Sex matters: Gamete-specific contribution of microRNA following parental exposure to hypoxia in zebrafish

Oxygen availability varies among aquatic environments, and oxygen concentration has been demonstrated to drive behavioral, metabolic, and genetic adaptations in numerous aquatic species. MicroRNAs (miRNAs) are epigenetic modulators that act at the interface of the environment and the transcriptome and are known to drive plastic responses following environmental stressors. An area of miRNA that has remained underexplored is the sex specific action of miRNAs following hypoxia exposure and its effects as gene expression regulator in fishes. This study aimed to identify differences in mRNA and miRNA expression in the F1 generation of zebrafish (Danio rerio) at 1 hpf after either F0 parental male or female were exposed to 2 weeks of continuous (45 %) hypoxia. In general, F1 embryos at 1 hpf demonstrated differences in mRNA and miRNAs expression related to the stressor and to the specific sex of the F0 that was exposed to hypoxia. Bioinformatic pathway analysis of predicted miRNA:mRNA relationships indicated responses in known hypoxia signaling and mitochondrial bioenergetic pathways. This research demonstrates the importance of examining the specific male and female contributions to phenotypic variation in subsequent generations and provides evidence that there is both maternal and paternal contribution of miRNA through eggs and sperm.

Genome assembly and annotation of the tambaqui (Colossoma macropomum): an emblematic fish of the Amazon River Basin

Colossoma macropomum, known as "tambaqui", is the largest Characiformes fish in the Amazon River Basin and a leading species in Brazilian aquaculture and fisheries. Good quality meat and excellent adaptability to culture systems are some of its remarkable farming features. To support studies into the genetics and genomics of the tambaqui, we have produced the first high-quality genome for the species. We combined Illumina and PacBio sequencing technologies to generate a reference genome, assembled with 39× coverage of long reads and polished to a consensus quality value (QV) of 36 with 130× coverage of short reads. The genome was assembled into 1269 scaffolds (a total of 1,221,847,006 bases), with a scaffold N50 size of 40 Mb, where 93% of all assembled bases were placed in the largest 54 scaffolds corresponding to the diploid karyotype of the tambaqui. Furthermore, the NCBI Annotation Pipeline annotated genes, pseudogenes, and non-coding transcripts using the RefSeq database as evidence, guaranteeing a high-quality annotation. A Genome Data Viewer for the tambaqui was produced, which will benefit groups interested in exploring the unique genomic features of the species. The availability of a highly accurate genome assembly for tambaqui provides the foundation for the discovery of novel ecological and evolutionary insights, and is a helpful resource for aquaculture.

Genome-wide association study reveals genes associated with the absence of intermuscular bones in tambaqui (Colossoma macropomum)

The presence of intermuscular bones in fisheries products limits the consumption and commercialization potential of many fish species, including tambaqui (Colossoma macropomum). These bones have caused medical emergencies and are an undesirable characteristic for fish farming because their removal is labor-intensive during fish processing. Despite the difficulty in identifying genes related to the lack of intermuscular bone in diverse species of fish, the discovery of individuals lacking intermuscular bones in a Neotropical freshwater characiform fish has provided a unique opportunity to delve into the genetic mechanisms underlying the pathways of intermuscular bone formation. In this study, we carried out a GWAS among boneless and wt tambaqui populations to identify markers associated with a lack of intermuscular bone. After analyzing 11 416 SNPs in 360 individuals (12 boneless and 348 bony), we report 675 significant (P_adj  < 0.003) associations for this trait. Of those, 13 associations were located near candidate genes related to the reduction of bone mass, promotion of bone formation, inhibition of bone resorption, central control of bone remodeling, bone mineralization and other related functions. To the best of our knowledge, for the first time, we have successfully identified genes related to a lack of intermuscular bones using GWAS in a non-model species.

Metabolic adjustment of Pyrrhulina aff. brevis exposed to different climate change scenarios

The increases in CO₂ concentrations and, consequently, temperature due to climate change are predicted to intensify. Understanding the physiological responses of Pyrrhulina aff. brevis to the climatic scenarios proposed by the IPCC (2014) for the next 100 years is of fundamental importance to determine its susceptibility. Thus, the present study aimed to evaluate the effects of the predicted climatic scenarios for the year 2100 on the metabolic adjustments of P. aff. brevis . Specifically, the rate of oxygen uptake, electron transport system capacity, glycogen and lactate content and the role of Na⁺K⁺-ATPases and H⁺-ATPase were evaluated. P. aff. brevis individuals were exposed for 15 days to the simulated climatic scenarios in climate scenario rooms, where temperature and CO₂ in the air were controlled. Two rooms were used to simulate the climatic scenarios predicted by the IPCC (2014): moderate (RCP 6; 2.5 °C and 400 μatm CO₂ above current levels) and extreme (RCP 8.5; 4.5 °C and 900 μatm CO₂ above current levels), in addition to the "control room" that represents the current scenario. There was an increase in the metabolic rate (MO₂) in the animals acclimated to the climate change scenarios (RCP 6 and RCP 8.5) compared to the current scenario. These responses showed a typical effect of temperature on energy demand in relation to the increase in temperature and CO₂. Our data showed an increase in O₂ consumption (MO₂), lactate levels and H⁺-ATPase activity of the animals acclimated to the moderate and extreme climate change scenarios. Such adjustments presented a clear metabolic imbalance, an alteration that may imply challenges for survival, growth, distribution and reproduction in the face of the expected environmental changes for the year 2100.

Protein synthesis is lowered by 4EBP1 and eIF2-α signaling while protein degradation may be maintained in fasting, hypoxic Amazonian cichlids Astronotus ocellatus

The Amazonian cichlid Astronotus ocellatus is highly tolerant to hypoxia, and is known to reduce its metabolic rate by reducing the activity of energetically expensive metabolic processes when oxygen is lacking in its environment. Our objectives were to determine how protein metabolism is regulated in A. ocellatus during hypoxia. Fish were exposed to a stepwise decrease in air saturation (100%, 20%, 10% and 5%) for 2 h at each level, and sampled throughout the experiment. A flooding dose technique using a stable isotope allowed us to observe an overall decrease in protein synthesis during hypoxia in liver, muscle, gill and heart. We estimate that this decrease in rates of protein synthesis accounts for a 20 to 36% decrease in metabolic rate, which would enable oscars to maintain stable levels of ATP and prolong survival. It was also determined for the first time in fish that a decrease in protein synthesis during hypoxia is likely controlled by signaling molecules (4EBP1 and eIF2-α), and not simply due to a lack of ATP. We could not detect any effects of hypoxia on protein degradation as the levels of NH₄ excretion, indicators of the ubiquitin proteasome pathway, and enzymatic activities of lysosomal and non-lysosomal proteolytic enzymes were maintained throughout the experiment.

Acute hypoxia up-regulates HIF-1α and VEGF mRNA levels in Amazon hypoxia-tolerant Oscar (Astronotus ocellatus)

Amazon fish maintain oxygen uptake through a variety of strategies considered evolutionary and adaptive responses to the low water oxygen saturation, commonly found in Amazon waters. Oscar (Astronotus ocellatus) is among the most hypoxia-tolerant fish in Amazon, considering its intriguing anaerobic capacity and ability to depress oxidative metabolism. Previous studies in hypoxia-tolerant and non-tolerant fish have shown that hypoxia-inducible factor-1α (HIF-1α) gene expression is positively regulated during low oxygen exposure, affecting vascular endothelial growth factor (VEGF) transcription and fish development or tolerance in different manners. However, whether similar isoforms exists in tolerant Amazon fish and whether they are affected similarly to others physiological responses to improve hypoxia tolerance remain unknown. Here we evaluate the hepatic HIF-1α and VEGF mRNA levels after 3 h of acute hypoxia exposure (0.5 mgO2/l) and 3 h of post-hypoxia recovery. Additionally, hematological parameters and oxidative enzyme activities of citrate synthase (CS) and malate dehydrogenase (MDH) were analyzed in muscle and liver tissues. Overall, three sets of responses were detected: (1) as expected, hematocrit, hemoglobin concentration, red blood cells, and blood glucose increased, improving oxygen carrying capacity and glycolysis potential; (2) oxidative enzymes from liver decreased, corroborating the tendency to a widespread metabolic suppression; and (3) HIF-1α and VEGF increased mRNA levels in liver, revealing their role in the oxygen homeostasis through, respectively, activation of target genes and vascularization. This is the first study to investigate a hypoxia-related transcription factor in a representative Amazon hypoxia-tolerant fish and suggests that HIF-1α and VEGF mRNA regulation have an important role in enhancing hypoxia tolerance in extreme tolerant species.

In vitro effects of increased temperature and decreased pH on blood oxygen affinity of 10 fish species of the Amazon

Blood-O2 affinities (P50 ) were measured over a physiologically relevant pH range at 31 (highest temperature average of Rio Negro over the last 8 years), 33 and 35° C for 10 species of the Rio Negro, aiming to test the acute effects of temperature foreseen by the IPCC (Intergovernmental Panel on Climate Change) for coming years. The animals were collected during an expedition to the Anavilhanas Islands of the Rio Negro, 110 km upstream from Manaus (2° 23' 41″ S; 60° 55' 14″ W). Hoplias malabaricus showed higher blood-O2 sensitivity to pH changes (Bohr effect, Φ = Δlog10  P50  ΔpH(-1) ) at both 31° C (Φ = -0·44) and 35° C (Φ = -0·26) compared to Osteoglossum bicirrhosum (Φ = -0·54 at 31° C and Φ = -0·58 at 35° C), but lower P50 under most conditions, and a greater sensitivity of P50 to temperature. Two out of the 10 analysed species had significant increases of P50 (lower blood-O2 affinity) at the highest temperature throughout the pH range tested. For all other species, a minor increase of P50 over the assay-tested temperatures was observed, although all presented a normal Bohr effect. Overall, a diversity of intensities of pH and temperature effects on blood-O2 affinities was observed, which seems to be connected to the biological characteristics of the analysed species. Thermal disturbances in their habitats, likely to occur due to the global warming, would impair blood-O2 binding and unloading in some of the analysed fish species. Copyright © 2016 John Wiley & Sons, Ltd.

Permanent genetic resources added to Molecular Ecology Resources Database 1 December 2010-31 January 2011

This article documents the addition of 238 microsatellite marker loci to the Molecular Ecology Resources Database. Loci were developed for the following species: Alytes dickhilleni, Arapaima gigas, Austropotamobius italicus, Blumeria graminis f. sp. tritici, Cobitis lutheri, Dendroctonus ponderosae, Glossina morsitans morsitans, Haplophilus subterraneus, Kirengeshoma palmata, Lysimachia japonica, Macrolophus pygmaeus, Microtus cabrerae, Mytilus galloprovincialis, Pallisentis (Neosentis) celatus, Pulmonaria officinalis, Salminus franciscanus, Thais chocolata and Zootoca vivipara. These loci were cross-tested on the following species: Acanthina monodon, Alytes cisternasii, Alytes maurus, Alytes muletensis, Alytes obstetricans almogavarii, Alytes obstetricans boscai, Alytes obstetricans obstetricans, Alytes obstetricans pertinax, Cambarellus montezumae, Cambarellus zempoalensis, Chorus giganteus, Cobitis tetralineata, Glossina fuscipes fuscipes, Glossina pallidipes, Lysimachia japonica var. japonica, Lysimachia japonica var. minutissima, Orconectes virilis, Pacifastacus leniusculus, Procambarus clarkii, Salminus brasiliensis and Salminus hilarii.

Anoxia- and hypoxia-induced expression of LDH-A* in the Amazon Oscar, Astronotus crassipinis

Adaptation or acclimation to hypoxia occurs via the modulation of physiologically relevant genes, such as erythropoietin, transferrin, vascular endothelial growth factor, phosphofructokinase and lactate dehydrogenase A. In the present study, we have cloned, sequenced and examined the modulation of the LDH-A gene after an Amazonian fish species, Astronotus crassipinis (the Oscar), was exposed to hypoxia and anoxia. In earlier studies, we have discovered that adults of this species are extremely tolerant to hypoxia and anoxia, while the juveniles are less tolerant. Exposure of juveniles to acute hypoxia and anoxia resulted in increased LDH-A gene expression in skeletal and cardiac muscles. When exposed to graded hypoxia juveniles show decreased LDH-A expression. In adults, the levels of LDH-A mRNA did not increase in hypoxic or anoxic conditions. Our results demonstrate that, when given time for acclimation, fish at different life-stages are able to respond differently to survive hypoxic episodes.

Fish and aquatic habitat conservation in South America: a continental overview with emphasis on neotropical systems

Fish conservation in South America is a pressing issue. The biodiversity of fishes, just as with all other groups of plants and animals, is far from fully known. Continuing habitat loss may result in biodiversity losses before full species diversity is known. In this review, the main river basins of South America (Magdalena, Orinoco, Amazon and Paraná-La Plata system), together with key aquatic habitats (mangrove-fringed estuaries of the tropical humid, tropical semi-arid and subtropical regions) are analysed in terms of their characteristics and main concerns. Habitat loss was the main concern identified for all South American ecosystems. It may be caused by damming of rivers, deforestation, water pollution, mining, poor agricultural practice or inadequate management practice. Habitat loss has a direct consequence, which is a decrease in the availability of living resources, a serious social and economic issue, especially for South American nations which are all developing countries. The introduction of exotic species and overfishing were also identified as widespread across the continent and its main freshwater, coastal and marine ecosystems. Finally, suggestions are made to find ways to overcome these problems. The main suggestion is a change of paradigm and a new design for conservation actions, starting with integrated research and aiming at the co-ordinated and harmonized management of the main transboundary waters of the continent. The actions would be focused on habitat conservation and social rescue of the less well-off populations of indigenous and non-indigenous peoples. Energy and freshwater demands will also have to be rescaled in order to control habitat loss.

Ion fluxes and hematological parameters of two teleosts from the Rio Negro, Amazon, exposed to hypoxia

The aim of this study was to describe the effect of hypoxia on whole body ion fluxes and hematological parameters in two Amazonian teleosts: Serrasalmus eigenmanni and Metynnis hypsauchen. The increase of Na+ and Cl- effluxes on M. hypsauchen exposed to hypoxia may be related to an increase of gill ventilation and effective respiratory surface area, to avoid a reduction in the oxygen uptake, and/or with the decrease of pHe, that could inhibit Na+ and Cl- transporters and, therefore, reduce influx of these ions. Effluxes of Na+ and Cl- were lower in hypoxia than in normoxia for S. eigenmanni, possibly because in hypoxia this species would reduce gill ventilation and oxygen uptake, which would lead to a decrease of gill ion efflux and, consequently, reducing ion loss. The increase on hematocrit (Ht) during hypoxia in M. hypsauchen probably was caused by an increase of the red blood cell volume (MCV). For S. eigenmanni the increase on glucose possibly results from the usage of glucose reserve mobilization. Metynnis hypsauchen showed to be more sensitive to hypoxia than Serrasalmus eigenmanni, since the first presented more significant alterations on these osmoregulatory and hematological parameters. Nevertheless, the alterations observed for both species are strategies adopted by fishes to preserve oxygen supply to metabolizing tissues during exposure to hypoxia.

Responses to hypoxia and recovery: repayment of oxygen debt is not associated with compensatory protein synthesis in the Amazonian cichlid,Astronotus ocellatus

Oxygen consumption, as an indicator of routine metabolic rate (RoMR), and tissue-specific changes in protein synthesis, as measured by 3H-labelled phenylalanine incorporation rates, were determined in Astronotus ocellatus to investigate the cellular mechanisms behind hypoxia-induced metabolic depression and recovery. RoMR was significantly depressed, by approximately 50%, when dissolved oxygen levels reached 10%saturation (0.67±0.01 mg l–1 at 28±1°C). This depression in RoMR was accompanied by a 50–60% decrease in liver,heart and gill protein synthesis, but only a 30% decrease in brain protein synthesis. During recovery from hypoxia, an overshoot in RoMR to 270% of the normoxic rate was observed, indicating the accumulation of an oxygen debt during hypoxia. This conclusion was consistent with significant increase in plasma lactate levels during the hypoxic exposure, and the fact that lactate levels rapidly returned to pre-hypoxic levels. In contrast, a hyperactivation of protein synthesis did not occur, suggesting the overshoot in oxygen consumption during recovery is attributed to an increase in cellular processes other than protein synthesis.

Carbohydrate management, anaerobic metabolism, and adenosine levels in the armoured catfish,Liposarcus pardalis (castelnau), during hypoxia

The armoured catfish, Liposarcus pardalis, tolerates severe hypoxia at high temperatures. Although this species can breathe air, it also has a strong anaerobic metabolism. We assessed tissue to plasma glucose ratios and glycogen and lactate in a number of tissues under "natural" pond hypoxia, and severe aquarium hypoxia without aerial respiration. Armour lactate content and adenosine in brain and heart were also investigated. During normoxia, tissue to plasma glucose ratios in gill, brain, and heart were close to one. Hypoxia increased plasma glucose and decreased tissue to plasma ratios to less than one, suggesting glucose phosphorylation is activated more than uptake. High normoxic white muscle glucose relative to plasma suggests gluconeogenesis or active glucose uptake. Excess muscle glucose may serve as a metabolic reserve since hypoxia decreased muscle to plasma glucose ratios. Mild pond hypoxia changed glucose management in the absence of lactate accumulation. Lactate was elevated in all tissues except armour following aquarium hypoxia; however, confinement in aquaria increased armour lactate, even under normoxia. A stress-associated acidosis may contribute to armour lactate sequestration. High plasma lactate levels were associated with brain adenosine accumulation. An increase in heart adenosine was triggered by confinement in aquaria, although not by hypoxia alone.

Metabolic adjustments in two Amazonian cichlids exposed to hypoxia and anoxia

The effects of graded hypoxia on the physiological and biochemical responses were examined in two closely related species of cichlids of the Amazon: Astronotus crassipinnis and Symphysodon aequifasciatus. Ten fish of each species were exposed to graded hypoxia for 8 h in seven oxygen concentrations (5.92, 3.15, 1.54, 0.79, 0.60, 0.34, and 0.06 mg O(2) L(-)(1)), with the aim to evaluate hypoxia tolerance and metabolic adjustments, where plasma glucose and lactate levels, hepatic and muscle glycogen contents, and maximum enzyme activities (PK, LDH, MDH and CS) in skeletal and cardiac muscles were measured. Another experimental set was done to quantify oxygen consumption (MO(2)) and opercular movements in two oxygen concentrations. Hypoxia tolerance differed between the two species. Astronotus crassipinnis was able to tolerate anoxia for 178 min while S. aequifasciatus was able to withstand 222 min exposure in deep hypoxia (0.75 mg O(2) L(-)(1)). Suppressed MO(2) was observed during exposure to 0.34 (A. crassipinnis) and 0.79 mg O(2) L(-)(1) (S. aequifasciatus), while opercular movements increased in both species exposed to hypoxia. Higher levels of muscle and liver glycogen and larger hypoxia-induced increases in plasma glucose and lactate were observed in A. crassipinnis, which showed a higher degree of hypoxia tolerance. Changes in enzyme levels were tissue-specific and differed between species suggesting differential abilities in down-regulating oxidative pathways and increasing anaerobic metabolism. Based on the present data, we conclude that these animals are good anaerobes and highly adapted to their environment, which is allowed by their abilities to regulate metabolic pathways and adjust their enzyme levels.

Specialized metabolism and biochemical suppression during aestivation of the extant South American lungfish--Lepidosiren paradoxa

Lepidosiren paradoxa (pirambóia) is the single representative of Dipnoan (lungfish) in South America. This species is considered a living fossil, in spite of some reports describing this fish as having a very specialized life style. It aestivates during the dry season, and has developed metabolic adaptations to cope with both flooding and drought. The literature describing its tissue ultra-structure shows high glycogen stored in the muscle, suggesting a strong dependence on anaerobic glycolysis. The present paper reports tissue enzyme levels of LDH, MDH, and CS, and isozymic tissue distribution of LDH, MDH, ADH, PGI, SOD, and PGM of 7 aestivating specimens from Lago do Canteiro in the Amazonas River. Animals were caught while burrowed in mud during the aestivation period. Our findings reveal high anaerobic capacity of both skeletal and heart muscles, even during the aestivation period, when enzymes showed suppressed levels compared to those of non-aestivating animals (data from the literature). Isozymic patterns suggest loss of duplicate condition in most analyzed loci, a characteristic that occurs mainly in higher vertebrate categories. These data indicate that, compared to the fish group, lungfish may be considered advanced, despite retaining primitive morphological characters.

Activity levels of enzymes of energy metabolism in heart and red muscle are higher in north-temperate-zone than in Amazonian teleosts

Fish living in the Amazon basin typically have body temperatures of about 30°C, whereas freshwater fishes of the north-temperate zone are eurythermal, with typical body temperatures of 10-20°C in summer. Enzyme activity levels in heart and red muscle of Amazonian species, which display various physiological mechanisms for dealing with hypoxic conditions, were compared with those in north-temperate-zone species. Five Amazonian species (acará-açu (Astronotus ocellatus), acari-bodó (Lipossarcus pardalis), tambaqui (Colossoma macropomum), tamoatá (Hoplosternum littorale), and pirarucu (Arapaima gigas)) and four north-temperate-zone species (American eel, bullhead, yellow perch, and rainbow trout) were studied. The Amazonian species included obligate and facultative air breathers. Activities of key indicator enzymes associated with carbohydrate metabolism, fatty acid metabolism, the citric acid cycle, and the electron-transport chain were determined. There was no obvious correlation between cardiac enzyme activity levels and the potential ability of fish to maintain blood oxygen levels in hypoxic water or the capacity of isolated heart preparations to survive anoxia. In heart, activity levels of hexokinase, phosphofructokinase, pyruvate kinase, lactate dehydrogenase, citrate synthase, cytochrome oxidase, and β-hydroxyacyl CoA dehydrogenase were about twice as high in north-temperate-zone species than in Amazonian species. Activities of red-muscle enzymes, especially those associated with aerobic fatty acid metabolism, were significantly higher in comparable north-temperate-zone species relative to Amazonian species. Increased enzyme activity levels in north-temperate-zone species relative to Amazonian species is considered to be an adaptation to generally lower body temperatures. This finding is consistent with earlier comparisions of Antarctic and north-temperate-zone species and with the results of studies of cold acclimation within north-temperate-zone fishes.

Anoxic cardiac performance in Amazonian and north-temperate-zone teleosts

Amazonian fish face periodic conditions of hypoxic water not commonly encountered by most other species. We examined the impact of simulated anoxia on cardiac performance of Amazonian species relative to north-temperate-zone species to assess whether the ability to maintain anoxic heart performance is related to either respiratory strategy or geographic location. Four Amazonian species (acará-açu (Astronotus ocellatus), acari-bodó (Lipossarcus pardalis), tambaqui (Colossoma macropomum), and tamoatá (Hoplosternum littorale)) and four north-temperate-zone species (American eel (Anguilla rostrata), bullhead (Ictalurus punctatus), yellow perch (Perca flavescens), and rainbow trout (Oncorhynchus mykiss)) were studied. The Amazonian species display a range of respiratory modes from obligate gill-breather to facultative air-breather. The performance of isolated ventricular strips under conditions of impaired oxidative phosphorylation was monitored under the same conditions of temperature (25°C) and contraction frequency (30 bpm) for all species. In all cases, ventricular strips showed a decrease in the force of contraction with sodium cyanide (NaCN) treatment. Ventricular strips from two Amazonian and one north-temperate-zone species showed signs of recovery from NaCN treatment. There was considerable diversity in the ability of ventricular strips to develop force under conditions of impaired oxidative phosphorylation that was not related to the ability to obtain oxygen from the air or to geographic location. However, there was a major difference between Amazonian and north-temperate-zone species in the ability of ventricular strips to maintain resting tension under NaCN treatment. Resting tension increased under conditions of simulated anoxia in ventricular strips from all north-temperate-zone species, but there was no change in resting tension in ventricular strips from Amazonian species. We propose that hearts from the Amazonian species are better able to reduce cytoplasmic calcium levels, possibly through a more highly developed sarcoplasmic reticulum.