Comparative metagenomic analysis of microbial community compositions and functions in cage aquaculture and its nearby non-aquaculture environments.

In the context of burgeoning global aquaculture, its environmental repercussions, particularly in marine ecosystems, have gained significant attentions. Cage aquaculture, a prominent method, has been observed to significantly influence marine environments by discharging substantial amounts of organic materials and pollutants. It is also one of the important reasons for water eutrophication. This study investigated the impacts of cage aquaculture on microbial diversity and functional potential using metagenomics. Specifically, a comparison was made of the physicochemical indicators and microbial diversity between three grouper aquaculture cage nets in Lingshui Xincun Port and three nearby non-aquaculture area surface waters. We found that compared to non-aquaculture areas, the eutrophication indicators in aquaculture environments significantly increased, and the abundances of Vibrio and Pseudoalteromonas in aquaculture environments significantly rose. Additionally, microbial functional genes related to carbon, nitrogen, and sulfur metabolisms were also found to be significantly affected by aquaculture activities. The correlation analysis between microbial populations and environmental factors revealed that the abundances of most microbial taxa showed positive correlations with dissolved inorganic nitrogen, soluble reactive phosphorus, NH4+, and negative correlations with dissolved oxygen. Overall, this study elucidated the significant impacts of aquaculture-induced eutrophication on the diversity and functions of planktonic bacterial communities.

Hydrological alteration drives chemistry of dissolved organic matter in the largest freshwater lake of China (Poyang Lake).

As the largest reactive organic carbon pool, dissolved organic matter (DOM) plays an important role in various biogeochemical processes in lake ecosystems. Recently, climate change-induced extreme events (e.g., floods and droughts) have significantly modified the hydrological patterns of lakes worldwide, and regulated the quality and quantity of DOM. However, the responses of DOM chemistry to hydrological alteration in lakes remain poorly understood. Here we investigated the influences of hydrological alteration on sources, composition, and characteristics of DOM in Poyang Lake, the largest freshwater lake in China, using a combination of bulk chemical, optical and Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) techniques. Results show various sources of DOM (autochthonous, allochthonous, and anthropogenic inputs) and significant variations in DOM chemistry across four hydrological periods (the retreating, dry, rising, and flooding periods) in Poyang Lake. During the retreating, rising, and flooding periods, DOM was characterized by higher aromaticity, humification degree, and recalcitrance, and exhibited pronounced allochthonous signatures. In contrast, DOM contained more S-containing molecules and aliphatic compounds during the dry period, displaying relatively stronger autochthonous features. Terrestrial inputs and the lignin-CHOS formation process are likely the primary underlying mechanisms shaping the differences in DOM chemistry in Poyang Lake. Our research demonstrates the significant impacts of hydrological alteration on DOM dynamics, and provides an improved understanding of DOM biogeochemical cycles and carbon cycling in large aquatic systems under global climate change.

Grouper RIP2 inhibits Singapore grouper iridovirus infection by modulating ASC-caspase-1 interaction.

Introduction: Receptor interacting protein 2 (RIP2), serves as a vital sensor of cell stress, is able to respond to cell survival or inflammation, and is involved in antiviral pathways. However, studies on the property of RIP2 in viral infections in fish have not been reported. Methods: In this paper, we cloned and characterized RIP2 homolog from orange-spotted grouper (Epinephelus coioides) (EcRIP2) and further discussed the relevance of EcRIP2 to EcASC, comparing the influences of EcRIP2 and EcASC on the modulation of inflammatory factors and the NF-κB activation to reveal the mechanism of EcRIP2 in fish DNA virus infection. Results: Encoded a 602 amino acid protein, EcRIP2 contained two structural domains: S-TKc and CARD. Subcellular localization signified that EcRIP2 existed in cytoplasmic filaments and dot aggregation patterns. After SGIV infection, the EcRIP2 filaments aggregated into larger clusters near the nucleus. The infection of SGIV could notably up-regulate the transcription level of the EcRIP2 gene compared with lipopolysaccharide (LPS) and red grouper nerve necrosis virus (RGNNV). Overexpression of EcRIP2 impeded SGIV replication. The elevated expression levels of inflammatory cytokines induced by SGIV were remarkably hindered by EcRIP2 treatment in a concentration-dependent manner. In contrast, EcASC treatment could up-regulate SGIV-induced cytokine expression in the presence of EcCaspase-1. Enhancing amounts of EcRIP2 could overcome the down regulatory effect of EcASC on NF-κB. Nevertheless, increasing doses of EcASC failed to restrain the NF-κB activation in the existence of EcRIP2. Subsequently, it was validated by a co-immunoprecipitation assay that EcRIP2 dose-dependently competed with EcASC binding to EcCaspase-1. With increasing time to SGIV infection, EcCaspase-1 gradually combined with more EcRIP2 than EcASC. Discussion: Collectively, this paper highlighted that EcRIP2 may impede SGIV-induced hyperinflammation by competing with EcASC for binding EcCaspase-1, thereby suppressing viral replication of SGIV. Our work supplies novel viewpoints into the modulatory mechanism of RIP2-associated pathway and offers a novel view of RIP2-mediated fish diseases.

Quantification adsorption mechanisms of arsenic by goethite-modified biochar in aqueous solution.

In this study, rice straw biochar (BC), goethite (GT), and goethite-modified biochar (GBC) were prepared and their differences in adsorption characteristics and mechanisms of arsenic were explored to provide theoretical and data reference for future design of modified biochar, aiming to address adsorption mechanism weakness and improve the efficiency of arsenic removal in water. Various characterization methods were employed to evaluate the influence of pH, adsorption kinetics, isotherms, and chemical analyses of the materials. At temperatures of 283 K, 298 K, and 313 K, the maximum actual adsorption capacity followed the order GBC > GT > BC, while at 313 K, the maximum Langmuir adsorption capacity of GBC reached 149.63 mg/g which was 95.92 times that of BC and 6.27 times of GT. Due to precipitation and complexation mechanisms, GBC exhibited more superior arsenic adsorption capacities than BC and GT, contributing to total adsorption ranging from 88.9% to 94.2%. BC was dominated by complexation and ion exchange mechanisms in arsenic adsorption, with contribution proportions of 71.8%-77.6% and 19.1%-21.9%, respectively. In GT, the precipitation mechanism played a significant role in total adsorption, contributing from 78.0% to 84.7%. Although GBC has significant potential for removing arsenic from aqueous solutions, the findings suggest that its ion exchange capacity needs improvement.

Exploring the optical properties and molecular characteristics of dissolved organic matter in a large river-connected lake (Poyang Lake, China) using optical spectroscopy and FT-ICR MS analysis.

River-connected lakes are complicated and dynamic ecosystems due to their distinctive hydrological pattern, which could significantly impact the generation, degradation, and transformation processes of dissolved organic matter (DOM) and further regulate DOM chemistry in lakes. However, the molecular compositions and characteristics of DOM in river-connected lakes are still poorly understood. Thus, here the spatial variations of optical properties and molecular characteristics of DOM in a large river-connected lake (Poyang Lake) were explored via spectroscopic techniques and Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS). The results showed high degree of spatial heterogeneity of DOM chemistry (variations in DOC concentrations, optical parameters, and molecular compounds) in Poyang Lake, and the diversity at the molecular level was primarily caused by the heteroatom compounds (N- and S- containing). Compared with classic lakes and rivers, DOM compositions of the river-connected lake had distinctive characteristics (differences in the AImod and DBE values, and CHOS proportions). And the composition characteristics of DOM between the southern and northern parts of Poyang Lake were different (such as the lability and molecular compounds), suggesting the changes of hydrologic conditions may affect the DOM chemistry. In addition, various sources of DOM (autochthonous, allochthonous, and anthropogenic inputs) were identified agreeably based on optical properties and molecular compounds. Overall, this study first characterizes the DOM chemistry and reveals its spatial variations in Poyang Lake at the molecular level, which could improve our understanding of DOM in large river-connected lake systems. Further studies are encouraged to investigate the seasonal variations of DOM chemistry under different hydrologic conditions in Poyang Lake to enrich the knowledge of carbon cycling in river-connected lake systems.

Grouper TIA-1 functions as a crucial antiviral molecule against nervous necrosis virus infection.

T-cell intracellular antigen (TIA)-1 is a prion-related RNA-binding protein involved in splicing and translational repression, and regulates translation in response to stress conditions by isolating target mRNAs in stress granules (SGs). However, little is known about the potential roles of fish TIA-1 and how it works in viral infection. In this study, the TIA-1 (EcTIA-1) homolog from orange-spotted grouper (Epinephelus coioides) was cloned and characterized. The open reading frame (ORF) sequence of EcTIA-1 encoded a 388 amino acid protein with predicted molecular mass of 42.73 kDa. EcTIA-1 contains three conserved domains of RNA recognition motif (RRM) that may interact with RNA via its second and third RRMs. Overexpression of EcTIA-1 inhibited red-spotted grouper nervous necrosis virus (RGNNV) replication and positively regulated interferon immune response, which was increased by knockdown of EcTIA-1. RGNNV induced formation of SGs in cells with EcTIA-1 overexpression. These results provide a novel insight into understanding the roles of fish TIA-1 in response to RNA viruses.

Fish RIP1 Mediates Innate Antiviral Immune Responses Induced by SGIV and RGNNV Infection.

Receptor interacting protein 1 (RIP1) is an essential sensor of cellular stress, which may respond to apoptosis or cell survival and participate in antiviral pathways. To investigate the roles of fish RIP1 in Singapore grouper iridovirus (SGIV) and red-spotted grouper nervous necrosis virus (RGNNV) infection, a RIP1 homolog from orange-spotted grouper (Epinephelus coioides) (EcRIP1) was cloned and characterized. EcRIP1 encoded a 679 amino acid protein that shares 83.28% identity with that of Perca flavescens and contained a homologous N-terminal kinase (S-TKc) domain, a RIP isotype interaction motif (RHIM), and a C-terminal domain (DD). EcRIP1 was predominantly detected in immune tissues, and its expression was induced by RGNNV or SGIV infection in vitro. Subcellular localization showed that EcRIP1 was distributed in the cytoplasm with point-like uniform and dot-like aggregation forms. Overexpression of EcRIP1 inhibited SGIV and RGNNV replication and positively regulated the expression levels of interferon (IFN) and IFN-stimulated genes and pro-inflammatory factors. EcRIP1 may interact with grouper tumor necrosis factor receptor type 1-associated DEATH domain protein (EcTRADD) to promote SGIV-induced apoptosis, and interact with grouper Toll/interleukin-1 receptor (TIR) domain containing adapter inducing interferon-ß (EcTRIF) and participate in Myeloid Differentiation Factor 88 (MyD88)-independent toll-like receptor (TLR) signaling. EcRIP1 may also interact with grouper tumor necrosis factor receptor-associated factors (TRAFs) as intracellular linker proteins and mediate the signaling of various downstream signaling pathways, including NF-κB and IFN. These results suggest that EcRIP1 may inhibit SGIV and RGNNV infection by regulating apoptosis and various signaling molecules. Our study offers new insights into the regulatory mechanism of RIP1-related signaling, and provides a novel perspective on fish diseases mediated by RIP1.

The roles of grouper TANK in innate immune defense against iridovirus and nodavirus infections.

The TRAF family member-associated nuclear factor (NF)-κB activator (TANK) was first identified as a TRAF-binding protein with both stimulatory and inhibitory properties in host innate immune activation. To elucidate the roles of TANK in teleosts, we cloned and characterized the TANK homologue of orange-spotted grouper (Epinephelus coioides). The open reading frame (ORF) of EcTANK consists of 1026 nucleotides encoding a 342 amino acid protein with a predicted molecular mass of 38.24 kDa. EcTANK shares 89.47% and 88.89% identity with Larimichthys crocea TANK and Lates calcarifer TANK, respectively. EcTANK was distributed in all 11 examined tissues. The expression of EcTANK in the spleen increased after infection with Singapore grouper iridovirus (SGIV) and red-spotted grouper nervous necrosis virus (RGNNV). EcTANK was mainly located in the cytoplasm of grouper spleen cells. EcTANK enhanced SGIV and RGNNV replication during viral infection in vitro. Overexpression EcTANK decreased the expression levels of interferon-associated cytokines and pro-inflammatory factors, and enhanced activation of NF-κB. Taken together, these results suggest that EcTANK may play an important role in antiviral innate immune activation in grouper.

Autophagy Participates in Lysosomal Vacuolation-Mediated Cell Death in RGNNV-Infected Cells.

Nervous necrosis virus (NNV) is the etiological agent of viral nervous necrosis (VNN), also known as viral encephalopathy and retinopathy (VER), which results in heavy economic losses to the aquaculture industry worldwide. Dramatic cytoplasmic vacuoles were observed during NNV infection both in vitro and in vivo; however, the origin and mechanism of cytoplasmic vacuolization remains unknown. In this report, we found that the cytoplasmic vacuole morphology became fused and enlarged during infection with red spotted grouper nervous necrosis virus (RGNNV), which was accompanied by increased cell death. Notably, Lyso-Tracker, but not Mito-Tracker or ER-Tracker, was accumulated in the vacuoles, and abnormal lysosome swelling was observed in RGNNV-infected cells, suggesting that the cytoplasmic vacuoles originated from lysosomal organelles. Cytoplasmic vacuolization and cell death in RGNNV-infected cells was completely blocked by the vacuolar H+-ATPase inhibitor (bafilomycin A1), and was significantly weakened by chloroquine (CQ), a lysosomotropic agent that induces the acidification of the lysosomes. This suggests that lysosome acidification was essential for vacuole formation. Significant inhibitory effects on vacuolization and cell death were also observed in the RGNNV-infected cells following treatment with nigericin and monensin (ionophores that uncouple the proton gradient present in lysosomes). This indicated that lysosome function was tightly associated with RGNNV infection-induced cell death. In addition, vacuoles were found to be partially co-localized with GFP-LC3II punctate dots during RGNNV infection. Moreover, the severity of vacuolization and cell death were both significantly decreased after treatment with the autophagy inhibitor, 3-MA, suggesting that autophagy was involved in lysosomal vacuolization and cell death evoked by RGNNV infection. Thus, our results demonstrate that autophagy participates in lysosomal vacuolation-mediated cell death during RGNNV infection, and provides new insight into our understanding of the potential mechanisms underlying nodavirus pathogenesis in vitro.

Characterization of orange-spotted grouper (Epinephelus coioides) ASC and caspase-1 involved in extracellular ATP-mediated immune signaling in fish.

Apoptosis-associated speck-like protein containing a CARD domain (ASC) is a critical adaptor molecule in multiple inflammasome protein complexes that mediate inflammation and host defense. Caspase-1 is a member of inflammatory caspases that play important roles in the innate immune system. However, few studies have been performed in lower vertebrates such as teleosts and implications of extracellular ATP-mediated immune signalling in fish. Here we identified and characterized novel ASC and caspase-1 genes (namely EcASC and EcCaspase-1) from the orange-spotted grouper (Epinephelus coioides). EcASC and EcCaspase-1 encode 204- and 388-aa proteins which shared 55.34% and 72.89% identity with those in Siniperca chuatsi and Perca flavescens, respectively. EcASC contained a PYRIN domain (aa 5-82) and CARD domain (aa 107-201). EcCaspase1 contained a CARD domain (aa 1-88) and a CASc domain (aa 127-376). Both EcASC and EcCaspase-1 were distributed in all tissues tested in the healthy grouper. The expression of EcASC and EcCaspase-1 was significantly upregulated in response to ATP infection. Subcellular localization analysis showed that EcCaspase-1 exhibited a clear distribution in both cytoplasm and nucleus. In contrast, EcASC was observed in the cytoplasm as speck-like structures, which are called "pyroptosomes". EcCaspase-1 co-localized with the spot-like protein (EcASC). Overexpression of EcASC and EcCaspase-1 inhibited NF-κB activation and promoted P53 activation in grouper spleen (GS) cells. Extracellular ATP was an effective signaling molecule that activates the innate immune response, rapidly upregulating the expression of EcASC and EcCaspase1, and enhancing their promotion of proinflammatory cytokine expression in GS cells. Both EcASC and EcCaspase-1 promoted ATP-induced apoptosis. Our results suggested that the interactions of inflammatory EcCaspase-1 with EcASC proteins were associated with extracellular ATP-mediated immune signaling in fish.

Grouper TRADD Mediates Innate Antiviral Immune Responses and Apoptosis Induced by Singapore Grouper Iridovirus (SGIV) Infection.

Tumor necrosis factor (TNF) receptor type 1-associated DEATH domain protein (TRADD) is a TNFR1-associated signal transducer and an essential component of the TNFR1 complex that is involved in activating both apoptotic and nuclear factor (NF)-κB pathways as an adaptor. It also is required for TNFR-1-initiated neuronal apoptosis following in vitro infection with virus as an essential component of the antiviral response. To date, few studies have investigated the function of TRADD in lower vertebrates and its antiviral response to DNA virus infection. In the present study, a TRADD gene (named as EcTRADD) from the orange-spotted grouper (Epinephelus coioides) was cloned and characterized. The full-length cDNA of EcTRADD consists of 1,370 base pairs (bp) and contains a 44 bp 5'-terminal untranslated region (UTR), a 450 bp 3'-UTR including a poly (A) tail, and an 876 bp open reading frame encoding a putative 291 amino acid protein. EcTRADD has two conserved domains of N-terminal domain (TRADD-N) and a death domain (DD). EcTRADD was detected in all examined tissues. EcTRADD was up-regulated in the spleen after infection with Singapore grouper iridovirus (SGIV). Subcellular localization analysis revealed that EcTRADD and EcTRADD-DD exhibited a clear pattern of discrete and interconnecting cytoplasmic filaments resembling the death-effector filaments, while EcTRADD-N was observed in the cytoplasm. After infection with SGIV, EcTRADD, and EcTRADD-DD were transferred to the nucleus. Overexpression of EcTRADD and its domains inhibited replication of SGIV in vitro. Both EcTRADD and EcTRADD-DD induced the caspase-dependent apoptosis in control and infected cells, while EcTRADD-N inhibited the apoptosis. Additionally, EcTRADD and EcTRADD-DD significantly promoted activation of NF-κB and reporter gene p53, whereas EcTRADD-N had no significant effect on p53. The results may provide new insights into the role of fish TRADD in fish virus infection.

Grouper IFIT1 inhibits iridovirus and nodavirus infection by positively regulating interferon response.

Interferon-induced protein with tetratricopeptide repeats 1 (IFIT1), one of the interferon stimulated genes (ISGs), is strongly induced by type I interferon (IFN), double-stranded RNAs and virus infection. To investigate the actions of fish IFIT1 in response to virus infection, we cloned an IFIT1 homolog from orange spotted grouper (EcIFIT1) and clarified its function in this study. The full-length cDNA of EcIFIT1 is 1839 bp, which is composed of 436 amino acid (aa) residues, with 77.8% and 22.8% identity to IFIT1 homolog of yellow perch (Perca flavescens) and humans (homo sapiens), respectively. Sequence alignment analysis showed that EcIFIT1 contained three tetratricopeptide repeats (TPRs). Tissue distribution analysis indicated that EcIFIT1 was abundant in intestine, spleen, liver, and heart. Moreover, EcIFIT1 was significantly up-regulated by Singapore grouper iridovirus (SGIV) or red-spotted grouper nervous necrosis virus (RGNNV) infection, and polyinosinic-polycytidylic acid (poly I:C) or lipopolysaccharide (LPS) treatment in vitro. Under fluorescence microscopy, EcIFIT1 was found to localize throughout the cytoplasm in transfected cells. EcIFIT1 overexpression significantly suppressed the replication of SGIV and RGNNV, demonstrated by decreasing the cytopathic effect (CPE) severity, viral gene transcription and the virus titers. Further studies showed that the ectopic expression of EcIFIT1 increased the transcription level of IFN related molecules, including IFN regulatory factor (IRF) 3, IRF7, IFN stimulated gene (ISG) 15 and myxovirus resistance gene (MX) I. Meanwhile, the expression levels of pro-inflammation cytokines were differently regulated by the ectopic expression of EcIFIT1. In addition, flow cytometry analysis suggested that EcIFIT1 overexpression affected cell cycle progression by mediating S/G2 transition. Taken together, our results indicated that EcIFIT1 might exert antiviral function against fish virus by up-regulating interferon response or affecting cell cycle.

Home range variation of two different-sized groups of golden snub-nosed monkeys (Rhinopithecus roxellana) in Shennongjia, China: implications for feeding competition.

Knowledge on the home range size of a species or population is important for understanding its behavioral and social ecology and improving the effectiveness of conservation strategies. We studied the home range size of two different-sized groups of golden snub-nosed monkeys (Rhinopithecus roxellana) in Shennongjia, China. The larger group (236 individuals) had a home range of 22.5 km2 from September 2007 to July 2008, whereas the smaller group (62 individuals) occupied a home range of 12.4 km2 from November 2008 to July 2009. Both groups exhibited considerable seasonal variation in their home range size, which was likely due to seasonal changes in food availability and distribution. The home range in any given season (winter, spring, summer, or winter+spring+summer) of the larger group was larger than that of the smaller group. As the two groups were studied in the same area, with the confounding effects of food availability thus minimized, the positive relationship between home range size and group size suggested that scramble feeding competition increased within the larger group.

Development of high-speed vacuum ultraviolet spectroscopy using a modified Seya-Namioka monochromator and channel electron multiplier detector in the HL-2A tokamak.

A high-speed vacuum ultraviolet monochromator is developed for the HL-2A tokamak through the introduction of a novel channel electron multiplier in a modified Seya-Namioka spectrometer. A good signal to noise ratio of above 2000 is attained in the development phase of the system with typical operating parameters for observing routine HL-2A plasmas. The wavelength calibration is performed using characteristic line emissions from a hollow cathode light source with helium and argon discharges. The first measurement result of the monochromator at a sample rate of 60 kHz is presented in comparison with the visible Dα signals.

A multiplexer-based multi-channel microwave Doppler backward scattering reflectometer on the HL-2A tokamak.

The Doppler backward scattering (DBS) reflectometer has become a well-established and versatile diagnostic technique for the measurement of density fluctuations and flows in magnetically confined fusion experiments. In this work, a novel multiple fixed-frequency array source with a multiplexer technique is developed and applied in the multi-channel DBS system. The details of the system design and laboratory tests are presented. Preliminary results of Doppler shift frequency spectra measured by the multi-channel DBS reflectometer systems are obtained. Characteristics of plasma rotation and turbulence before and after supersonic molecular beam injection are analyzed.

A novel multi-channel quadrature Doppler backward scattering reflectometer on the HL-2A tokamak.

A novel 16-channel fixed frequency Doppler backward scattering (DBS) reflectometer system has been developed on the HL-2A tokamak. This system is based on the filter-based feedback loop microwave source (FFLMS) technique, which has lower phase noise and lower power variation compared with present tunable frequency generation and comb frequency array generation techniques [J. C. Hillesheim et al. Rev. Sci. Instrum. 80, 083507 (2009) and W. A. Peebles et al. Rev. Sci. Instrum. 81, 10D902 (2010)]. The 16-channel DBS system is comprised of four × four-frequency microwave transmitters and direct quadrature demodulation receivers. The working frequencies are 17-24 GHz and 31-38 GHz with the frequency interval of 1 GHz. They are designed to measure the localized intermediate wave-number (k⊥ρ ∼ 1-2, k⊥ ∼ 2-9 cm-1) density fluctuations and the poloidal rotation velocity profile of turbulence. The details of the system design and laboratory tests are presented. Preliminary results of Doppler spectra measured by the multi-channel DBS reflectometer systems are obtained. The plasma rotation and turbulence distribution during supersonic molecular beam injection are analyzed.

Congener diversity, topographic heterogeneity and human-assisted dispersal predict spread rates of alien herpetofauna at a global scale.

Understanding the factors that determine rates of range expansion is not only crucial for developing risk assessment schemes and management strategies for invasive species, but also provides important insight into the ability of species to disperse in response to climate change. However, there is little knowledge on why some invasions spread faster than others at large spatiotemporal scales. Here, we examine the effects of human activities, species traits and characteristics of the invaded range on spread rates using a global sample of alien reptile and amphibian introductions. We show that spread rates vary remarkably among invaded locations within a species, and differ across biogeographical realms. Spread rates are positively related to the richness of native congeneric species and human-assisted dispersal in the invaded range but are negatively correlated with topographic heterogeneity. Our findings highlight the importance of environmental characteristics and human-assisted dispersal in developing robust frameworks for predicting species' range shifts.