Characterization and expression profiles of toll-like receptor genes (TLR2 and TLR5) in immune tissues of hybrid yellow catfish under bacterial infection.

The yellow catfish (Pelteobagrus fulvidraco) is one of the most economically important freshwater species in Asia. However, pathogenic bacterial infections often cause high rates of mortality and economic losses in practical aquaculture. Previous studies in mammals have shown that Toll-like receptor 2 (TLR2) and Toll-like receptor 5 (TLR5) are involved in the recognition of cell wall components such as lipopolysaccharides and flagella of various bacteria, thereby acting as key regulators in the innate immunity response. However, TLR2 and TLR5 in yellow catfish have not been characterized. In the present study, TLR2 and TLR5 were examined through comparative genomic approaches. The gene structure, collinearity, protein spatial structure, and phylogenetic relationships were compared with those in multiple representative vertebrates. Meanwhile, quantitative real-time PCR was conducted to explore transcriptional changes in TLR2 and TLR5 in immune tissues after infection with exogenous A. hydrophila and E. tarda. The results demonstrated the presence of TLR2 and TLR5 in yellow catfish. However, a systematic analysis showed that TLR2 was not associated with the arrangement of diverse neighboring genes. The expression of hybrid yellow catfish TLR2 transcripts in multiple tissues (including liver, spleen, kidney, and intestine) was significantly up-regulated after infection with A. hydrophila and E. tarda, suggesting that hybrid yellow catfish TLR2 and TLR5 may participate in the immune process. Taken together, the results indicate that TLR2 and TLR5 are conserved in terms of evolution and possess significant antibacterial activity as well as regulatory properties in immune-related tissues and thus play key roles in host defense against pathogen invasion.

Gene expressions between obligate bamboo-eating pandas and non-herbivorous mammals reveal converged specialized bamboo diet adaptation.

BACKGROUND: It is inevitable to change the function or expression of genes during the environmental adaption of species. Both the giant panda (Ailuropoda melanoleuca) and red panda (Ailurus fulgens) belong to Carnivora and have developed similar adaptations to the same dietary switch to bamboos at the morphological and genomic levels. However, the genetic adaptation at the gene expression level is unclear. Therefore, we aimed to examine the gene expression patterns of giant and red panda convergent specialized bamboo-diets. We examined differences in liver and pancreas transcriptomes between the two panda species and other non-herbivorous species. RESULTS: The clustering and PCA plots suggested that the specialized bamboo diet may drive similar expression shifts in these two species of pandas. Therefore, we focused on shared liver and pancreas DEGs (differentially expressed genes) in the giant and red panda relative to other non-herbivorous species. Genetic convergence occurred at multiple levels spanning carbohydrate metabolism, lipid metabolism, and lysine degradation. The shared adaptive convergence DEGs in both organs probably be an evolutionary response to the high carbohydrate, low lipid and lysine bamboo diet. Convergent expression of those nutrient metabolism-related genes in both pandas was an intricate process and subjected to multi-level regulation, including DNA methylation and transcription factor. A large number of lysine degradation and lipid metabolism related genes were hypermethylated in promoter regions in the red panda. Most genes related to carbohydrate metabolism had reduced DNA methylation with increased mRNA expression in giant pandas. Unlike the red panda, the core gene of the lysine degradation pathway (AASS) doesn't exhibit hypermethylation modification in the giant panda, and dual-luciferase reporter assay showed that transcription factor, NR3C1, functions as a transcriptional activator in AASS transcription through the binding to AASS promoter region. CONCLUSIONS: Our results revealed the adaptive expressions and regulations of the metabolism-related genes responding to the unique nutrients in bamboo food and provided data accumulation and research hints for the future revelation of complex mechanism of two pandas underlying convergent adaptation to a specialized bamboo diet.

Characterization and expression profiling of fadd gene in response to exogenous Aeromonas hydrophila or Edwardsiella tarda challenge in the hybrid yellow catfish (Pelteobagrus fulvidraco ♀ × P. vachelli ♂).

In mammals, fas-associated protein with death domain (FADD) is involved in the process of cell apoptosis and plays a key role in innate immune signaling. Nevertheless, its detailed molecular mechanisms underlying apoptosis and immune responses to exogenous bacterial infections in teleosts remain largely unknown. In this study, a group of 60 hybrid yellow catfish (with the body weight of 25 ± 0.5 g) were used in subsequent experiments, we examined the expression profiling of fadd gene through comparative genomics and comparative immunological methods. Our results showed that fadd in the hybrid yellow catfish (hycfadd) exhibited similar gene and spatial structures to those in other vertebrates, and formed an independent clade in phylogeny. An expression pattern analysis revealed that hycfadd widely transcribed in various tissues, with the highest transcription level in the liver. Furthermore, expression profiling of hycfadd when intraperitoneally infected with 50 µL of exogenous Aeromonas hydrophila (2.0 × 107 CFU/mL) or Edwardsiella tarda (2.0 × 107 CFU/mL) within 48 h were significantly up-regulated in the kidney, spleen, liver and intestine. Important genes in the toll like receptor (tlr) 1-tlr2- myeloid differentiation primary response 88 (MyD88)-fadd-caspase (casp) 8 cascades of TLR signaling pathway in liver were significantly up-regulated after the A. hydrophila stimulation, suggesting that apoptosis through the TLR signaling pathway may have been triggered and activated, which were further verified in the liver, kidney, spleen, intestine and gill by a TUNEL assay. Overall, this study provides solid evidence for the bacterial induction of fadd-related apoptosis in teleosts.

Comparative analyses reveal potential genetic mechanisms for high-altitude adaptation of Schizopygopsis fishes based on chromosome-level genomes.

The schizothoracine fishes, widely distributed in the Qinghai-Tibetan Plateau and its adjacent areas, are considered as ideal models for investigation of high-altitude adaptation. Schizophygopsis are one group of the highly specialized schizothoracine fishes, and the genetic basis for their high-altitude adaptation is poorly understood. In this study, we performed comparative genomics analyses to investigate the potential genetic mechanisms for high-altitude adaptation of Schizopygopsis malacanthus and Schizopygopsis pylzovi based on the chromosome-level genomes. Functional enrichment analysis revealed that many expanded gene families in Schizopygopsis were associated with immune response while many contracted gene families were functionally associated with olfaction. Among the 123 positively selected genes (PSGs), angpt2a was detected in HIF-1 signaling pathway and possibly related to the hypoxia adaptation of Schizopygopsis. Furthermore, two PSGs cox15 and ndufb10 were distributed in thermogenesis, and there was a Schizopygopsis-specific missense mutation in cox15 (Gln115Glu), which possibly contributed to the cold temperature adaptation of the Schizopygopsis. Kyoto Encyclopedia of Genes and Genomes enrichment of the PSGs revealed three significant pathways including metabolic pathways, cell cycle, and homologous recombination and Gene Ontology enrichment analysis of the PSGs revealed several categories associated with DNA repair, cellular response to DNA damage stimulus, and metabolic process. Chromosome-scale characterization of olfactory receptor (OR) repertoires indicated that Schizopygopsis had the least number of OR genes, and the OR gene contraction was possibly caused by the limited food variety and the environmental factors such as lower air pressure, lower humidity, and lower temperature. Our study will help expand our understanding of the potential adaptive mechanism of Schizopygopsis to cope with the high-altitude conditions.

Epigenomic profiling indicates a role for DNA methylation in the postnatal liver and pancreas development of giant pandas.

Giant pandas are unique within Carnivora with a strict bamboo diet. Here, the epigenomic profiles of giant panda liver and pancreas tissues collected from three important feeding stages were investigated using BS-seq. Few differences in DNA methylation profiles were exhibited between no feeding and suckling groups in both tissues. However, we observed a tendency toward a global loss of DNA methylation in the gene-body and promoter region of metabolism-related genes from newborn to adult. Correlation analysis revealed a significant negative correlation between the changes in methylation levels within gene promoters and gene expression. The majority of genes related to nutrition metabolism had lost DNA methylation with increased mRNA expression in adult giant pandas. The few galactose metabolism and unsaturated fatty acid metabolism related genes that were hypomethylated and highly-expressed at early stages of giant panda development may meet the nutritional requirement of this species' highly altricial neonates.

Seasonal variation significantly influenced the stochasticity of community assembly of amphibian symbiotic bacteria.

Seasonal variation has been shown to influence symbiotic bacterial community composition and structure in amphibians. It is still unknown how the symbiotic bacterial community assembly changes during different seasons, especially for amphibians who are particularly sensitive to environmental change. We found significant differences in the composition and diversity (alpha and beta diversity) of amphibian skin and gut bacteria. Co-occurrences network analysis showed that seasonal variation reduced the microbial network complexity of amphibians from summer to autumn. The normalized stochastic ratio (NST) and phylogenetic bin-based null model analysis (iCAMP) models showed that the same result that stochastic processes was the major factor regulating the symbiotic bacterial community assembly mechanisms of amphibians. From summer to autumn, the symbiotic bacterial community assembly mechanisms declined in the contribution of stochastic processes, while increasing in the contribution of deterministic processes. Dispersal limitation was the dominant microbial assembly mechanism, followed by homogeneous selection, and then heterogeneous selection in the symbiotic bacterial community communities of amphibians between summer and autumn. Furthermore, higher niche width of the symbiotic bacterial community of amphibians was found in summer than autumn. Overall, these results demonstrated that seasonal variation influenced amphibian symbiotic bacterial community between summer and autumn.

Genome-wide characterization of microsatellite DNA in fishes: survey and analysis of their abundance and frequency in genome-specific regions.

BACKGROUND: Microsatellite repeats are ubiquitous in organism genomes and play an important role in the chromatin organization, regulation of gene activity, recombination and DNA replication. Although microsatellite distribution patterns have been studied in most phylogenetic lineages, they are unclear in fish species. RESULTS: Here, we present the first systematic examination of microsatellite distribution in coding and non-coding regions of 14 fish genomes. Our study showed that the number and type of microsatellites displayed nonrandom distribution for both intragenic and intergenic regions, suggesting that they have potential roles in transcriptional or translational regulation and DNA replication slippage theories alone were insufficient to explain the distribution patterns. Our results showed that microsatellites are dominant in non-coding regions. The total number of microsatellites ranged from 78,378 to 1,012,084, and the relative density varied from 4925.76 bp/Mb to 25,401.97 bp/Mb. Overall, (A + T)-rich repeats were dominant. The dependence of repeat abundance on the length of the repeated unit (1-6 nt) showed a great similarity decrease, whereas more tri-nucleotide repeats were found in exonic regions than tetra-nucleotide repeats of most species. Moreover, the incidence of different repeated types appeared species- and genomic-specific. These results highlight potential mechanisms for maintaining microsatellite distribution, such as selective forces and mismatch repair systems. CONCLUSIONS: Our data could be beneficial for the studies of genome evolution and microsatellite DNA evolutionary dynamics, and facilitate the exploration of microsatellites structural, function, composition mode and molecular markers development in these species.

Pathogen of Vibrio harveyi infection and C-type lectin proteins in whiteleg shrimp (Litopenaeus vannamei).

Diseases caused by Vibrio harveyi in shrimps have gradually become one group of the most serious threats to shrimp production, while related molecular mechanisms of infections with Vibrio harveyi are still not known well in shrimps. Here, we performed proteomic sequencing of hepatopancreas in whiteleg shrimps (Litopenaeus vannamei) infected with exogenous Vibrio harveyi, and subsequent functional annotation and calculation of differentially expressed proteins (DEPs) in this study. A total of 145 DEPs were obtained, among them 36 were up-regulated and 109 were down-regulated after the infection. Meanwhile, our results showed that after the infection of Vibrio harveyi, expression levels of a variety of C-type lectins (CTLs) were changed significantly. In-depth functional domain analysis and spatial structure prediction of these CTLs revealed that amino acid sequences and spatial structures of the C-type lectin domain (CTLD) shared by the CTL-S and IML proteins were variant, suggesting differential functions between the two CTLs. In summary, various members of the CTL family have different epidemic responses to Vibrio harveyi infection, which provides a theoretical guidance for deep-going investigations on practical immunity reactions and pathogen infections in shrimps.

Improved aerobic and anaerobic swimming performance after exercise training and detraining in Schizothorax wangchiachii: Implications for fisheries releases.

Swimming performance (aerobic and anaerobic) is often used to predict the ability of fish to adapt and survive. Fish raised in captivity are typically poor swimmers and have lower survival rates than wild conspecifics when released into the natural environment. We investigated the potential for exercise training to enhance the swimming performance of Schizothorax wangchiachii held in captivity. Juvenile fish (mean body mass 1.40 ± 0.13 g, mean body length 4.36 ± 0.24 cm) were trained under five different regimes [3 cm·s-1 control group (C), 10 cm·s-1 for 6 (L6) and 12 h (L12) per day and 20 cm·s-1 for 6 (H6) and 12 h (H12) per day] for 30 days and then detrained for 20 days (i.e. no training). Aerobic (i.e. critical swimming speed, Ucrit), anaerobic swimming performance (i.e. endurance time at 1.2 or 1.5 Ucrit), and morphological parameters were measured at the beginning (T0), after 30 days of exercise training (T30) and after 20 days of detraining (DT20). Aerobic exercise training significantly improved the Ucrit, endurance time at 1.2 and 1.5 Ucrit of juvenile S. wangchiachii (P < .05). After 20 days of detraining, both the aerobic and anaerobic swimming performance of the H6 and H12 groups declined and no longer differed from the control group indicating a failure to maintain improved swimming performance, whereas improved swimming performance was maintained in L6 and L12 groups. No significant difference in swimming performance was found between 6 and 12 hours training at 10 cm·s-1. Thus, exercise at close to 10 cm·s-1 for 6 h per day for 30 days or a longer time periods prior to release appears to be a suitable regime for swimming performance enhancement, potentially increasing survivability of released S. wangchiachii in wild.

Evolutionary melting pots and reproductive isolation: A ring-shaped diversification of an odorous frog (Odorrana margaratea) around the Sichuan Basin.

Quaternary climatic oscillations and geography are of primary importance in shaping intraspecific genetic diversity. We examined the diversification patterns and inferred processes for the green odorous frog (Odorrana margaretae) of western China. Species distribution modelling showed that the species has a continuous circular distribution around the Sichuan Basin while the basin itself is largely uninhabitable. Population genetic and phylogenetic analyses revealed that the species has a ring-shaped divergent pattern. While the chain of populations around the Basin maintains a mostly gradual and continuous genetic variation, populations between the north and west showed little gene exchange. Two processes, glacial refugial history and geography, likely contributed to the observed patterns. Our genetic clustering analysis revealed two clusters, suggesting two refugial groups among the populations, one from the west and the other from the east. Postglacial expansion may have created two contact zones. One at the south had extensive population admixture and produced a gradual transition between the western and eastern populations. Consequently, this region has the highest genetic diversity and represents an evolutionary "melting pot." In contrast, the second contact zone at the northwestern side of the Basin has limited admixture, suggesting partial reproductive isolation between the northern and western populations. Furthermore, an isolation-by-distance analysis revealed a strong correlation (Mantel r = 0.745) between the genetic and geographic distances, when we assumed that populations were connected following the circular distribution without gene flow across the NW contact zone. We also explored alternative explanations, such as a one-refugium scenario. With its micro-ring, the green odorous frog is poised to make an excellent model system for understanding the process of speciation.

Strong population structure of Schizopygopsis chengi and the origin of S. chengi baoxingensis revealed by mtDNA and microsatellite markers.

The Tibetan Plateau underwent dramatic geological and climatic changes, which had important implications for genetic divergence and population dynamics of freshwater fish populations. Fluctuations of the ecogeographical environment and major hydrographic formations might have promoted the formation of new subspecies or species. In order to understand the impact of plateau uplift on freshwater fish evolutionary history, we estimated the genetic diversity and population structure in two subspecies of Schizopygopsis chengi (S. c. chengi and S. c. baoxingensis) in upper Yangtze River in Tibetan Plateau area using mitochondrial DNA control region and eight microsatellite markers, which suggested that there was a close genetic relationship. S. chengi showed some significant genetic structure that did not correlate with geographic distance. Bayesian assignment tests indicated that S. chengi samples in the study could be divided into four populations: upstream population, midstream population, tributary population and S. c. baoxingensis population. S. c. chengi and S. c. baoxingensis showed significant genetic divergence. However, phylogenetic analysis, population structure analysis and historical gene flow estimation suggested that there was close genetic relationship between S. c. baoxingensis and the Dawei population which belongs to populations of S. c. chengi. The time that Dawei population suffered from a bottleneck and S. c. baoxingensis underwent population expansion was congruent with the last glacial period on the Tibetan Plateau. The results confirmed the hypothesis that the Dawei River and Baoxing River were once connected, and the Dawei and Baoxing populations originated from a single population, but were isolated into separate populations because of crustal movements and the Baoxing population evolved as S. c. baoxingensis.

Molecular cloning and expression of two heat-shock protein genes (HSC70/HSP70) from Prenant's schizothoracin (Schizothorax prenanti).

Through the RT-PCR and rapid amplification of cDNA ends, two complementary deoxyribonucleic acid (cDNA) clones encoding heat-shock cognate 70 (HSC70, designated Sp-HSC70) and inducible heat-shock protein 70 (HSP70, designated Sp-HSP70) were isolated from the liver of Prenant's schizothoracin (Schizothorax prenanti). The cDNAs were 2344- and 2292-bp in length and contained 1950- and 1932-bp open reading frames, encoded proteins of 649 and 643 amino acids, respectively. Amino acid sequence analysis indicated that both Sp-HSC70 and Sp-HSP70 contained three signature sequences of HSP70 family, two partial overlapping bipartite nuclear localization signal sequences (an ATP-binding site motif, a bipartite nuclear targeting signal), and a cytoplasmic characteristic motif EEVD. Homology analysis revealed that Sp-HSC70 and Sp-HSP70 shared 77.5% identity and Sp-HSC70 shared more than 81.1% identity with the known HSC70s of other vertebrates, while Sp-HSP70 shared more than 77.5 % identity with the known HSP70s of other vertebrates. Fluorescent real-time quantitative RT-PCR showed that Sp-HSC70 and Sp-HSP70 mRNAs were found in all tested tissues, including blood, brain, heart, liver, spleen, head kidney, white muscle, skin, gonad, hypophysis, red muscle, and gill. The Sp-HSC70 and Sp-HSP70 mRNA expression level in blood and head kidney displayed a significant increase in vibrio-challenged group with the bacterium Aeromonas hydrophila at 24 h post-infection compared to a control group. Temporally, there was a clear time-dependent expression pattern of Sp-HSC70 or Sp-HSP70 gene after bacterial challenge, and the expression of Sp-HSC70 and Sp-HSP70 mRNAs reached a maximum level at 12 and 6 h post-challenge, respectively. Both returned to control level after 7 × 24 h. The results suggest that Sp-HSC70 and Sp-HSP70 genes may play important roles in mediating the immune responses of A. hydrophila-related diseases in the Prenant's schizothoracin.

Integrated miRNA and mRNA Sequencing Reveals the Sterility Mechanism in Hybrid Yellow Catfish Resulting from Pelteobagrus fulvidraco (♀) × Pelteobagrus vachelli (♂).

The hybrid yellow catfish exhibits advantages over pure yellow catfish in terms of fast growth, fast development, a high feeding rate, and strong immunity; additionally, it is almost sterile, thus ensuring the conservation of the genetic stock of fish populations. To investigate the sterility mechanism in hybrid yellow catfish (P. fulvidraco (♀) × P. vachelli (♂)), the mRNA and miRNA of the gonads of P. fulvidraco, P. vachelli, and a hybrid yellow catfish were analyzed to characterize the differentially expressed genes; this was carried out to help establish gene expression datasets to assist in the further determination of the mechanisms of genetic sterility in hybrid yellow catfish. In total, 1709 DEGs were identified between the hybrid and two pure yellow catfishes. A KEGG pathway analysis indicated that several genes related to reproductive functions were upregulated, including those involved in the cell cycle, progesterone-mediated oocyte maturation, and oocyte meiosis, and genes associated with ECM-receptor interaction were downregulated. The spermatogenesis-related GO genes CFAP70, RSPH6A, and TSGA10 were identified as being downregulated DEGs in the hybrid yellow catfish. Sixty-three DEmiRNAs were identified between the hybrid and the two pure yellow catfish species. The upregulated DEmiRNAs ipu-miR-194a and ipu-miR-499 were found to target the spermatogenesis-related genes CFAP70 and RSPH6A, respectively, playing a negative regulatory role, which may underscore the miRNA-mRNA regulatory mechanism of sterility in hybrid yellow catfish. The differential expression of ipu-miR-196d, ipu-miR-125b, and ipu-miR-150 and their target genes spidr, cep85, and kcnn4, implicated in reproductive processes, was verified via qRT-PCR, consistent with the transcriptome sequencing expression trends. This study provides deep insights into the mechanism of hybrid sterility in vertebrate groups, thereby contributing to achieving a better understanding and management of fish conservation related to hybrid sterility.

Deterministic processes dominate microbial assembly mechanisms in the gut microbiota of cold-water fish between summer and winter.

Exploring the effects of seasonal variation on the gut microbiota of cold-water fish plays an important role in understanding the relationship between seasonal variation and cold-water fish. Gut samples of cold-water fish and environmental samples were collected during summer and winter from the lower reaches of the Yalong River. The results of the 16S rRNA sequencing showed that significant differences were identified in the composition and diversity of gut bacteria of cold-water fish. Co-occurrence network complexity of the gut bacteria of cold-water fish was higher in summer compared to winter (Sum: nodes: 256; edges: 20,450; Win: nodes: 580; edges: 16,725). Furthermore, from summer to winter, the contribution of sediment bacteria (Sum: 5.3%; Win: 23.7%) decreased in the gut bacteria of cold-water fish, while the contribution of water bacteria (Sum: 0%; Win: 27.7%) increased. The normalized stochastic ratio (NST) and infer community assembly mechanisms by phylogenetic bin-based null model analysis (iCAMP) showed that deterministic processes played a more important role than stochastic processes in the microbial assembly mechanism of gut bacteria of cold-water fish. From summer to winter, the contribution of deterministic processes to gut bacteria community assembly mechanisms decreased, while the contribution of stochastic processes increased. Overall, these results demonstrated that seasonal variation influenced the gut bacteria of cold-water fish and served as a potential reference for future research to understand the adaptation of fish to varying environments.

Plant functional traits mediate the response magnitude of plant-litter-soil microbial C: N: P stoichiometry to nitrogen addition in a desert steppe.

Global nitrogen deposition is significantly altering the carbon (C), nitrogen (N) and phosphorus (P) stoichiometry in terrestrial ecosystems, yet how N deposition simultaneously affects plant-litter-soil-soil microbial stoichiometry in arid grassland is still unclear. In a five-year experimental study conducted in a desert steppe in Northern China, we investigated the effects of N addition on the C:N:P stoichiometry of plants, litter, soil, and soil microbes. We also used structural equation modelling (SEM) exploring the direct or indirect effects of N addition, plant species diversity, functional traits and diversity, soil microbial diversity, soil pH, soil electrical conductivity (EC) and moisture on the stoichiometry in plant-soil system. The results showed that N addition increased the N, P concentrations and N:P in plants, the N concentration and N:P in litter, and the C, N concentrations, C:P and N:P in microbes. Conversely, it decreased the C:N and C:P in plants, and litter C:N. Functional traits, functional dispersion (FDis), soil pH and EC accounted for a substantial proportion of the observed variations in elemental concentrations (from 42 % to 69 %) and stoichiometry (from 9 % to 73 %) across different components. SEM results showed that N addition decreased C:N and C:P in plants and litter by increasing FDis and leaf N content, while increased plant and litter N:P by decreasing leaf C content and increasing specific leaf area, respectively. Furthermore, N addition increased microbial C:P by increasing leaf thickness. We also found the mediating effects of soil pH and EC on C:N, C:P of litter and microbial N:P. Overall, our research suggests that plant functional traits as key predictors of nutrient cycling responses in desert steppes under N addition. This study extends the application of plant functional traits, enhances our understanding of C and nutrient cycling and facilitates predicting the response of desert steppes to N deposition.

Grassland stability decreases with increasing number of global change factors: A meta-analysis.

Experiments manipulating a single global change factor (GCF) have provided increasing evidence that global environmental changes, such as eutrophication, precipitation change, and warming, generally affect the temporal stability of grassland productivity. Whether the combined impact of global changes on grassland stability increases as the number of global changes increases remains unknown. Using a meta-analysis of 673 observations from 143 sites worldwide, including 7 different GCFs, we examined the responses of grassland temporal stability of productivity to increasing numbers of GCFs. We quantified the links between community stability, biotic factors (i.e., species richness, species stability, and species asynchrony), and abiotic factors (i.e., aridity index, experimental duration, and experimental intensity). Although inconsistent responses of community stability were found with different GCF types and combinations, when integrating existing GCFs studies and ignoring the identity of GCFs, we found a general decrease in community stability as the number of GCFs increases, but the main drivers of community stability varied with the numbers of GCFs. Specifically, one GCF mainly reduced species stability through species richness and thus weakened community stability. Two GCFs weakened community stability via independently weakening species stability and species asynchrony. Three GCFs reduce community stability mainly via independently weakening species asynchrony. Moreover, for single factor, the impact of GCFs on community stability was weaker under dryer conditions, but stronger when two or three factors were manipulated. In addition, the negative effect of GCFs on community stability was weaker with increasing experimental duration. Our study reveals that reduced community stability with increasing numbers of GCFs is caused by a shift from reduced species stability to reduced species asynchrony, suggesting that persistent global changes will destabilize grassland productivity by reducing asynchronous dynamics among species in response to natural environmental fluctuations.

Deterministic processes dominate microbial community assembly in artificially bred Schizothorax wangchiachii juveniles after being released into wild.

Fish artificial breeding and release is an important method to restore wild populations of endemic fish species around the world. Schizothorax wangchiachii (SW) is an endemic fish in the upper Yangtze River and is one of the most important species for the artificial breeding and release program implemented in the Yalong River drainage system in China. It is unclear how artificially bred SW adapts to the changeable wild environment post-release, after being in a controlled and very different artificial environment. Thus, the gut samples were collected and analyzed for food composition and microbial 16S rRNA in artificially bred SW juveniles at day 0 (before release), 5, 10, 15, 20, 25, and 30 after release to the lower reaches of the Yalong River. The results indicated that SW began to ingest periphytic algae from the natural habitat before day 5, and this feeding habit is gradually stabilized at day 15. Prior to release, Fusobacteria are the dominant bacteria in the gut microbiota of SW, while Proteobacteria and Cyanobacteria generally are the dominant bacteria after release. The results of microbial assembly mechanisms illustrated that deterministic processes played a more prominent role than stochastic processes in the gut microbial community of artificially bred SW juveniles after releasing into the wild. Overall, the present study integrates the macroscopic and microscopic methods to provide an insight into the food and gut microbial reorganization in the released SW. This study will be an important research direction to explore the ecological adaptability of artificially bred fish after releasing into the wild.

Toll-like Receptor 3 in the Hybrid Yellow Catfish (Pelteobagrus fulvidraco ♀ × P. vachelli ♂): Protein Structure, Evolution and Immune Response to Exogenous Aeromonas hydrophila and Poly (I:C) Stimuli.

As a major mediator of cellular response to viral infection in mammals, Toll-like receptor 3 (TLR3) was proved to respond to double-stranded RNA (dsRNA). However, the molecular mechanism by which TLR3 functions in the viral infection response in teleosts remains to be investigated. In this study, the Toll-like receptor 3 gene of the hybrid yellow catfish was identified and characterized by comparative genomics. Furthermore, multiple sequence alignment, genomic synteny and phylogenetic analysis suggested that the homologous TLR3 genes were unique to teleosts. Gene structure analysis showed that five exons and four introns were common components of TLR3s in the 12 examined species, and interestingly the third exon in teleosts was the same length of 194 bp. Genomic synteny analysis indicated that TLR3s were highly conserved in various teleosts, with similar organizations of gene arrangement. De novo predictions showed that TLR3s were horseshoe-shaped in multiple taxa except for avian (with a round-shaped structure). Phylogenetic topology showed that the evolution of TLR3 was consistent with the evolution of the studied species. Selection analysis showed that the evolution rates of TLR3 proteins were usually higher than those of TLR3-TIR domains, indicating that the latter were more conserved. Tissue distribution analysis showed that TLR3s were widely distributed in the 12 tested tissues, with the highest transcriptions in liver and intestine. In addition, the transcription levels of TLR3 were significantly increased in immune-related tissues after infection of exogenous Aeromonas hydrophila and poly (I:C). Molecular docking showed that TLR3 in teleosts forms a complex with poly (I:C). In summary, our present results suggest that TLR3 is a pattern recognition receptor (PRR) gene in the immune response to pathogen infections in hybrid yellow catfish.

The organism fate of inland freshwater system under micro-/nano-plastic pollution: A review of past decade.

Micro- and nano-plastics (MPs/NPs) are characterized by their small size and extensive surface area, making them global environmental pollutants with adverse effects on organisms at various levels, including organs, cells, and molecules. Freshwater organisms, such as microalgae, emerging plants, zooplankton, benthic species, and fish, experience varying impacts from MPs/NPs, which are prevalent in both terrestrial and aquatic inland environments. MPs/NPs significantly impact plant physiological processes, including photosynthesis, antioxidant response, energy metabolism, and nitrogen removal. Extended exposure and ingestion to MPs/NPs might cause metabolic and behavioral deviations in zooplankton, posing an extinction risk. Upon exposure to MPs/NPs, both benthic organisms and fish display behavioral and metabolic disturbances, due to oxidative stress, neural toxicity, intestinal damage, and metabolic changes. Results from laboratory and field investigations have confirmed that MPs/NPs can be transported across multiple trophic levels. Moreover, MPs/NPs-induced alterations in zooplankton populations can impede energy transfer, leading to food scarcity for filter-feeding fish, larvae of benthic organism and fish, thus jeopardizing aquatic ecosystems. Furthermore, MPs/NPs can harm the nervous systems of aquatic organisms, influencing their feeding patterns, circadian rhythms, and mobility. Such behavioral alterations might also introduce unforeseen ecological risks. This comprehensive review aims to explore the consequences of MPs/NPs on freshwater organisms and their interconnected food webs. The investigation encompasses various aspects, including behavioral changes, alterations in physiology, impacts on metabolism, transgenerational effects, and the disruption of energy transfer within the ecosystem. This review elucidated the physiological and biochemical toxicity of MPs/NPs on freshwater organisms, and the ensuing risks to inland aquatic ecosystems.

Characterization of TLR1 and expression profiling of TLR signaling pathway related genes in response to Aeromonas hydrophila challenge in hybrid yellow catfish (Pelteobagrus fulvidraco ♀ × P. vachelli ♂).

Toll-like receptor 1 (TLR1) mediates the innate immune response to a variety of microbes through recognizing cell wall components (such as bacterial lipoproteins) in mammals. However, the detailed molecular mechanism of TLR1 involved in pathogen immunity in the representative hybrid yellow catfish (Pelteobagrus fulvidraco ♀ × P. vachelli ♂) has not been well studied. In the present study, we identified the TLR1 gene from the hybrid yellow catfish, and further comparative synteny data from multiple species confirmed that the TLR1 gene is highly conserved in teleosts. Phylogenetic analysis revealed distinguishable TLR1s in diverse taxa, suggesting consistence in evolution of the TLR1 proteins with various species. Structural prediction indicated that the three-dimensional structures of TLR1 proteins are relatively conserved among different taxa. Positive selection analysis showed that purifying selection dominated the evolutionary process of TLR1s and TLR1-TIR domain in both vertebrates and invertebrates. Expression pattern analysis based on the tissue distribution showed that TLR1 mainly transcribed in the gonad, gallbladder and kidney, and the mRNA levels of TLR1 in kidney were remarkably up-regulated after Aeromonas hydrophila stimulation, indicating that TLR1 participates in the inflammatory responses to exogenous pathogen infection in hybrid yellow catfish. Homologous sequence alignment and chromosomal location indicated that the TLR signaling pathway is very conserved in the hybrid yellow catfish. The expression patterns of TLR signaling pathway related genes (TLR1- TLR2 - MyD88 - FADD - Caspase 8) were consistent after pathogen stimulation, revealing that the TLR signaling pathway is triggered and activated after A. hydrophila infection. Our findings will lay a solid foundation for better understanding the immune roles of TLR1 in teleosts, as well as provide basic data for developing strategies to control disease outbreak in hybrid yellow catfish.