Institute of Hydrobiology, Chinese Academy Of Sciences
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Molecular characterization of a cyprinid fish (Ancherythroculter nigrocauda) TBK1 and its kinase activity in IFN regulation
No full textTANK-binding kinase 1 (TBK1) plays a vital role in activating interferon (IFN) production and positively regulating antiviral response in mammals. Research on more species of fish is necessary to clarify whether the function of fish TBK1 is conserved compared to that in mammals. Here, a cyprinid fish (Ancherythroculter nigrocauda) TBK1 (AnTBK1) was functionally identified and characterized. The full-length open reading frame (ORF) of AnTBK1 consists of 2184 nucleotides encoding 727 amino acids and contains a conserved Serine/Threonine protein kinase catalytic domain (S_TKc) in the N-terminal, similar to TBK1 in other species. The transcripts of AnTBK1 were found in all the tissues evaluated and the cellular distribution indicated that AnTBK1 was localized in the cytoplasm. In terms of functional identification, AnTBK1 induced a variety of IFN promoter activities as well as the expression of downstream IFN-stimulated genes (ISGs). In addition, AnTBK1 interacted with and significantly phosphorylated IFN regulatory factor 3 (IRF3), exhibiting the canonical kinase activity of TBK1. Finally, AnTBK1 presented strong antiviral activity against spring viremia of carp virus (SVCV) infection. Taken together, our research on the features and functions of AnTBK1 demonstrated that AnTBK1 plays a central role in IFN induction against SVCV infection
Microplastics in freshwater sediment: A review on methods, occurrence, and sources
No full textThere is a rising concern regarding the accumulation of microplastics in the aquatic ecosystems. However, compared to the marine environment, the occurrence, transport, and diffusion of microplastics in freshwater sediment are still open questions. This paper summarizes and compares the methods used in previous studies and provides suggestions for sampling and analysis of microplastics in freshwater sediment. This paper also reviews the findings on microplastics in freshwater sediment, including abundance, morphological characteristics, polymer types, sources, and factors affecting the abundance of microplastics in freshwater sediment. The results show that microplastics are ubiquitous in the investigated sediment of rivers, lakes, and reservoirs, with an abundance of 2-5 orders of magnitude across different regions. Low microplastics concentration was observed in the Ciwalengke River with an average abundance of 30.3 +/- 15.9 items/kg. In particular, an extremely high abundance of microplastics was recorded in the urban recipient in Norway reaching 12,000-200,000 items/kg. Fibers with particle size less than 1 mm are the dominant shape for microplastics in freshwater sediment. In addition, the most frequently recorded colors and types are white/transparent, and PE/PS, respectively. Finally, we conclude that the consistency of morphological characteristics and components of microplastics between the beach or marine sediments and freshwater sediments may be an indicator of these interlinkages and source-pathways. Microplastics in freshwater sediment need further research and exploration to identify its spatial and temporal variations and driving force through further field sampling and implementation of standard and uniform analytical methodologies. (C) 2020 Elsevier B.V. All rights reserved
Production, functional stability, and effect of rhamnolipid biosurfactant from Klebsiella sp. on phenanthrene degradation in various medium systems
No full textThe present study investigated the stability and efficacy of a biosurfactant produced by Klebsiella sp. KOD36 under extreme conditions and its potential for enhancing the solubilization and degradation of phenanthrene in various environmental matrices. Klebsiella sp. KOD36 produced a mono-rhamnolipids biosurfactant with a low critical micelle concentration (CMC) value. The biosurfactant was stable under extreme conditions (60 degrees C, pH 10 and 10% salinity) and could lower surface tension by 30% and maintained an emulsification index of > 40%. The emulsion index was also higher (17-43%) in the presence of petroleum hydrocarbons compared to synthetic surfactant Triton X-100. Investigation on phenanthrene degradation in three different environmental matrices (aqueous, soil-slurry and soil) confirmed that the biosurfactant enhanced the solubilization and biodegradation of phenanthrene in all matrices. The high functional stability and performance of the biosurfactant under extreme conditions on phenanthrene degradation show the great potential of the biosurfactant for remediation applications under harsh environmental conditions
The new chimeric chiron genes evolved essential roles in zebrafish embryonic development by regulating NAD(+) levels
No full textThe origination of new genes is important for generating genetic novelties for adaptive evolution and biological diversity. However, their potential roles in embryonic development, evolutionary processes into ancient networks, and contributions to adaptive evolution remain poorly investigated. Here, we identified a novel chimeric gene family, the chiron family, and explored its genetic basis and functional evolution underlying the adaptive evolution of Danioninae fishes. The ancestral chiron gene originated through retroposition of nampt in Danioninae 48-54 million years ago (Mya) and expanded into five duplicates (chiron1-5) in zebrafish 1-4 Mya. The chiron genes (chirons) likely originated in embryonic development and gradually extended their expression in the testis. Functional experiments showed that chirons were essential for zebrafish embryo development. By integrating into the NAD(+) synthesis pathway, chirons could directly catalyze the NAD(+) rate-limiting reaction and probably impact two energy metabolism genes (nmnat1 and naprt) to be under positive selection in Danioninae fishes. Together, these results mainly demonstrated that the origin of new chimeric chiron genes may be involved in adaptive evolution by integrating and impacting the NAD(+) biosynthetic pathway. This coevolution may contribute to the physiological adaptation of Danioninae fishes to widespread and varied biomes in Southeast Asian
Microbial fuel cell improves restoration of Hydrilla verticillata in an algae-rich sediment microcosm system
No full textSettled algae may be used as nutrient for macrophyte establishment, but also can induce marked macrophyte decline during deep anaerobic decomposition. Sediment microbial fuel cells (SMFCs) may promote the utilization of algae-derived nutrients and relieve bio-toxicity from settled algae to submerged macrophytes, thus facilitating plant production. To test these hypotheses, a 62-day comparative study was designed and conducted in microcosms with the following six treatments: control (open-circuit SMFC), plant (open-circuit SMFC with plants), algae (open-circuit SMFC with algae), algae-plant (open-circuit SMFC with algae and plants), algae-SMFC (closed-circuit SMFC with algae), and algae-plant-SMFC (closed-circuit SMFC with algae and plants). The results showed that the presence of Hydrilla verticillata improved the power generation of SMFCs when algae were used as substrates during the whole operation. The decomposition of sedimented algae experienced two periods since the injection. During the slight decomposition period (14-38 day), the algal retention in sediments was enhanced by H. verticillata as a nutrient source. Nitrogen (N) assimilation in plant shoots was facilitated under electrogenesis due to a simultaneous increase of algae-derived dissolved inorganic carbon (DIC) and ammonium (NH4+) in the water column. At the end of the 38th day, the biomass of H. verticillata were increased by 21.4% and 52.3%, respectively, in the algae-plant and algae-plant-SMFC, compared with that in plant treatment. Obvious NH4+-stress was exerted on H. verticillata during the following intense algal decomposition period (38-62 day). Compared with shoots, roots of H. verticillata were more sensitive to the biotoxicity of algae-derived NH4+. The electrogenetic process diverted the degradation pathway from acetoclastic methanogenesis to electrogenesis via redox cycle, resulting in delayed algal decomposition in algae-SMFC treatment. In addition, electrogenesis enhanced the removal of algae-derived N. As a result, NH4+ toxicity to plant roots was effectively alleviated, and sedimented algae served as a stable nutrient source for plant development. Stable transfer rate of algae-derived N from sediments to plant roots was observed, while the assimilation rate of algae-derived N from water column to plant shoots showed a constant increase in the algae-plant-SMFC treatment. Electrogenesis enhanced N-fixing capacity belonged to rhizosphere of H. verticillata, evidenced by greater enrichment of some plant growth-promoting rhizobacteria (PGPRs), including Bradyrhizobium, Mycobacterium, Paenibacillus, Mesorhizobium, and Roseomonas in the algae-plant-SMFC treatment. At the end of the experiment, marked increases in the production of H. verticillata in algae-plant-SMFC were observed, with 90.1% and 32.8%, respectively, when compared with algae-plant and plant treatments (p < 0.05). SMFC application could be used as a strategy to promote the growth of submerged macrophytes in algae-rich sediments. (C) 2020 Elsevier Ltd. All rights reserved
Bibliometrics and visualization analysis regarding research on the development of microplastics (Jan, 10.1007/s11356-021-12366-2, 2021)
No full textA correction to this paper has been published: 10.1007/s11356-021-12767-
A global perspective on the influence of the COVID-19 pandemic on freshwater fish biodiversity
No full textThe COVID-19 global pandemic and resulting effects on the economy and society (e.g., sheltering-in-place, alterations in transportation, changes in consumer behaviour, loss of employment) have yielded some benefits and risks to biodiversity. Here, we considered the ways the COVID-19 pandemic has influenced (or may influence) freshwater fish biodiversity (e.g., richness, abundance). In many cases, we could only consider potential impacts using documented examples (often from the media) of likely changes, because anecdotal observations are still emerging and data-driven studies are yet to be completed or even undertaken. We evaluated the potential for the pandemic to either mitigate or amplify widely acknowledged, pre-existing threats to freshwater fish biodiversity (i.e., invasive species, pollution, fragmentation, flow alteration, habitat loss and alteration, climate change, exploitation). Indeed, we identified examples spanning the extremes of positive and negative outcomes for almost all known threats. We also considered the pandemic's impact on freshwater fisheries demand, assessment, research, compliance monitoring, and management interventions (e.g., restoration), with disruptions being experienced in all domains. Importantly, we provide a forward-looking synthesis that considers the potential mechanisms and pathways by which the consequences of the pandemic may positively and negatively impact freshwater fishes over the longer term. We conclude with a candid assessment of the current management and policy responses and the extent to which they ensure freshwater fish populations and biodiversity are conserved for human and aquatic ecosystem benefits in perpetuity
Identification of Dermocystidium anguillae Spangenberg, 1975 from the American eel Anguilla rostrata (Lesueur, 1817) and Chinese perch Siniperca chuatsi (Basilewsky, 1855)
No full textRecently, mass mortality of the American eel Anguilla rostrata (Lesueur, 1817) and Chinese perch Siniperca chuatsi (Basilewsky, 1855) caused by dermocystidiosis has occurred in China. In the present study, a Dermocystidium species from American eels and Chinese perch was identified. Sequence analysis revealed that the small subunit ribosomal DNA (SSU rDNA) of Dermocystidium specimens infecting American eels was identical to those of Dermocystidium specimens infecting Chinese perch, which indicates the conspecificity of these Dermocystidium specimens from different hosts. When the present Dermocystidium specimens infecting gills of American eels was compared with all reported Dermocystidium species, it is found that the present species has closely related host fish, identical infection site, and overlapped size with D. anguillae Spangenberg, 1975 described from gills of European eel A. anguilla (Linnaeus, 1758), which suggests these two Dermocystidium isolations from the American eels and European eels may be considered as same species. Surprisingly, BLAST search showed that all the newly obtained SSU rDNA of D. anguillae were most similar to that of D. fennicum Pekkarinen, Lom, Murphy, Ragan, Dykova, 2003 infecting common perch Perca fluviatilis Linnaeus, 1758. However, their sequence variation should be within the degree of intraspecific sequence variation, being 99.61% to 99.71% similarities, suggesting that D. fennicum is synonymous with D. anguillae. Phylogenetically, all species in the Dermocystidium genus were clustered in the Dermocystidium clade. However, Amphibiocystidium ranae Pascolini, Daszak, Cunningham, Fagotti, Tei, Vagnetti, Bucci et Rosa, 2003 infecting frog Rana esculenta Linnaeus, 1785. was also placed in this clade, which may either imply the non-monophyly of the species in the Dermocystidium or the requirement for further phylogenetic study on these two genera
Construction of a high-density genetic linkage map and fine mapping of QTLs for growth and sex-related traits in red-tail catfish (Hemibagrus wyckioides)
No full textHigh-density genetic linkage map based on single nucleotide polymorphisms (SNPs) are essential for fine mapping of QTLs and identification of trait-related genes in aquaculture fish species. In this study, the first high density genetic linkage map of red-tail catfish (Hemibagrus wyckioides) based on 2b-RAD sequencing technology was constructed using one F1 family composed of 165 offspring and their parents. A total of 2369 SNP markers were assigned to 29 linkage groups (LGs) and the map spanned 2067.35 cM with an average SNP marker interval of 0.87 cM and genome coverage of 98.16%. QTL mapping analysis revealed that 2 significant and 15 suggestive QTLs for all four morphometric traits were identified on 10 LGs, explaining 7.4-13.3% of phenotypic variations. Some candidate growth-related genes such as ttc39b, lrp1, gng3, aspp2, mgp and rusc2 were identified within QTL intervals, and a SNP in ttc39b was found to be significantly associated with body weight in different genetically unrelated populations of red-tail catfish. In addition, one genome-wide significance sex-related QTL was detected on the LG20 with a contribution to phenotypic variation of 44.2-85.7%. A total of 10 potential sex dimorphic genes, such as vps54, tsg10, pld6, psmd8 and gpa33, were also identified within or near the sex QTL markers in LG20. It suggests that the LG20 may be a sex-related LG in red-tail catfish. This high-density genetic map not only enables us to fine-map these genes related with the economic traits, but also provides effective information for future marker-assisted selection and sex-control breeding in this species
Construction of a high-density genetic linkage map and fine mapping of QTLs for growth and sex-related traits in red-tail catfish (Hemibagrus wyckioides)
No full textHigh-density genetic linkage map based on single nucleotide polymorphisms (SNPs) are essential for fine mapping of QTLs and identification of trait-related genes in aquaculture fish species. In this study, the first high density genetic linkage map of red-tail catfish (Hemibagrus wyckioides) based on 2b-RAD sequencing technology was constructed using one F1 family composed of 165 offspring and their parents. A total of 2369 SNP markers were assigned to 29 linkage groups (LGs) and the map spanned 2067.35 cM with an average SNP marker interval of 0.87 cM and genome coverage of 98.16%. QTL mapping analysis revealed that 2 significant and 15 suggestive QTLs for all four morphometric traits were identified on 10 LGs, explaining 7.4-13.3% of phenotypic variations. Some candidate growth-related genes such as ttc39b, lrp1, gng3, aspp2, mgp and rusc2 were identified within QTL intervals, and a SNP in ttc39b was found to be significantly associated with body weight in different genetically unrelated populations of red-tail catfish. In addition, one genome-wide significance sex-related QTL was detected on the LG20 with a contribution to phenotypic variation of 44.2-85.7%. A total of 10 potential sex dimorphic genes, such as vps54, tsg10, pld6, psmd8 and gpa33, were also identified within or near the sex QTL markers in LG20. It suggests that the LG20 may be a sex-related LG in red-tail catfish. This high-density genetic map not only enables us to fine-map these genes related with the economic traits, but also provides effective information for future marker-assisted selection and sex-control breeding in this species