Environmental DNA-based biodiversity profiling along the Houdong River in north-eastern Taiwan.

Background: This paper describes two datasets: species occurrences, which were determined by environmental DNA (eDNA) metabarcoding and their associated DNA sequences, originating from a research project which was carried out along the Houdong River (), Jiaoxi Township, Yilan, Taiwan. The Houdong River begins at an elevation of 860 m and flows for approximately 9 km before it empties into the Pacific Ocean. Meandering through mountains, hills, plains and alluvial valleys, this short river system is representative of the fluvial systems in Taiwan. The primary objective of this study was to determine eukaryotic species occurrences in the riverine ecosystem through the use of the eDNA analysis. The second goal was, based on the current dataset, to establish a metabarcoding eDNA data template that will be useful and replicable for all users, particularly the Taiwan community. The species occurrence data are accessible at the Global Biodiversity Information Facility (GBIF) portal and its associated DNA sequences have been deposited in the European Nucleotide Archive (ENA) at EMBL-EBI, respectively. A total of 12 water samples from the study yielded an average of 1.5 million reads. The subsequent species identification from the collected samples resulted in the classification of 432 Operational Taxonomic Units (OTUs) out of a total of 2,734. Furthermore, a total of 1,356 occurrences with taxon matches in GBIF were documented (excluding 4,941 incertae sedis, accessed 05-12-2023). These data will be of substantial importance for future species and habitat monitoring within the short river, such as assessment of biodiversity patterns across different elevations, zonations and time periods and its correlation to water quality, land uses and anthropogenic activities. Further, these datasets will be of importance for regional ecological studies, in particular the freshwater ecosystem and its status in the current global change scenarios. New information: The datasets are the first species diversity description of the Houdong River system using either eDNA or traditional monitoring processes.

Single-worm long-read sequencing reveals genome diversity in free-living nematodes.

Obtaining sufficient genetic material from a limited biological source is currently the primary operational bottleneck in studies investigating biodiversity and genome evolution. In this study, we employed multiple displacement amplification (MDA) and Smartseq2 to amplify nanograms of genomic DNA and mRNA, respectively, from individual Caenorhabditis elegans. Although reduced genome coverage was observed in repetitive regions, we produced assemblies covering 98% of the reference genome using long-read sequences generated with Oxford Nanopore Technologies (ONT). Annotation with the sequenced transcriptome coupled with the available assembly revealed that gene predictions were more accurate, complete and contained far fewer false positives than de novo transcriptome assembly approaches. We sampled and sequenced the genomes and transcriptomes of 13 nematodes from early-branching species in Chromadoria, Dorylaimia and Enoplia. The basal Chromadoria and Enoplia species had larger genome sizes, ranging from 136.6 to 738.8 Mb, compared with those in the other clades. Nine mitogenomes were fully assembled, and displayed a complete lack of synteny to other species. Phylogenomic analyses based on the new annotations revealed strong support for Enoplia as sister to the rest of Nematoda. Our result demonstrates the robustness of MDA in combination with ONT, paving the way for the study of genome diversity in the phylum Nematoda and beyond.

Cellular mechanisms underlying extraordinary sulfide tolerance in a crustacean holobiont from hydrothermal vents.

The shallow-water hydrothermal vent system of Kueishan Island has been described as one of the world's most acidic and sulfide-rich marine habitats. The only recorded metazoan species living in the direct vicinity of the vents is Xenograpsus testudinatus, a brachyuran crab endemic to marine sulfide-rich vent systems. Despite the toxicity of hydrogen sulfide, X. testudinatus occupies an ecological niche in a sulfide-rich habitat, with the underlying detoxification mechanism remaining unknown. Using laboratory and field-based experiments, we characterized the gills of X. testudinatus that are the major site of sulfide detoxification. Here sulfide is oxidized to thiosulfate or bound to hypotaurine to generate the less toxic thiotaurine. Biochemical and molecular analyses demonstrated that the accumulation of thiosulfate and hypotaurine is mediated by the sodium-independent sulfate anion transporter (SLC26A11) and taurine transporter (Taut), which are expressed in gill epithelia. Histological and metagenomic analyses of gill tissues demonstrated a distinct bacterial signature dominated by Epsilonproteobacteria. Our results suggest that thiotaurine synthesized in gills is used by sulfide-oxidizing endo-symbiotic bacteria, creating an effective sulfide-buffering system. This work identified physiological mechanisms involving host-microbe interactions that support life of a metazoan in one of the most extreme environments on our planet.

Multigenerational inspections of environmental thermal perturbations promote metabolic trade-offs in developmental stages of tropical fish.

Global warming both reduces global temperature variance and increases the frequency of extreme weather events. In response to these ambient perturbations, animals may be subject to trans- or intra-generational phenotype modifications that help to maintain homeostasis and fitness. Here, we show how temperature-associated transgenerational plasticity in tilapia affects metabolic trade-offs during developmental stages under a global warming scenario. Tropical tilapia reared at a stable temperature of 27 °C for a decade were divided into two temperature-experience groups for four generations of breeding. Each generation of one group was exposed to a single 15 °C cold-shock experience during its lifetime (cold-experienced CE group), and the other group was kept stably at 27 °C throughout their lifetimes (cold-naïve CN group). The offspring at early life stages from the CE and CN tilapia were then assessed by metabolomics-based profiling, and the results implied that parental cold-experience might affect energy provision during reproduction. Furthermore, at early life stages, progeny may be endowed with metabolic traits that help the animals cope with ambient temperature perturbations. This study also applied the feature rescaling and Uniform Manifold Approximation and Projection (UMAP) to visualize metabolic dynamics, and the result could effectively decompose the complex omic-based datasets to represent the energy trade-off variability. For example, the carbohydrate to free amino acid conversion and enhanced compensatory features appeared to be hypothermic-responsive traits. These multigenerational metabolic effects suggest that the tropical ectothermic tilapia may exhibit transgenerational phenotype plasticity, which could optimize energy allocation under ambient temperature challenges. Knowledge about such metabolism-related transgenerational plasticity effects in ectothermic aquatic species may allow us to better predict how adaptive mechanisms will affect fish populations in a climate with narrow temperature variation and frequent extreme weather events.

In Vivo Functional Assay in Fish Gills: Exploring Branchial Acid-Excreting Mechanisms in Zebrafish.

Molecular and physiological analyses in ionoregulatory organs (e.g., adult gills and embryonic skin) are essential for studying fish ion regulation. Recent progress in the molecular physiology of fish ion regulation was mostly obtained in embryonic skin; however, studies of ion regulation in adult gills are still elusive and limited because there are no direct methods for in vivo functional assays in the gills. The present study applied the scanning ion-selective electrode technique (SIET) in adult gills to investigate branchial H+-excreting functions in vivo. We removed the opercula from zebrafish and then performed long-term acid acclimation experiments. The results of Western blot and immunofluorescence showed that the protein expression of H+-ATPase (HA) and the number of H+-ATPase-rich ionocytes were increased under acidic situations. The SIET results proved that the H+ excretion capacity is indeed enhanced in the gills acclimated to acidic water. In addition, both HA and Na+/H+ exchanger (Nhe) inhibitors suppressed the branchial H+ excretion capacity, suggesting that H+ is excreted in association with HA and Nhe in zebrafish gills. These results demonstrate that SIET is effective for in vivo detection in fish gills, representing a breakthrough approach for studying the molecular physiology of fish ion regulation.

Adaptive metabolic responses in a thermostabilized environment: Transgenerational trade-off implications from tropical tilapia.

Relatively warm environments caused by global warming enhance the productivity of aquaculture activities in tropical/subtropical regions; however, the intermittent cold stress (ICS) caused by negative Arctic Oscillation can still result in major economic losses. In contrast to endotherms, ectothermic fishes experience ambient temperature as an abiotic factor that is central to performance and survival. Therefore, the occurrence of extreme temperatures caused by climate change has ignited a surge of scientific interest from ecologists, economists and physiologists. In this study, we test the transgenerational effects of rearing cold-experienced (CE) and cold-naïve (CN) strains of tropical tilapia. Our results show that compared to CN tilapia, the CE strain preferentially converts carbohydrates into lipids in liver at a regular temperature of 27 °C. Besides, at a low temperature of 22 °C, the CE strain exhibits a broader aerobic scope than CN fish, and their metabolite profile suggests a metabolic shift towards the utilization of glutamate derivatives. Therefore, in response to thermal perturbations, this transgenerational metabolic adjustment provides evidence into the adaptive trade-off mechanisms in tropical fish. Nevertheless, global warming may result in less thermal variation each year, and the stabilized ambient temperature may cause tropical tilapia to gradually exhibit lower energy deposits in liver. In addition to those habitants in cold and temperate regions, a lack of cold exposure to multiple generations of fish may decrease the native cold-tolerance traits of subtropical/tropical organisms; this notion has not been previously explored in terms of the biological effects under anthropogenic climate change.

Effects of emersion on acid-base regulation, osmoregulation, and nitrogen physiology in the semi-terrestrial mangrove crab, Helice formosensis.

Emersion limits water availability and impairs the gill function of water-breathing animals resulting in a reduced capacity to regulate respiratory gas exchange, acid-base balance, and nitrogenous waste excretion. Semi-terrestrial crustaceans such as Helice formosensis mitigate these physiological consequences by modifying and recycling urine and branchial water shifting some branchial workload to the antennal glands. To investigate how this process occurs, Helice formosensis were emersed for up to 160 h and their hemolymph and urinary acid-base, nitrogenous waste, free amino acids, and osmoregulatory parameters were investigated. Upon emersion, crabs experienced a respiratory acidosis that is restored by bicarbonate accumulation and ammonia reduction within the hemolymph and urine after 24 h. Prolonged emersion caused an overcompensatory metabolic alkalosis potentially limiting the crab's ability to remain emersed. During the alkalosis, hemolymph ammonia was maintained at control levels while urinary ammonia remained reduced by 60% of control values. During emersion, ammonia may be temporarily converted to alanine as part of the Cahill cycle until re-immersion where crabs can revert alanine to ammonia for excretion coinciding with the crabs' observed delayed ammonia excretion response. The presence of high hemolymph alanine concentrations even when immersed may indicate this cycle's use outside of emersion or in preparation for emersion. Furthermore, H. formosensis appears to be uniquely capable of actively suppressing its rate of desiccation in absence of behavioral changes, in part by creating hyperosmotic urine that mitigates evaporative water loss.

Resveratrol Induces Expression of Metabolic and Antioxidant Machinery and Protects Tilapia under Cold Stress.

Exposures to low ambient temperature require ectothermic fish to not only adjust their metabolic machinery but also to mount protective responses against oxidative stress. In this study, we tested whether diets supplemented with resveratrol (RSV), a naturally occurring polyphenol known to stimulate metabolic and protective responses in various animals, would be beneficial to tilapia (Oreochromis mossambicus) under hypothermic challenge. Feeding tilapia with RSV-supplemented diet promoted liver expression of sirtuins and their known targets, including metabolic/antioxidative enzymes. After exposure to 15 °C cold conditions for three days, the oxygen-nitrogen (O:N) ratio was decreased in the control-diet-fed tilapia but not in their RSV-fed counterparts. Moreover, at 27 °C, RSV-fed tilapia showed significantly higher prolonged swim speed compared with controls. RSV feeding produced no significant effect on upper and bottom layer preference between the control- and RSV-treated tilapia at either 27 °C or 15 °C. Together, these findings suggest that RSV stimulates beneficial metabolic/antioxidative adjustments in teleosts and may serve as a valuable feed supplement for tropical fish exposed to cold stress during winter.

The Air-Breathing Paradise Fish (Macropodus opercularis) Differs From Aquatic Breathers in Strategies to Maintain Energy Homeostasis Under Hypoxic and Thermal Stresses.

Two major strategies are used by most fish to maintain energy homeostasis under hypoxia. One is to utilize alternative metabolic pathways to increase energy production, and the other is to limit energy expenditure by suppressing energy-consuming processes, especially ionoregulation. Some anabantoid fishes live in tropical rivers, where hypoxic environments occur frequently. We previously found that under ambient hypoxia, anabantoid fishes do not downregulate Na+/K+-ATPase (NKA) activity to conserve energy in gills but instead increase the frequency of air-breathing respiration (ABR). In addition to the hypoxic condition, another factor that may cause cellular hypoxia in fish is abnormally high environmental temperatures. The frequency of such extreme thermal events has increased due to global climate change. In the present study, we examined whether the anabantoid fish, Macropodus opercularis employs the two strategies mentioned above to resist both ambient hypoxic and elevated thermal (cellular hypoxic) conditions. Results indicate that neither glucose metabolism nor gill NKA activity were altered by hypoxia (DO = 1.5 ± 1 mg/L), but glucose metabolism was increased by thermal stress (34 ± 1°C). NH4 + excretion and ABR frequency were both increased under hypoxia, thermal or hypoxic-and-thermal treatments. In fish that were restricted from breathing air, increased mortality and glucose metabolism were observed under hypoxic or thermal treatments. These results suggest that for M. opercularis, increasing ABR is an important strategy for coping with unmet oxygen demand under hypoxic or thermal stress. This behavioral compensation allows anabantoid fish to physiologically withstand hypoxic and thermal stresses, and constitutes a mechanism of stress resistance that is unavailable to water-breathing fishes.

Norepinephrine reversibly regulates the proliferation and phenotypic transformation of vascular smooth muscle cells.

OBJECTIVE: To investigate the effect of norepinephrine (NE) on the proliferation and phenotypic transformation of vascular smooth muscle cells (VSMCs) and the mechanisms underlying this effect. METHODS: VSMCs were isolated from the rat abdominal aorta. VSMCs cultured in both serum-containing or in a serum-free medium were treated with NE, oxidized low-density lipoprotein (ox-LDL), alpha-adrenergic receptor agonist (alpha1-R(-)), beta1-adrenergic receptor antagonist (beta1-R(-)) and various combinations of these factors. VSMC proliferation was determined by bromodeoxyuridine (BrdU) assays. The mRNA expression level of HRG-1 and SM22 alpha were determined by reverse transcription-polymerase chain reaction (RT-PCR). RESULTS: The expressions of HRG-1 and SM22 alpha mRNA in NE- or OX-LDL-treated VSMCs was down-regulated, and the proliferation of BrdU-labeled cells increased; the expression of the above mentioned genes in the VSMCs treated with a combination of NE, alpha1-R, and beta1-R was significantly up-regulated. However, NE was observed to up-regulate the expression of HRG-1 and SM22 alpha mRNA in serum-starved VSMCs. CONCLUSION: NE could reversibly regulate the proliferation and phenotypic transformation of VSMCs. This regulation might be mediated via its receptors.