摘要: Aquatic habitat analysis is crucial in determining the relationship between river flow and habitat availability for aquatic species. This helps in identifying the environmental flow requirements of rivers. However, conducting habitat analysis in Indian rivers is challenging because of the unavailability of reliable and high-resolution terrain data. To address this challenge, a study was conducted to explore the possibilities of using Digital Elevation Models (DEMs) to extract required hydraulic data and to evaluate their accuracies. The extracted data were coupled with ecological data of a keystone fish species, namely Golden Mahseer ( Tor putitora), to develop habitat analysis models for the Upper Ganga Basin (UGB) in India. The study adopted a hierarchical three-step approach for evaluating the accuracy and performance of DEMs as surrogate data sources. Firstly, cross sections at selected sites in the UGB were extracted from three different DEMs (SRTM, ASTER, and CARTOSAT) and evaluated against surveyed cross-section data with turning point tests and correlation coefficients. These data were then used to establish hydraulic and habitat analysis models. Four parameters (top width, flow cross-sectional area, hydraulic mean depth, and wetted perimeter) were evaluated using five error estimators to determine the accuracy and performance of hydraulic modelling. Finally, the hydraulic parameters were coupled with ecological requirements to develop a habitat model for different life stages of Golden Mahseer, namely fingerling, juvenile, and adult stages. We found that the SRTM predictions were better than those of the other DEMs, indicating its suitability to replicate channel geometry with higher accuracy, thus better predicting hydraulic parameters at all flow ranges. In habitat area estimation for adult Golden Mahseer, all the DEMs performed reasonably well (within +20%) within the flow range of 100 m3/s, which covers the low to average flow season. Beyond this flow range, ASTER and CARTOSAT resulted in considerable underestimations, averaging 22% and 54%, respectively. It is important to note that DEM-based cross sections lack high-resolution channel information, resulting in unstable habitat predictions for younger life stages like fingerling. However, overall, the study established that DEM-based data can be relied upon for habitat modelling-based assessment of environmental flows with some precautions for sensitive cases. Remote sensing presents a promising avenue for habitat analysis studies of Indian species, offering the potential to unlock significant progress in environmental flows (E-Flows) assessments and thus providing ecological benefits.

摘要: Schizothoracine fishes are distributed in the Nagqu region, which is the hinterland of the Tibetan Plateau. They have adapted to the cold and strongly ultraviolet environment of the plateau and show diverse morphologies, which makes them ideal for studying the relationship between phenotype and environment. However, traditional morphological measurements are time consuming and labor costly. In this study, we propose a deep-learning-based method for acquiring high-throughput phenotypic data of fishes, including image dataset construction of schizothoracine fishes (including front, side, and top views), fish keypoint detection based on the You Only Look Once (YOLO) model, and reconstruction of 2D and 3D keypoint coordinates based on multiple views. A total of 7050 phenotypic data points consisting of keypoint distances and angles were constructed for each fish and were highly correlated (>0.98) with the corresponding data measured manually. We obtained phenotypic data for a total of 525 fishes from three schizothoracine fish groups inhabiting riverine, lacustrine, and river-lake transitional environments using the proposed phenotypic data acquisition method. We employed a random forest algorithm to classify the groups, achieving a classification accuracy of 96%, and identified 15 morphometric indices that exhibited statistically significant differences., of which 6 were related to head morphology, 6 related to body shape, and 3 related to tail morphology, based on the random forest algorithm. Specifically, river-living schizothoracine fishes showed a blunt head, robust body, and elongated caudal peduncle which may reflect adaptations to the turbulence of the river, while the lake-living schizothoracine fishes have the opposite effect. Schizothoracine fishes at the river-lake transitional zones were phenotypically characterized as being in the middle of the two phenotypes, and these presumably reflect adaptations to their lake habitat. This study provides a methodological reference for obtaining high-throughput phenotypic data on fish and a theoretical basis for understanding the adaptation of very high-altitude schizothoracine fishes to their environment.

摘要: The adaptive strategies of prey against predation risk have been pivotal in non-consumptive effects. However, the adaptive strategies of prey and the response mechanisms to various predation risk cues remain unclear. We hypothesized that prey adopt a similar adaptive strategy to address different predation risks, but their response mechanisms depend on the attributes of predation risk cues. To test this hypothesis, we used Didinium-Paramecium as a predator-prey model to first evaluate the effects of various predation risk cues, including homogenates of predators (TD) and prey (TP) alone or in combination (TM), and the density of conspecific prey on the specific growth rate (SGR) to determine their adaptive strategies and their underlying response mechanisms based on transcriptomic analysis. Our results show that predation risk cues considerably enhance prey SGR, with effects in descending order of TM, TD, and TP. However, such effects gradually decrease as the density of conspecific prey increases until they disappear. The trend in the levels of differentially expressed genes (DEGs) in prey exposed to different predation risk cues is similar to that of SGRs. In particular, pathways based on DEG enrichment mediated by predation risk cues involve cellular processes, nutrient metabolism, and synthesis of biological macromolecules. However, they differ in type, number, and location within specific biological processes. In conclusion, Paramecium uses early reproduction strategies to address the risk of predation caused by different cues, and differences in its response mechanisms depend on the attributes of the cues of predation risk, resulting in differences in the SGR of the prey.

摘要: Olfaction, the sense of smell, is vital for the survival of many species and serves as an excellent system for investigating the molecular basis of behavior. Fishes possess a well-developed olfactory system that governs various behaviors related to feeding, reproduction, and fear. However, the cellular diversity and heterogeneity of the fish olfactory epithelium remains largely unexplored. This study presents a single-cell atlas of the zebrafish olfactory epithelium using single-cell RNA sequencing (scRNA-seq). Through scRNA-seq analysis of approximately 10,587 cells, we identified nine distinct cell types with unique transcriptional profiles, including immature and mature olfactory sensory neurons (OSNs), horizontal basal cells, globose basal cells, and sustentacular cells, as well as lymphocyte and myeloid cells expressing immune signals. Further subcluster analysis revealed selective and combinatorial expression of key components in odorant-mediated signal transduction by distinct OSN populations. Additionally, we discovered transcriptional changes specific to certain OSN populations following exposure to a conspecific alarm substance. The single-cell transcriptional atlas of the zebrafish olfactory epithelium provided in this study serves as a valuable tool for exploring cell diversity and assessing genetic profiles from functional and behavioral perspectives in fish.

摘要: Understanding the distribution of species is highly important for optimizing future conservation priorities and strategies at the regional scale. Relatively little attention has been given to multi-taxon aquatic biota in extreme alpine environments. We examined the spatial and temporal patterns of alpha and beta diversity, site-specific contributions to beta diversity and assembly mechanisms of four taxonomic groups (fishes, macroinvertebrates, zooplankton and phytoplankton) from the source to the estuary of the Za'gya Zangbo River above 4500 m AMSL (above mean sea level) on the northern Qinghai-Tibetan (Q-T) Plateau. A total of 4 fish species, 45 macroinvertebrate taxa, 17 zooplankton taxa and 56 phytoplankton taxa were found in the study area. No consistent patterns in taxonomic richness were observed across taxa from upstream to estuary. The fish communities had the lowest dissimilarity between communities, the phytoplankton community had the highest dissimilarity in the dry season, and the macroinvertebrate community had the highest dissimilarity in the wet season. The relative importance of the turnover and nestedness components varied considerably across taxa and along spatial gradients. The diversity patterns of macroinvertebrate, zooplankton and phytoplankton communities were significantly correlated with several environmental factors, whereas only the beta diversity of fish was correlated with altitude. Stochastic processes dominated in shaping the macroinvertebrate communities whereas deterministic processes dominated the assembly of the phytoplankton communities. Weak congruence of diversity patterns across taxonomic groups suggested that biological groups cannot serve as reliable surrogates for one another and that multiple biological groups should be included in the biomonitoring of high-altitude rivers on the Q-T Plateau. The relatively unique species in the upstream area and estuary of the Za'gya Zangbo River harbor should receive more attention in future conservation and management schemes.

摘要: Environmental factors and anthropogenic activity are key factors that shape the distribution of bacteria and antibiotic resistance genes (ARGs) in natural environments. However, few studies have focused on the occurrence of bacteria and ARGs in remote and pristine environments. In this study, the distribution of bacteria and ARGs in two typical rivers of the western Qinghai Lake basin was investigated. Results showed that cold-resistant Planomicrobium sp. was the predominant genus due to the low temperature, followed by unclassified_f_Planococcaceae. High nitrogen nutrients increased the abundance and diversity of the bacteria community and denitrification was the dominant means of bacterial nitrate reduction. Tetracycline resistance genes including tetA, tetB, and tetC were the dominant ARGs in the western Qinghai Lake basin, ranging from 2.30 x 103 to 1.91 x 108 copies/L, while the low abundances of intI1, and ARGs such as sul1 indicated low anthropogenic activity in the western Qinghai Lake basin. Finally, the strong positive correlation between ARGs and intI1 highlights the potential transmission risk of ARGs through cross- or co-selection by horizontal gene transfer. Our study emphasized the adaptation of bacteria to the environment and the facilitation of anthropogenic activity in the propagation of ARGs in natural environments.

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摘要: This study investigated the effects of dietary supplementation with the probiotic Bacillus pumilus on coho salmon (Oncorhynchus kisutch). A total of 360 juvenile fish, with an average initial weight of 130.75 f 1.33 g, were randomly assigned to four treatment groups, each with three replicates of 30 fish. The fish were then fed for 70 days using formulated diets containing four concentrations of B. pumilus: 0 (control group), 2 x 106, 4 x 108, and 8 x 1010 CFU/g. We then evaluated growth, nutrient metabolism, immune-related serum biochemical markers, enzyme activity, gene expression, and muscle composition. Additionally, we assessed intestinal histology and microbiota composition. Our findings revealed that B. pumilus significantly improved growth, protein and fat metabolism, and immune function compared to the control group. It also had a positive effect on the structure and function of the intestinal microbiota. The group receiving 4 x 108 CFU/g showed the greatest improvements. Overall, B. pumilus appears to be a promising probiotic for enhancing the health and performance of coho salmon in aquaculture.

摘要: Autophagosome generation, development and maturation are largely dependent on Atg9a, an important member of the autophagy-related protein family. However, the potential role of fish Atg9a in viral infections is poorly understood. This research involved cloning and characterizing an Atg9a homologue from the orange-spotted grouper (Epinephelus coioides), known as EcAtg9a. The ORF (open reading frame) of EcAtg9a is composed of 2583 nucleotides and encodes 860 amino acids. EcAtg9a was detected in every tissue that was analyzed, and was particularly abundant in liver, kidney, head and blood. EcAtg9a expression levels in grouper spleen (GS) cells increased following infection with SGIV and RGNNV. EcAtg9a was uniformly present in the cytoplasm, while found to co-exist with the endoplasmic reticulum (ER), Golgi apparatus, mitochondria and lysosomes. EcAtg9a suppressed the expression of interferon-related genes and factors linked to inflammation while promoting the replication of SGIV as well as RGNNV in GS cells. In addition, EcAtg9a could interact with the key molecules of the cGAS-STING pathway including EccGAS, EcTBK1, EcSTING, and even EcIRF3. EcAtg9a facilitated the upregulation of Beclin1 and LC3-II synthesis within cells, resulting in an augmented formation of LC3 fluorescent aggregates. The level of eIF2 alpha phosphorylation (S51) was increased in EcAtg9a-overexpressing cells, and the p53 protein moved from the cytoplasm into the nucleus. Findings may offer insight into how grouper's innate immunity works against viral infections.

摘要: Life history theory predicts that species-specific life history traits are shaped by variations in environmental conditions. Understanding the key environmental factors determining life history strategies can provide insights into the mechanisms of community assembly and identify potential biodiversity threats by predicting selective responses to environmental perturbations. We collected life history traits for fish species from 14 river basins across 5 continents to identify their life history strategies and explore the related key environmental factors. Our results showed that fishes from all the river basins conformed to a triangular life history strategy model including periodic, opportunistic, and equilibrium endpoints. However, the proportions of these three strategies varied significantly amongst river basins. For example, the Rhine River basin had a high proportion of fish with the periodic strategy and a low proportion of fish with the opportunistic strategy, whereas the Mississippi River basin displayed the opposite pattern. At the river basin extent, linear regression analysis revealed that the proportion of species with the opportunistic strategy increased with mean annual temperature, annual variation in river discharge, and annual precipitation, and was negatively associated with latitude. In contrast, species with the periodic strategy were negatively related to annual variation in river discharge and positively with latitude. These findings corroborate that opportunistic species are adapted to unpredictable environments, whereas periodic species are adapted to predictable environments. We then used molecular phylogeny to reconstruct the ancestral state of Yangtze fishes and analyzed the percentage composition of the three life history strategies across geological times. We found dominance of the equilibrium strategy in the Upper Cretaceous followed by dominance of periodic fishes before the Paleocene. Opportunistic fish species began to dominate the Yangtze River basin after the Miocene, with more than half of the fish species being opportunistic. This implies that the environmental conditions in the Yangtze River basin evolved from stable (low annual variation in river discharge) to unstable (high annual variation in river discharge and high annual precipitation) states, possibly associated with the onset of seasonality expressed as prevalence of a monsoon climate and the overall alteration of precipitation patterns. Life history theory can give hints for assessing river ecological conditions because changes in strategy proportions may indicate the alteration of environmental conditions. Such changes can aid in developing suitable strategies for river ecological protection and fish resource management.