Diversity of Inner Ears in Fishes: Possible Contribution Towards Hearing Improvements and Evolutionary Considerations

Advance and Application of Single-cell Transcriptomics in Auditory Research

Hearing loss and deafness, as a worldwide disability disease, have been troubling human beings. However, the auditory organ of the inner ear is highly heterogeneous and has a very limited number of cells, which are largely uncharacterized in depth. Recently, with the development and utilization of single-cell RNA sequencing (scRNA-seq), researchers have been able to unveil the complex and sophisticated biological mechanisms of various types of cells in the auditory organ at the single-cell level and address the challenges of cellular heterogeneity that are not resolved through by conventional bulk RNA sequencing (bulk RNA-seq). Herein, we reviewed the application of scRNA-seq technology in auditory research, with the aim of providing a reference for the development of auditory organs, the pathogenesis of hearing loss, and regenerative therapy. Prospects about spatial transcriptomic scRNA-seq, single-cell based genome, and Live-seq technology will also be discussed.

Noise-induced damage in the zebrafish inner ear endorgans: evidence for higher acoustic sensitivity of saccular and lagenar hair cells

The three otolithic endorgans of the inner ear are known to be involved in sound detection in different teleost fishes, yet their relative roles for auditory-vestibular functions within the same species remain uncertain. In zebrafish (Danio rerio), the saccule and utricle are thought to play key functions in encoding auditory and vestibular information, respectively, but the biological function of the lagena is not clear. We hypothesized that the zebrafish saccule serves as a primary auditory endorgan, making it more vulnerable to noise exposure, and that the lagena might have an auditory function given its connectivity to the saccule and the dominant vestibular function of the utricle. We compared the impact of acoustic trauma (continuous white noise at 168 dB for 24 h) between the sensory epithelia of the three otolithic endorgans. Noise treatment caused hair cell loss in both the saccule and lagena but not in the utricle. This effect was identified immediately after acoustic treatment and did not increase 24 h post-trauma. Furthermore, hair cell loss was accompanied by a reduction in presynaptic activity measured based on ribeye b presence, but mainly in the saccule, supporting its main contribution for noise-induced hearing loss. Our findings support the hypothesis that the saccule plays a major role in sound detection and that the lagena is also acoustically affected, extending the species hearing dynamic range.

From the morphospace to the soundscape: Exploring the diversity and functional morphology of the fish inner ear, with a focus on elasmobranchsa)

Fishes, including elasmobranchs (sharks, rays, and skates), present an astonishing diversity in inner ear morphologies; however, the functional significance of these variations and how they confer auditory capacity is yet to be resolved. The relationship between inner ear structure and hearing performance is unclear, partly because most of the morphological and biomechanical mechanisms that underlie the hearing functions are complex and poorly known. Here, we present advanced opportunities to document discontinuities in the macroevolutionary trends of a complex biological form, like the inner ear, and test hypotheses regarding what factors may be driving morphological diversity. Three-dimensional (3D) bioimaging, geometric morphometrics, and finite element analysis are methods that can be combined to interrogate the structure-to-function links in elasmobranch fish inner ears. In addition, open-source 3D morphology datasets, advances in phylogenetic comparative methods, and methods for the analysis of highly multidimensional shape data have leveraged these opportunities. Questions that can be explored with this toolkit are identified, the different methods are justified, and remaining challenges are highlighted as avenues for future work.

A comparative analysis of form and function in Centrarchidae hearing ability: Does otolith variation affect auditory responsiveness?

There exists a wealth of knowledge on hearing ability in individual fish species, but the role of interspecific variation, and drivers behind it, remains understudied, making it difficult to understand evolutionary drivers. The current study quantified hearing thresholds for three species of sunfish in the family Centrarchidae [bluegill sunfish (Lepomis macrochirus), pumpkinseed sunfish (Lepomis gibbosus), and rock bass (Ambloplites rupestris)] using auditory evoked potentials and behavioral trials and saccular otolith size and hair cell density. In auditory physiological experiments, 10-ms tone bursts were played and responses monitored to measure hearing. In behavioral experiments, fish were exposed to the same tone bursts for 1 s, and changes in fish behaviors were monitored. Saccular otolith morphology and hair cell densities were also quantified. Physiological thresholds varied between species, but behavioral thresholds did not. Rock bass had larger S:O ratio (percentage of the saccular otolith surface occupied by the sulcus), but no differences in hair cell densities were found. Our study allows for a direct comparison between confamilial species, allowing a deeper understanding of sound detection abilities and possible mechanisms driving differential hearing. Using both approaches also allows future research into how these species may be impacted by increasing levels of anthropogenic noise.

Quantitative assessment of inner ear variation in elasmobranchs

Considerable diversity has been documented in most sensory systems of elasmobranchs (sharks, rays, and skates); however, relatively little is known about morphological variation in the auditory system of these fishes. Using magnetic resonance imaging (MRI), the inner ear structures of 26 elasmobranchs were assessed in situ. The inner ear end organs (saccule, lagena, utricle, and macula neglecta), semi-circular canals (horizontal, anterior, and posterior), and endolymphatic duct were compared using phylogenetically-informed, multivariate analyses. Inner ear variation can be characterised by three primary axes that are influenced by diet and habitat, where piscivorous elasmobranchs have larger inner ears compared to non-piscivorous species, and reef-associated species have larger inner ears than oceanic species. Importantly, this variation may reflect differences in auditory specialisation that could be tied to the functional requirements and environmental soundscapes of different species.

Hearing in catfishes: 200 years of research

Ernst Weber stated in 1819, based on dissections, that the swimbladder in the European wels (Silurus glanis, Siluridae) and related cyprinids serves as an eardrum and that the ossicles connecting it to the inner ear function as hearing ossicles similar to mammals. In the early 20th century, K. von Frisch showed experimentally that catfishes and cyprinids (otophysines) indeed hear excellently compared to fish taxa lacking auxiliary hearing structures (ossicles, eardrums). Knowledge on hearing in catfishes progressed in particular in the 21st century. Currently, hearing abilities (audiograms) are known in 28 species out of 13 families. Recent ontogenetic and comparative studies revealed that the ability to detect sounds of low-level and high frequencies (4-6 kHz) depends on the development of Weberian ossicles. Species with a higher number of ossicles and larger bladders hear better at higher frequencies (>1 kHz). Hearing sensitivities are furthermore affected by ecological factors. Rising temperatures increase, whereas various noise regimes decrease hearing. Exposure to high-noise levels (>150 dB) for hours result in temporary thresholds shifts (TTS) and recovery of hearing after several days. Low-noise levels reduce hearing abilities due to masking without a TTS. Furthermore, auditory evoked potential (AEP) experiments reveal that the temporal patterns of fish-produced pulsed stridulation and drumming sounds are represented in their auditory pathways, indicating that catfishes are able to extract important information for acoustic communication. Further research should concentrate on inner ears to determine whether the diversity in swimbladders and ossicles is paralleled in the inner ear fine structure.

A regulatory network of Sox and Six transcription factors initiate a cell fate transformation during hearing regeneration in adult zebrafish

Using adult zebrafish inner ears as a model for sensorineural regeneration, we ablated the mechanosensory receptors and characterized the single-cell epigenome and transcriptome at consecutive time points during hair cell regeneration. We utilized deep learning on the regeneration-induced open chromatin sequences and identified cell-specific transcription factor (TF) motif patterns. Enhancer activity correlated with gene expression and identified potential gene regulatory networks. A pattern of overlapping Sox- and Six-family TF gene expression and binding motifs was detected, suggesting a combinatorial program of TFs driving regeneration and cell identity. Pseudotime analysis of single-cell transcriptomic data suggested that support cells within the sensory epithelium changed cell identity to a “progenitor” cell population that could differentiate into hair cells. We identified a 2.6 kb DNA enhancer upstream of the sox2 promoter that, when deleted, showed a dominant phenotype that resulted in a hair-cell-regeneration-specific deficit in both the lateral line and adult inner ear.

Jimenez et al. interrogate the epigenomic and transcriptomic landscape of regenerating adult zebrafish inner-ear sensory epithelia. They show that the support-cell population transitions to an intermediate “progenitor” cell state that becomes new hair cells, and they demonstrate that the cell fate decisions may be driven by the coordinate regulation and spatial co-binding of Sox and Six transcription factors. By functionally validating a predicted regeneration-responsive enhancer upstream of sox2, they show that precise timing of sox2 expression is critical for hearing regeneration in zebrafish.

Physical effects of sound exposure from underwater explosions on Pacific mackerel (Scomber japonicus): Effects on the inner ear

Studies of the effects of sounds from underwater explosions on fishes have not included examination of potential effects on the ear. Caged Pacific mackerel (Scomber japonicus) located at seven distances (between approximately 35 and 800 m) from a single detonation of 4.5 kg of C4 explosives were exposed. After fish were recovered from the cages, the sensory epithelia of the saccular region of the inner ears were prepared and then examined microscopically. The number of hair cell (HC) ciliary bundles was counted at ten preselected 2500 μm² regions. HCs were significantly reduced in fish exposed to the explosion as compared to the controls. The extent of these differences varied by saccular region, with damage greater in the rostral and caudal ends and minimal in the central region. The extent of effect also varied in animals at different distances from the explosion, with damage occurring in fish as far away as 400 m. While extrapolation to other species and other conditions (e.g., depth, explosive size, and distance) must be performed with extreme caution, the effects of explosive sounds should be considered when environmental impacts are estimated for marine projects.

An overview of fish bioacoustics and the impacts of anthropogenic sounds on fishes

Fishes use a variety of sensory systems to learn about their environments and to communicate. Of the various senses, hearing plays a particularly important role for fishes in providing information, often from great distances, from all around these animals. This information is in all three spatial dimensions, often overcoming the limitations of other senses such as vision, touch, taste and smell. Sound is used for communication between fishes, mating behaviour, the detection of prey and predators, orientation and migration and habitat selection. Thus, anything that interferes with the ability of a fish to detect and respond to biologically relevant sounds can decrease survival and fitness of individuals and populations. Since the onset of the Industrial Revolution, there has been a growing increase in the noise that humans put into the water. These anthropogenic sounds are from a wide range of sources that include shipping, sonars, construction activities (e.g., wind farms, harbours), trawling, dredging and exploration for oil and gas. Anthropogenic sounds may be sufficiently intense to result in death or mortal injury. However, anthropogenic sounds at lower levels may result in temporary hearing impairment, physiological changes including stress effects, changes in behaviour or the masking of biologically important sounds. The intent of this paper is to review the potential effects of anthropogenic sounds upon fishes, the potential consequences for populations and ecosystems and the need to develop sound exposure criteria and relevant regulations. However, assuming that many readers may not have a background in fish bioacoustics, the paper first provides information on underwater acoustics, with a focus on introducing the very important concept of particle motion, the primary acoustic stimulus for all fishes, including elasmobranchs. The paper then provides background material on fish hearing, sound production and acoustic behaviour. This is followed by an overview of what is known about effects of anthropogenic sounds on fishes and considers the current guidelines and criteria being used world-wide to assess potential effects on fishes. Most importantly, the paper provides the most complete summary of the effects of anthropogenic noise on fishes to date. It is also made clear that there are currently so many information gaps that it is almost impossible to reach clear conclusions on the nature and levels of anthropogenic sounds that have potential to cause changes in animal behaviour, or even result in physical harm. Further research is required on the responses of a range of fish species to different sound sources, under different conditions. There is a need both to examine the immediate effects of sound exposure and the longer-term effects, in terms of fitness and likely impacts upon populations.

The importance of particle motion to fishes and invertebrates

This paper considers the importance of particle motion to fishes and invertebrates and the steps that need to be taken to improve knowledge of its effects. It is aimed at scientists investigating the impacts of sounds on fishes and invertebrates but it is also relevant to regulators, those preparing environmental impact assessments, and to industries creating underwater sounds. The overall aim of this paper is to ensure that proper attention is paid to particle motion as a stimulus when evaluating the effects of sound upon aquatic life. Directions are suggested for future research and planning that, if implemented, will provide a better scientific basis for dealing with the impact of underwater sounds on marine ecosystems and for regulating those human activities that generate such sounds. The paper includes background material on underwater acoustics, focusing on particle motion; the importance of particle motion to fishes and invertebrates; and sound propagation through both water and the substrate. Consideration is then given to the data gaps that must be filled in order to better understand the interactions between particle motion and aquatic animals. Finally, suggestions are provided on how to increase the understanding of particle motion and its relevance to aquatic animals.

Shaping of inner ear sensory organs through antagonistic interactions between Notch signalling and Lmx1a

The mechanisms of formation of the distinct sensory organs of the inner ear and the non-sensory domains that separate them are still unclear. Here, we show that several sensory patches arise by progressive segregation from a common prosensory domain in the embryonic chicken and mouse otocyst. This process is regulated by mutually antagonistic signals: Notch signalling and Lmx1a. Notch-mediated lateral induction promotes prosensory fate. Some of the early Notch-active cells, however, are normally diverted from this fate and increasing lateral induction produces misshapen or fused sensory organs in the chick. Conversely Lmx1a (or cLmx1b in the chick) allows sensory organ segregation by antagonizing lateral induction and promoting commitment to the non-sensory fate. Our findings highlight the dynamic nature of sensory patch formation and the labile character of the sensory-competent progenitors, which could have facilitated the emergence of new inner ear organs and their functional diversification in the course of evolution.

Wave Mechanics of the Vestibular Semicircular Canals

The semicircular canals are biomechanical sensors responsible for detecting and encoding angular motion of the head in 3D space. Canal afferent neurons provide essential inputs to neural circuits responsible for representation of self-position/orientation in space, and to compensatory circuits including the vestibulo-ocular and vestibulo-collic reflex arcs. In this work we derive, to our knowledge, a new 1D mathematical model quantifying canal biomechanics based on the morphology, dynamics of the inner ear fluids, and membranous labyrinth deformability. The model takes the form of a dispersive wave equation and predicts canal responses to angular motion, sound, and mechanical stimulation. Numerical simulations were carried out for the morphology of the human lateral canal using known physical properties of the endolymph and perilymph in three diverse conditions: surgical plugging, rotation, and mechanical indentation. The model reproduces frequency-dependent attenuation and phase shift in cases of canal plugging. During rotation, duct deformability extends the frequency bandwidth and enhances the high frequency gain. Mechanical indentation of the membranous duct at high frequencies evokes traveling waves that move away from the location of indentation and at low frequencies compels endolymph displacement along the canal. These results demonstrate the importance of the conformal perilymph-filled bony labyrinth to pressure changes and to high frequency sound and vibration.

Methods to study the development, anatomy, and function of the zebrafish inner ear across the life course

The inner ear is a remarkably intricate structure able to detect sound, motion, and gravity. During development of the zebrafish embryo, the ear undergoes dynamic morphogenesis from a simple epithelial vesicle into a complex labyrinth, consisting of three semicircular canals and three otolithic sensory organs, each with an array of differentiated cell types. This microcosm of biology has led to advances in understanding molecular and cellular changes in epithelial patterning and morphogenesis, through to mechanisms of mechanosensory transduction and the origins of reflexive behavior. In this chapter, we describe different methods to study the zebrafish ear, including high-speed imaging of otic cilia, confocal microscopy, and light-sheet fluorescent microscopy. Many dyes, antibodies, and transgenic lines for labeling the ear are available, and we provide a comprehensive review of these resources. The developing ear is amenable to genetic, chemical, and physical manipulations, including injection and transplantation. Chemical modulation of developmental signaling pathways has paved the way for zebrafish to be widely used in drug discovery. We describe two chemical screens with relevance to the ear: a fluorescent-based screen for compounds that protect against ototoxicity, and an in situ-based screen for modulators of a signaling pathway involved in semicircular canal development. We also describe methods for dissection and imaging of the adult otic epithelia. We review both manual and automated methods to test the function of the inner ear and lateral line, defects in which can lead to altered locomotor behavior. Finally, we review a collection of zebrafish models that are generating new insights into human deafness and vestibular disorders.