn, and As in various food ingredients, which should be considered in the coming studies related to nutrition and risk assessment of trace elements.

Immunogenicity and protective efficacy of a multi-epitope recombinant toxin antigen of Pasteurella multocida against virulent challenge in mice.

Pasteurella multocida (P. multocida) infection frequently results in porcine atrophic rhinitis and swine plague, leading to large economic losses for the swine industry worldwide. P. multocida toxin (PMT, 146 kDa) is a highly virulent key virulence factor that plays a vital role in causing lung and turbinate lesions. This study developed a multi-epitope recombinant antigen of PMT (rPMT) that showed excellent immunogenicity and protection in a mouse model. Using bioinformatics to analyse the dominant epitopes of PMT, we constructed and synthesized rPMT containing 10 B-cell epitopes, 8 peptides with multiple B-cell epitopes and 13 T-cell epitopes of PMT and a rpmt gene (1,974 bp) with multiple epitopes. The rPMT protein (97 kDa) was soluble and contained a GST tag protein. Immunization of mice with rPMT stimulated significantly elevated serum IgG titres and splenocyte proliferation, and serum IFN-γ and IL-12 were upregulated by 5-fold and 1.6-fold, respectively, but IL-4 was not. Furthermore, the rPMT immunization group exhibited alleviated lung tissue lesions and a significantly decreased degree of neutrophil infiltration compared with the control groups post-challenge. In the rPMT vaccination group, 57.1% (8/14) of the mice survived the challenge, similar to the bacterin HN06 group, while all the mice in the control groups succumbed to the challenge. Thus, rPMT could be a suitable candidate antigen for developing a subunit vaccine against toxigenic P. multocida infection.

Pseudorabies virus exploits N6-methyladenosine modification to promote viral replication.

Introduction: Pseudorabies virus (PRV) is the pathogenic virus of porcine pseudorabies (PR), belonging to the Herpesviridae family. PRV has a wide range of hosts and in recent years has also been reported to infect humans. N6-methyladenosine (m6A) modification is the major pathway of RNA post-transcriptional modification. Whether m6A modification participates in the regulation of PRV replication is unknown. Methods: Here, we investigated that the m6A modification was abundant in the PRV transcripts and PRV infection affected the epitranscriptome of host cells. Knockdown of cellular m6A methyltransferases METTL3 and METTL14 and the specific binding proteins YTHDF2 and YTHDF3 inhibited PRV replication, while silencing of demethylase ALKBH5 promoted PRV output. The overexpression of METTL14 induced more efficient virus proliferation in PRV-infected PK15 cells. Inhibition of m6A modification by 3-deazaadenosine (3-DAA), a m6A modification inhibitor, could significantly reduce viral replication. Results and Discussion: Taken together, m6A modification played a positive role in the regulation of PRV replication and gene expression. Our research revealed m6A modification sites in PRV transcripts and determined that m6A modification dynamically mediated the interaction between PRV and host.

Initial results of the meteorological data from the first 325 sols of the Tianwen-1 mission.

As the Zhurong rover landed on the surface of Mars in 2021, it began a months-long collection of Mars data. Equipped with highly sensitive sensors, Zhurong is capable of being a meteorological station at the surface of Mars. The Mars Climate Station, one of the onboard sensors with high sensitivity, helps the Tianwen-1 lander to collect meteorological data at the Martian surface, via which the air temperature, atmospheric pressure, wind speed and direction are measured. In this paper, we present results of surface pressure, air temperature and wind data from the Mars Climate Station at Zhurong's landing site. The data is collected in 176 solar days out of the entire rover's mission time, 325 solar days. We use a trigonometric function to fit the relationship between the solar longitude (Ls) and the pressure, after which we compare the results with those of Viking I. Our analysis of the temperature shows that seasonal evolution is similar to the patterns concluded in previous Mars missions at different landing sites. We discover that wind speed appears the maximum in early summer near Zhurong's landing site, and analyze the occurrence of dust storms by combining the data of wind and temperature. Our results provide some evidence of the seasonal changes in meteorological pattern at Tianwen-1's landing site, south of Utopia Planitia. With the mission ongoing further, more results are expected in the future.

The Plaque Microbiota Community of Giant Panda (Ailuropoda melanoleuca) Cubs With Dental Caries.

Dental caries severely hinders efficient access to adequate energy in wildlife. Different food supplies will develop characteristic plaque, and the microorganisms of these plaque are closely related to dental health. Here, plaque samples from panda cubs with caries and caries-free were collected for 16S rRNA high-throughput sequencing. All sequences clustered into 337 operational taxonomic units (OTUs; 97% identity), representing 268 independent species belonging to 189 genera, 98 families, 51 orders, 24 classes, and 13 phyla. Two groups shared 218 OTUs, indicating the presence of a core plaque microbiome. α diversity analysis showed that the microbial diversity in plaques with caries exceeded that of caries-free. The dominant phyla of plaque microbiota included Proteobacteria, Bacteroidetes, Firmicutes, Fusobacteria, and Actinobacteria. The dominant genera included unclassified Neisseriaceae, Actinobacillus, Lautropia, Neisseria, Porhyromonas, unclassified Pasteurellaceae, Moraxella, Streptococcus, Bergeywlla and Capnocytophaga. ß diversity analysis showed that the plaque microbial community structure was different between two groups. Using LEfSe analysis, 19 differentially abundant taxa were identified as potential biomarkers. Finally, function predictions analysis showed All the energy related metabolic pathways on KEGG level 2 were enriched in caries-active group. Consistent with the mainstream caries-causing narrative, our results illuminate the lack of information regarding the oral microflora composition and function within giant panda cubs.

Identifying the shared genes and KEGG pathways of Resolvin D1-targeted network and osteoarthritis using bioinformatics.

Osteoarthritis (OA) is a common chronic degenerative disease characterized by the loss of articular cartilage, which causes loss of joint function and reduce quality of life. Resolvin D1 (RvD1) has shown interesting anti-inflammatory effects; however, the mechanism of action of RvD1 in OA remains unclear. The aim of this study was to investigate the potential mechanism of RvD1 in OA by bioinformatics and partial in vitro mechanisms. Here, 106 shared differentially expressed genes (DEGs) were identified based on the GSE82107, GSE55235, GSE55457 dataset; 700 DEGs were identified based on GSE169077. Enrichment analyses of these genes were then successively conducted. RvD1-targeted genes and KEGG pathways are identified by STITCH. 27 shared KEGG pathways were identified among RvD1-targeted pathways and OA. Furthermore, cell apoptosis assay, western blotting, real-time fluorescent quantitative PCR (qRT-PCR), enzyme linked immunosorbent assay (ELISA) were used to confirm the expression levels of the key genes of shared Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways between RvD1-targeted and OA in IL-1ß treated rat knee chondrocytes. The results showed that RvD1-targeted pathways and the expression of nuclear p65, p53, and p-JNK were inhibited in the RvD1 group compared with the IL-1ß group. Thus, the findings indicate that RvD1 may inhibit the development of OA through NF/kB, p53, MAPK/JNK, PI3K-AKT signaling pathways, and act as a treatment for OA.

Resolvin D1 inhibits the proliferation of osteoarthritis fibroblast-like synoviocytes through the Hippo-YAP signaling pathway.

OBJECTIVE: Osteoarthritis (OA) is a disease characterized by cartilage degradation and structural destruction. Resolvin D1 (RvD1), a specialized proresolving mediator (SPM) derived from omega-3 fatty acids, has been preliminarily proven to show anti-inflammatory and antiapoptotic effects in OA. However, the mechanisms of RvD1 in osteoarthritis fibroblast-like synoviocytes (OA-FLSs) need to be clarified. METHODS: Synovial and fibroblast-like synoviocytes were obtained from OA patients and healthy individuals. MTT and EdU assays were performed to determine cell cytotoxicity and proliferation. The protein expression levels of cyclin D1, cyclin B1, PCNA, p53, MMP-13, YAP, p-YAP, and LATS1 were detected by western blot analysis. The release levels of IL-1ß were detected by ELISA. The cell cycle was assessed by flow cytometry. Immunofluorescence was used to detect the levels of YAP in OA-FLSs. RESULTS: RvD1 inhibited OA-FLS proliferation and reduced MMP-13 and IL-1ß secretion in the concentrations of 20 nM and 200 nM. Furthermore, RvD1 induced G2 cell cycle arrest in OA-FLSs via the Hippo-YAP signaling pathway and promoted YAP phosphorylation. However, RvD1 had no effects on normal FLSs. CONCLUSIONS: RvD1 inhibits OA-FLS proliferation by promoting YAP phosphorylation and protects chondrocytes by inhibiting the secretion of MMP-13 and IL-1ß, providing an experimental basis for RvD1 treatment of OA.

Newly identified HMO-2011-type phages reveal genomic diversity and biogeographic distributions of this marine viral group.

Viruses play critical roles in influencing biogeochemical cycles and adjusting host mortality, population structure, physiology, and evolution in the ocean. Marine viral communities are composed of numerous genetically distinct subfamily/genus-level viral groups. Among currently identified viral groups, the HMO-2011-type group is known to be dominant and broadly distributed. However, only four HMO-2011-type cultivated representatives that infect marine SAR116 and Roseobacter strains have been reported to date, and the genetic diversity, potential hosts, and ecology of this group remain poorly elucidated. Here, we present the genomes of seven HMO-2011-type phages that were isolated using four Roseobacter strains and one SAR11 strain, as well as additional 207 HMO-2011-type metagenomic viral genomes (MVGs) identified from various marine viromes. Phylogenomic and shared-gene analyses revealed that the HMO-2011-type group is a subfamily-level group comprising at least 10 discernible genus-level subgroups. Moreover, >2000 HMO-2011-type DNA polymerase sequences were identified, and the DNA polymerase phylogeny also revealed that the HMO-2011-type group contains diverse subgroups and is globally distributed. Metagenomic read-mapping results further showed that most HMO-2011-type phages are prevalent in global oceans and display distinct geographic distributions, with the distribution of most HMO-2011-type phages being associated with temperature. Lastly, we found that members in subgroup IX, represented by pelagiphage HTVC033P, were among the most abundant HMO-2011-type phages, which implies that SAR11 bacteria are crucial hosts for this viral group. In summary, our findings substantially expand current knowledge regarding the phylogenetic diversity, evolution, and distribution of HMO-2011-type phages, highlighting HMO-2011-type phages as major ecological agents that can infect certain key bacterial groups.

Genomic diversity, life strategies and ecology of marine HTVC010P-type pelagiphages.

SAR11 bacteria dominate ocean surface bacterioplankton communities, and play an important role in marine carbon and nutrient cycling. The biology and ecology of SAR11 are impacted by SAR11 phages (pelagiphages) that are highly diverse and abundant in the ocean. Among the currently known pelagiphages, HTVC010P represents an extremely abundant but under-studied phage group in the ocean. In this study, we have isolated seven new HTVC010P-type pelagiphages, and recovered 77 nearly full-length HTVC010P-type metagenomic viral genomes from marine metagenomes. Comparative genomic and phylogenomic analyses showed that HTVC010P-type pelagiphages display genome synteny and can be clustered into two major subgroups, with subgroup I consisting of strictly lytic phages and subgroup II mostly consisting of phages with potential lysogenic life cycles. All but one member of the subgroup II contain an integrase gene. Site-specific integration of subgroup II HTVC010P-type pelagiphage was either verified experimentally or identified by in silico genomic sequence analyses, which revealed that various SAR11 tRNA genes can serve as the integration sites of HTVC010P-type pelagiphages. Moreover, HTVC010P-type pelagiphage integration was confirmed by the detection of several Global Ocean Survey (GOS) fragments that contain hybrid phage-host integration sites. Metagenomic recruitment analysis revealed that these HTVC010P-type phages were globally distributed and most lytic subgroup I members exhibited higher relative abundance. Altogether, this study significantly expands our knowledge about the genetic diversity, life strategies and ecology of HTVC010P-type pelagiphages.

Toxicity of gabapentin-lactam on the early developmental stage of zebrafish (Danio rerio).

Gabapentin-lactam (GBP-L) is a transformation product (TP) of gabapentin (GBP), a widely used anti-epileptic pharmaceutical. Due to its high persistence, GBP-L has been frequently detected in the surface water. However, the effects of GBP-L on aquatic organisms have not been thoroughly investigated. In the present study, zebrafish (Danio rerio) embryos as a model organism were used to study the impacts of GBP-L in terms of embryos LC50, spontaneous movement at 24 hpf (hours post fertilization), heartbeat rates at 48 hpf, and body length at 72 hpf, with the concentrations of GBP-L down to 0.01 µg/L, covering its environmental concentrations. Various biomarkers from nervous, antioxidant and immune systems of zebrafish larvae were analyzed, including acetylcholinesterase, acetylcholine, dopamine, gamma-aminobutyric acid, superoxide dismutase, catalase, glutathione S-transferase, C reactive protein, and lysozyme, to assess its toxicity on these systems. RT-qPCR was then used to further verify the results and explain the toxicological mechanism at the gene level. The results demonstrated that GBP-L is much more toxic than its parent compound, and could lead to adverse impacts on the aquatic organisms even at every low concentrations.

Genomic Characterization and Distribution Pattern of a Novel Marine OM43 Phage.

Bacteriophages have a significant impact on the structure and function of marine microbial communities. Phages of some major bacterial lineages have recently been shown to dominate the marine viral communities. However, phages that infect many important bacterial clades still remained unexplored. Members of the marine OM43 clade are methylotrophs that play important roles in C1 metabolism. OM43 phages (phages that infect the OM43 bacteria) represent an understudied viral group with only one known isolate. In this study, we describe the genomic characterization and biogeography of an OM43 phage that infects the strain HTCC2181, designated MEP301. MEP301 has a genome size of 34,774 bp. We found that MEP301 is genetically distinct from other known phage isolates and only displays significant sequence similarity with some metagenomic viral genomes (MVGs). A total of 12 MEP301-type MVGs were identified from metagenomic datasets. Comparative genomic and phylogenetic analyses revealed that MEP301-type phages can be separated into two subgroups (subgroup I and subgroup II). We also performed a metagenomic recruitment analysis to determine the relative abundance of reads mapped to these MEP301-type phages, which suggested that subgroup I MEP301-type phages are present predominantly in the cold upper waters with lower salinity. Notably, subgroup II phages have an inverse different distribution pattern, implying that they may infect hosts from a distinct OM43 subcluster. Our study has expanded the knowledge about the genomic diversity of marine OM43 phages and identified a new phage group that is widespread in the ocean.