The chromosome-level genome assembly of the Japanese yellowtail jack Seriola aureovittata provides insights into genome evolution and efficient oxygen transport

Fishes of the genus Seriola are widely farmed and highly valued in global aquaculture production. To further understand their economically important traits and help improve aquaculture product quality and sustainability, we performed a chromosome-level genome construction for Seriola aureovittata. Combining two technologies, PacBio and BGISEQ-500, we assembled 649.86 Mb S. aureovittata genome sequences with a contig N50 of 22.21 Mb, and 98% of BUSCO genes were detected in total. The initial assembly was then further scaffolded into 24 pseudochromosomes using Hi-C data, indicating the high quality of the genome. Genome evolution analysis showed that many genes related to fatty acid metabolism and oxygen binding, or transport were expanded, which provided insights into the metabolic characteristics of fatty acids and efficient oxygen transport. Based on the genome data, we confirmed the evolutionary relationship of S. aureovittata, S. dorsalis and S. lalandi and identified chr12 as the putative sex chromosome of S. aureovittata. Our chromosome-level genome assembly provides a genetic foundation for the phylogenetic and taxonomic investigation of different Seriola species. Moreover, the genome will provide an important genomic resource for further biological and aquaculture studies of S. aureovittata.

Tunabot Flex: a tuna-inspired robot with body flexibility improves high-performance swimming

Tunas are flexible, high-performance open ocean swimmers that operate at high frequencies to achieve high swimming speeds. Most fish-like robotic systems operate at low frequencies (≤3 Hz) resulting in low swim speeds (≤1.5 body lengths per second), and the cost of transport (COT) is often one to four orders of magnitude higher than that of tunas. Furthermore, the impact of body flexibility on high-performance fish swimming remains unknown. Here we design and test a research platform based on yellowfin tuna (Thunnus albacares) to investigate the role of body flexibility and to close the performance gap between robotic and biological systems. This single-motor platform, termed Tunabot Flex, measures 25.5 cm in length. Flexibility is varied through joints in the tail to produce three tested configurations. We find that increasing body flexibility improves self-propelled swimming speeds on average by 0.5 body lengths per second while reducing the minimum COT by 53%. The most flexible configuration swims 4.60 body lengths per second with a tail beat frequency of 8.0 Hz and a COT measuring 18.4 J kg^-1m^-1. We then compare these results in addition to the midline kinematics, stride length, and Strouhal number with yellowfin tuna data. The COT of Tunabot Flex's most flexible configuration is less than a half-order of magnitude greater than that of yellowfin tuna across all tested speeds. Tunabot Flex provides a new baseline for the development of future bio-inspired underwater vehicles that aim to explore a fish-like, high-performance space and close the gap between engineered robotic systems and fish swimming ability.

Physiological Responses of Fish to Oil Spills

Millions of tons of oil are spilled in aquatic environments every decade, and this oil has the potential to greatly impact fish populations. Here, we review available information on the physiological effects of oil and polycyclic aromatic hydrocarbons on fish. Oil toxicity affects multiple biological systems, including cardiac function, cholesterol biosynthesis, peripheral and central nervous system function, the stress response, and osmoregulatory and acid-base balance processes. We propose that cholesterol depletion may be a significant contributor to impacts on cardiac, neuronal, and synaptic function as well as reduced cortisol production and release. Furthermore, it is possible that intracellular calcium homeostasis-a part of cardiotoxic and neuronal function that is affected by oil exposure-may be related to cholesterol depletion. A detailed understanding of oil impacts and affected physiological processes is emerging, but knowledge of their combined effects on fish in natural habitats is largely lacking. We identify key areas deserving attention in future research.

Short-term feed and light deprivation reduces voluntary activity but improves swimming performance in rainbow trout Oncorhynchus mykiss

Rainbow trout Oncorhynchus mykiss (~ 180 g, 16 °C and < 5 kg m^-3) that were feed deprived and kept in total darkness showed a significant increase in critical swimming speed (U _crit) between 1 and 12 days of deprivation (from 3.35 to 4.46 body length (BL) s^-1) with no increase in maximum metabolic rate (MMR). They also showed a significant decrease in the estimated metabolic rate at 0 BL s^-1 over 12 days which leads to a higher factorial aerobic metabolic scope at day 12 (9.38) compared to day 1 (6.54). Routine metabolic rates were also measured in ~ 90 g rainbow trout that were swimming freely in large circular respirometers at 16 °C. These showed decreasing consumption oxygen rates and reductions in the amount of oxygen consumed above standard metabolic rate (a proxy for spontaneous activity) over 12 days, though this happened significantly faster when they were kept in total darkness when compared to a 12:12-h light-dark (LD) photoperiod. Weight loss during this period was also significantly reduced in total darkness (3.33% compared to 4.98% total body weight over 12 days). Immunological assays did not reveal any consistent up- or downregulation of antipathogenic and antioxidant enzymes in the serum or skin mucus of rainbow trout between 1 and 12 days of feed and light deprivation. Overall, short periods of deprivation do not appear to significantly affect the performance of rainbow trout which appear to employ a behavioural energy-sparing strategy, albeit more so in darkness than under a 12:12-h LD regime.

Sensing the flow beneath the fins

Flow sensing, maneuverability, energy efficiency and vigilance of surroundings are the key factors that dictate the performance of marine animals. Be it swimming at high speeds, attack or escape maneuvers, sensing and survival hydrodynamics are a constant feature of life in the ocean. Fishes are capable of performing energy efficient maneuvers, including capturing energy from vortical structures in water. These impressive capabilities are made possible by the uncanny ability of fish to sense minute pressure and flow variations on their body. This is achieved by arrays of biological neuromast sensors on their bodies that 'feel' the surroundings through 'touch at a distance' sensing. The main focus of this paper is to review the various biomimetic material approaches in developing superficial neuromast inspired ultrasensitive MEMS sensors. Principals and methods that translate biomechanical filtering properties of canal neuromasts to benefit artificial MEMS sensors have also been discussed. MEMS sensors with ultrahigh flow sensitivity and accuracy have been developed mainly through inspiration from the hair cell and cupula structures in the neuromast. Canal-inspired packages have proven beneficial in hydrodynamic flow filtering in artificial sensors enabling signal amplification and noise attenuation. A special emphasis has been placed on the recent innovations that closely mimic the structural and material designs of stereocilia of neuromasts by exploring soft polymers.

Boundary layer control by a fish: Unsteady laminar boundary layers of rainbow trout swimming in turbulent flows

The boundary layers of rainbow trout, Oncorhynchus mykiss [0.231±0.016 m total body length (L) (mean±s.d.); N=6], swimming at 1.6±0.09 L s⁻¹ (N=6) in an experimental flow channel (Reynolds number, Re=4×10⁵) with medium turbulence (5.6% intensity) were examined using the particle image velocimetry technique. The tangential flow velocity distributions in the pectoral and pelvic surface regions (arc length from the rostrum, l_x=71±8 mm, N=3, and l_x=110±13 mm, N=4, respectively) were approximated by a laminar boundary layer model, the Falkner−Skan equation. The flow regime over the pectoral and pelvic surfaces was regarded as a laminar flow, which could create less skin-friction drag than would be the case with turbulent flow. Flow separation was postponed until vortex shedding occurred over the posterior surface (l_x=163±22 mm, N=3). The ratio of the body-wave velocity to the swimming speed was in the order of 1.2. This was consistent with the condition of the boundary layer laminarization that had been confirmed earlier using a mechanical model. These findings suggest an energy-efficient swimming strategy for rainbow trout in a turbulent environment.

Summary: The boundary layer laminarization of rainbow trout swimming in turbulent flows was confirmed. The results suggested an energy-efficient swimming strategy of this species in the turbulent flow environment.

PFOS, PFNA, and PFOA sub-lethal exposure to embryonic zebrafish have different toxicity profiles in terms of morphometrics, behavior and gene expression

Polyfluorinated compounds (PFC) are a class of anthropogenic, persistent and toxic chemicals. PFCs are detected worldwide and consist of fluorinated carbon chains of varying length, terminal groups, and industrial uses. Previous zebrafish studies in the literature as well as our own studies have shown that exposure to these chemicals at a low range of concentrations (0.02-2.0μM; 20-2000ppb) resulted in chemical specific developmental defects and reduced post hatch survival. It was hypothesized that sub-lethal embryonic exposure to perfluorooctanesulfonic acid (PFOS), perfluorononanoic acid (PFNA), or perfluorooctanoic acid (PFOA) would result in different responses with regard to morphometric, behavior, and gene expression in both yolk sac fry and larval zebrafish. Zebrafish were exposed to PFOS, PFOA, and PFNA (0.02, 0.2, 2.0μM) for the first five days post fertilization (dpf) and analyzed for morphometrics (5 dpf, 14 dpf), targeted gene expression (5 dpf, 14 dpf), and locomotive behavior (14 dpf). All three PFCs commonly resulted in a decrease in total body length, increased tfc3a (muscle development) expression and decreased ap1s (protein transport) expression at 5dpf, and hyperactive locomotor activity 14 dpf. All other endpoints measured at both life-stage time points varied between each of the PFCs. PFOS, PFNA, and PFOA exposure resulted in significantly altered responses in terms of morphometric, locomotion, and gene expression endpoints, which could be manifested in field exposed teleosts.

Lateral line layout correlates with the differential hydrodynamic pressure on swimming fish

The lateral line of fish includes the canal subsystem that detects hydrodynamic pressure gradients and is thought to be important in swimming behaviors such as rheotaxis and prey tracking. Here, we explore the hypothesis that this sensory system is concentrated at locations where changes in pressure are greatest during motion through water. Using high-fidelity models of rainbow trout, we mimic the flows encountered during swimming while measuring pressure with fine spatial and temporal resolution. The variations in pressure for perturbations in body orientation and for disturbances to the incoming stream are seen to correlate with the sensory network. These findings support a view of the lateral line as a "hydrodynamic antenna" that is configured to retrieve flow signals and also suggest a physical explanation for the nearly universal sensory layout across diverse species.

Accommodating the cost of growth and swimming in fish-the applicability of exercise-induced growth to juvenile hapuku (Polyprion oxygeneios)

Induced-swimming can improve the growth and feed conversion efficiency of finfish aquaculture species, such as salmonids and Seriola sp., but some species, such as Atlantic cod, show no or a negative productivity response to exercise. As a possible explanation for these species-specific differences, a recent hypothesis proposed that the applicability of exercise training, as well as the exercise regime for optimal growth gain (ERopt growth), was dependent upon the size of available aerobic metabolic scope (AMS). This study aimed to test this hypothesis by measuring the growth and swimming metabolism of hapuku, Polyprion oxygeneios, to different exercise regimes and then reconciling the metabolic costs of swimming and specific dynamic action (SDA) against AMS. Two 8-week growth trials were conducted with ERs of 0.0, 0.25, 0.5, 0.75, 1, and 1.5 body lengths per second (BL s(-1)). Fish in the first trial showed a modest 4.8% increase in SGR over static controls in the region 0.5-0.75 BL s(-1) whereas the fish in trial 2 showed no significant effect of ER on growth performance. Reconciling the SDA of hapuku with the metabolic costs of swimming showed that hapuku AMS is sufficient to support growth and swimming at all ERs. The current study therefore suggests that exercise-induced growth is independent of AMS and is driven by other factors.

Unilateral ablation of trunk superficial neuromasts increases directional instability during steady swimming in the yellowtail kingfish Seriola lalandi

Detailed swimming kinematics of the yellowtail kingfish Seriola lalandi were investigated after unilateral ablation of superficial neuromasts (SNs). Most kinematic variables, such as tail-beat frequency, stride length, caudal fin-beat amplitude and propulsive wavelength, were unaffected but lateral amplitude at the tip of the snout (A0 ) was significantly increased in SN-disrupted fish compared with sham-operated controls. In addition, the orientation of caudal fin-tip relative to the overall swimming direction of SN-disrupted fish was significantly deflected (two-fold) in comparison with sham-operated control fish. In some fish, SN disruption also led to a phase distortion of the propulsive body-wave. These changes would be expected to increase both hydrodynamic drag and thrust production which is consistent with the finding that SN-disrupted fish had to generate significantly greater thrust power when swimming at ≥1·3 fork lengths (LF ) s(-1) . In particular, hydrodynamic drag would increase as a result of any increase in rotational (yaw) perturbation and sideways slip resulting from the sensory disturbance. In conclusion, unilateral SN ablation produced directional instability of steady swimming and altered propulsive movements, suggesting a role for sensory feedback in correcting yaw and slip disturbances to maintain efficient locomotion.