International Journal of Aquaculture 2024, Vol.14, No.5 http://www.aquapublisher.com/index.php/ija © 2024 AquaPublisher, registered at the publishing platform that is operated by Sophia Publishing Group, founded in British Columbia of Canada. All Rights Reserved. Publisher
International Journal of Aquaculture 2024, Vol.14, No.5 http://www.aquapublisher.com/index.php/ija © 2024 AquaPublisher, registered at the publishing platform that is operated by Sophia Publishing Group, founded in British Columbia of Canada. All Rights Reserved. Publisher Aqua Publisher Editedby Editorial Team of International Journal of Aquaculture Email: edit@ija.aquapublisher.com Website: http://www.aquapublisher.com/index.php/ija Address: 11388 Stevenston Hwy, PO Box 96016, Richmond, V7A 5J5, British Columbia Canada International Journal of Aquaculture (ISSN 1927-5773) is an open access, peer reviewed journal published online by AquaPublisher. The journal publishes all the latest and outstanding research articles, letters and reviews in all working and studying within varied areas of aquaculture, containing the latest developments and techniques for practice in aquaculture; information about the entire area of applied aquaculture, including breeding and genetics, physiology, aquaculture-environment, hatchery design and management, utilization of primary and secondary resources in aquaculture, production and harvest, the biology and culture of aquaculturally important and emerging species. All the articles published in International Journal of Aquaculture are Open Access, and are distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. AquaPublisher uses CrossCheck service to identify academic plagiarism through the world’s leading plagiarism prevention tool, iParadigms, and to protect the original authors' copyrights. Aqua Publisher is an international Open Access publisher specializing in the field of marine science and aquaculture registered at the publishing platform that is operated by Sophia Publishing Group (SPG), founded in British Columbia of Canada.
International Journal of Aquaculture (online), 2024, Vol. 14 ISSN 1927-6648 http://aquapublisher.com/index.php/ija © 2024 AquaPublisher, registered at the publishing platform that is operated by Sophia Publishing Group, founded in British Columbia of Canada. All Rights Reserved. Latest Content 2024, Vol. 14, No.5 【Research Article】 Emerging Contaminants in Aquatic Ecosystems: Sources, Effects, and Mitigation Approaches 232-240 Xueli Zhang, Xiaohong Liu, Chunyang Zhan DOI: 10.5376/ija.2024.14.0023 【Research Insight】 Comparative Genomics of Aquatic Organisms: Insights into Biodiversity Origins 241-248 Wenli Li, Jiamin Zhang, Fan Wang DOI: 10.5376/ija.2024.14.00024 Epigenetic Regulation in Algae: Implications for Growth, Development, and Stress Response 257-265 Zhongxian Zhao, Guoping Chen, Linhua Zhang DOI: 10.5376/ija.2024.14.0026 【Research Report】 Optimizing Feed Formulations for Enhanced Growth and Environmental Sustainability in Common Carp Aquaculture 249-256 Weidong Liu, Xiaoya Wang, Liqing Chen DOI: 10.5376/ija.2024.14.0025 The Effects of Vitamin A Supplementation in Female Broodstock Diets of African Catfish on Egg Quality, Egg and Liver Retinol, Ovary Estradiol, and Larval Survival 266-279 Okure G.P., Udo I.U., Afia O.E. DOI: 10.5376/ija.2024.14.0027
International Journal of Aquaculture, 2024, Vol.14, No.5, 232-240 http://www.aquapublisher.com/index.php/ija 232 Research Article Open Access Emerging Contaminants in Aquatic Ecosystems: Sources, Effects, and Mitigation Approaches Xueli Zhang, Xiaohong Liu, Chunyang Zhan Hainan Institute of Biotechnology, Haikou, 570206, Hainan, China Corresponding author: chunyang.zhan@hitar.org International Journal of Aquaculture, 2024, Vol.14, No.5 doi: 10.5376/ija.2024.14.0023 Received: 20 Jun., 2024 Accepted: 31 Jul., 2024 Published: 10 Sep., 2024 Copyright © 2024 Zhang et al., This is an open access article published under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Preferred citation for this article: Zhang X.L., Liu X.H., and Zhan C.Y., 2024, Emerging contaminants in aquatic ecosystems: sources, effects, and mitigation approaches, International Journal of Aquaculture, 14(5): 232-240 (doi: 10.5376/ija.2024.14.0023) Abstract This study explores emerging pollutants in aquatic ecosystems, their sources, impacts, and mitigation methods. With the progress of industrialization and population growth, more and more emerging pollutants (such as drug residues, pesticides, heavy metals, etc.) enter water bodies through various pathways, which have a profound impact on aquatic species and ecosystem services. The problem with the study is that the accumulation and continuous exposure of these pollutants not only pose a toxicological threat to aquatic organisms, but may also affect human health through the food chain and water sources. Therefore, it is important to identify the sources and pathways of emerging pollutants and their impacts on ecology and health, develop effective monitoring and treatment technologies, and promote adaptive policies on a global scale, providing a basis for further governance and protection work. Keywords Emerging contaminants; Aquatic ecosystems; Bioaccumulation; Toxicological impact; Mitigation approaches 1 Introduction Aquatic ecosystems, encompassing both marine and freshwater environments, cover over two-thirds of the Earth's surface and are vital for maintaining global climate stability and supporting biodiversity. These ecosystems provide essential services, including water purification, habitat for numerous species, and resources for human consumption and recreation (Álvarez-Ruiz and Picó, 2020; Häder et al., 2020). Freshwater systems, although covering only a small fraction of the Earth's surface, host a significant proportion of the planet's biodiversity, including many species that are not found anywhere else (Reid et al., 2018). The increasing presence of emerging pollutants (EPs) in aquatic ecosystems poses a significant threat to both environmental and human health. These pollutants, which include pharmaceuticals, personal care products, heavy metals, pesticides, and microplastics, can be bioaccumulated and biomagnified, leading to adverse effects on aquatic biota and potential risks to humans through the consumption of contaminated water and organisms (Impellitteri et al., 2023). The impact of these contaminants is exacerbated by their ability to alter the physicochemical properties of water, disrupt food webs, and contribute to the decline of biodiversity (Gallardo et al., 2016; Reid et al., 2018). Understanding the sources, effects, and mitigation strategies for EPs is crucial for developing effective environmental policies and conservation efforts (Mierzejewska and Urbaniak, 2020). This study provides a comprehensive overview of the current knowledge status of newly emerging pollutants in aquatic ecosystems. It will explore the various sources of these pollutants, their ecological and physiological impacts on aquatic organisms, and potential mitigation methods that can be used to reduce their effects; Emphasize the urgent need for stricter environmental regulations and innovative solutions to protect aquatic ecosystems and ensure their sustainability for future generations. 2 Identification of Emerging Contaminants 2.1 Definition and classification Emerging contaminants (ECs), also known as contaminants of emerging concern (CECs), are a diverse group of chemicals that have recently been detected in the environment, primarily due to advancements in analytical
International Journal of Aquaculture, 2024, Vol.14, No.5, 232-240 http://www.aquapublisher.com/index.php/ija 233 techniques that allow for the identification of these substances even at trace levels (Stefanakis and Becker, 2020). These contaminants include a wide range of substances such as pharmaceuticals, personal care products, pesticides, hormones, nanomaterials, and microplastics (Naidu et al., 2016; Srikanth, 2019). ECs can be of synthetic origin or naturally occurring, and their environmental and public health risks are not yet fully understood due to limited data on their interactions and toxicological impacts (Hossein, 2019). The classification of ECs is broad and encompasses various categories, including but not limited to antibiotics, endocrine disruptors, industrial chemicals, and biological contaminants like bacteria and viruses (Gavrilescu et al., 2015; Nilsen et al., 2018). The continuous detection of new chemicals over time raises significant concerns regarding their fate, transport, transformations, and impacts on aquatic environments and human health. 2.2 Sources and pathways The sources and pathways of emerging contaminants into aquatic ecosystems are diverse and complex. ECs can enter the environment through various anthropogenic activities, including agricultural runoff, wastewater effluents, industrial discharges, and urban runoff (Srikanth, 2019; Rathi et al., 2020). Wastewater treatment plants are significant point sources, as they often release pharmaceuticals, personal care products, and other chemicals directly into water bodies (Carere et al., 2021). Additionally, non-point sources such as agricultural fields contribute pesticides and fertilizers, which can leach into groundwater or be carried by surface runoff into rivers and lakes. The presence of ECs in the environment is further exacerbated by the continuous release of new chemicals, which are not routinely monitored and thus remain undetected until advanced analytical methods are applied. Once in the aquatic environment, these contaminants can persist and be transported across different environmental matrices, including water, soil, and sediments, potentially affecting a wide range of ecological receptors (Deere et al., 2021). The pathways of ECs are influenced by various factors, including their chemical properties, environmental conditions, and the presence of other contaminants, which can complicate their fate and behavior in the ecosystem. Understanding these sources and pathways is crucial for developing effective management and mitigation strategies to protect aquatic ecosystems and human health from the adverse effects of emerging contaminants. 3 Effects on Aquatic Life and Ecosystems 3.1 Toxicological impact on aquatic species 3.1.1 Endocrine disruption Emerging contaminants (ECs), particularly endocrine-disrupting compounds (EDCs), have been shown to cause significant endocrine disruption in aquatic species. These compounds, which include pharmaceuticals and personal care products (PPCPs), can interfere with the hormonal systems of aquatic organisms, leading to reproductive and developmental abnormalities (Yuan, 2024). For instance, exposure to EDCs such as estrone (E1), estriol (E3), and 17α-ethynylestradiol (EE2) has been linked to feminization of male fish, reduced fertility, and altered sex ratios in fish populations (Su et al., 2020). The effects of these disruptions are often permanent and can impair the development of the endocrine system and the organs that respond to endocrine signals, leading to long-term consequences for affected species (Talib and Randhir, 2016). 3.1.2 Bioaccumulation Bioaccumulation of ECs in aquatic organisms is another critical concern. Pharmaceuticals, personal care products, and other ECs can accumulate in the tissues of aquatic species, leading to toxic effects over time. Studies have shown that compounds such as azithromycin, DEET, diphenhydramine, and fluoxetine are frequently detected in aquatic environments and can bioaccumulate in fish and other organisms (Deere et al., 2021). This bioaccumulation can lead to sublethal effects, including behavioral changes, growth inhibition, and increased susceptibility to diseases (Saidulu et al., 2021). The persistence of these contaminants in the environment and their ability to bioaccumulate pose significant risks to aquatic life and can disrupt entire food webs. 3.2 Impacts on ecosystem services The presence of ECs in aquatic ecosystems can have profound impacts on ecosystem services. These
International Journal of Aquaculture, 2024, Vol.14, No.5, 232-240 http://www.aquapublisher.com/index.php/ija 234 contaminants can alter the structure and function of aquatic communities, affecting biodiversity, water quality, and the overall health of the ecosystem. For example, ECs such as pharmaceuticals and personal care products can affect the growth and reproduction of key species, leading to changes in community composition and reductions in biodiversity (Prichard and Granek, 2016). Additionally, the presence of ECs can impair the ability of aquatic ecosystems to provide essential services such as water purification, nutrient cycling, and habitat provision (Bilal et al., 2019). The disruption of these services can have cascading effects on both aquatic and terrestrial ecosystems, highlighting the need for effective management and mitigation strategies to protect these vital resources (Gogoi et al., 2018). 4 Human Health Implications 4.1 Exposure pathways Emerging contaminants in aquatic ecosystems can reach humans through various exposure pathways. One of the primary routes is through the consumption of contaminated seafood, which can lead to bioaccumulation and biomagnification of harmful substances such as mercury. Mercury, particularly in its methylmercury form, is a significant concern due to its potential for causing acute and chronic health issues in humans (Rodrigues et al., 2019). Additionally, the increase in water temperature due to global warming can exacerbate the toxicity of environmental contaminants, further affecting the food chain and ultimately human health (Manciocco et al., 2014). Contaminants can also be transferred from aquatic to terrestrial ecosystems through both biotic and abiotic pathways, such as emerging adult aquatic insects or flood events, which can then affect terrestrial food webs and human health (Schulz and Bundschuh, 2020). Moreover, the presence of microplastics in aquatic environments poses a risk as they can be ingested by aquatic organisms, which are then consumed by humans, leading to potential health risks (Foley et al., 2018). 4.2 Potential health risks The potential health risks associated with emerging contaminants in aquatic ecosystems are diverse and significant. Mercury contamination, for instance, can lead to neurological and developmental issues, particularly in vulnerable populations such as pregnant women and young children (Rodrigues et al., 2019). The ingestion of contaminated fish and shellfish can result in the accumulation of various harmful substances, including heavy metals and persistent organic pollutants, which can cause a range of health problems from acute poisoning to long-term chronic diseases (Häder et al., 2020). The presence of microplastics in the food chain can also lead to physical and chemical hazards, as these particles can carry toxic chemicals and pathogens, potentially leading to gastrointestinal and other systemic health issues (Foley et al., 2018). Furthermore, the continuous release of pharmaceuticals, personal care products, and other emerging contaminants into aquatic environments can disrupt endocrine systems and lead to reproductive and developmental problems in humans (Impellitteri et al., 2023). The complexity of these contaminants and their interactions within the food web make it challenging to fully assess and mitigate their health risks, highlighting the need for advanced analytical methods and stricter environmental regulations (Lapworth et al., 2012; Hernández et al., 2019). 5 Detection and Monitoring 5.1 Analytical techniques for detection 5.1.1 Advanced spectroscopy Advanced spectroscopy techniques have become indispensable in the detection of emerging contaminants in aquatic ecosystems. High-resolution mass spectrometry (HRMS) is particularly effective for the suspect and non-target screening of halogenated contaminants and their transformation products, which often exist in trace amounts (Badea et al., 2020). Additionally, techniques such as surface-enhanced Raman spectroscopy (SERS) and fluorescence spectroscopy offer significant advantages over traditional methods. These include high sensitivity, selectivity, and the ability to monitor contaminants in real-time, making them suitable for rapid and low-cost detection (Manivannan et al., 2020). Low-Resolution Raman Spectroscopy (LRRS) has also shown promise in detecting low concentrations of harmful cyanobacterial species within dense algal cultures, demonstrating its potential for real-time monitoring in bioreactors and other aquatic environments (Olubunmi et al., 2021).
International Journal of Aquaculture, 2024, Vol.14, No.5, 232-240 http://www.aquapublisher.com/index.php/ija 235 5.1.2 Biomonitorin Biomonitoring involves the use of living organisms to assess the presence and impact of contaminants in the environment. This approach is crucial for detecting a wide array of undetected contaminants that may be mobile and persistent across various environmental matrices, including water, soil, and sediments (Gavrilescu et al., 2015). The development of biosensors capable of real-time environmental monitoring is an emerging field that holds promise for the detection of multiple species of contaminants. These biosensors can exploit specialized microbes or enzymes to degrade endocrine disruptors and other micropollutants, thereby providing a more comprehensive understanding of the ecological and health risks posed by these contaminants (Lohmann et al., 2017). 5.2 Monitoring strategies Effective monitoring strategies are essential for managing the risks associated with emerging contaminants in aquatic ecosystems. The Aquatic Global Passive Sampling (AQUA-GAPS) network exemplifies a strategic approach to global monitoring. This decentralized network uses passive sampling techniques to detect persistent organic pollutants (POPs) and other contaminants of concern in freshwater and coastal marine sites (Figure 1), thereby providing consistent and comparable data on a global scale (Lohmann et al., 2017). Another innovative approach involves the use of Effect-Based Methods (EBMs), which combine chemical analysis with eco-genotoxicological assays to assess the genotoxic activity of chemicals in urban river stretches. This method has proven effective in identifying the presence of pharmaceuticals, pesticides, and personal care products, even at low concentrations, and can inform future monitoring and remediation efforts (Carere et al., 2021). Figure 1 Passive samplers will be deployed, equipped with both polyethylene and silicone rubber samplers (Adopted from Lohmann et al., 2017)
International Journal of Aquaculture, 2024, Vol.14, No.5, 232-240 http://www.aquapublisher.com/index.php/ija 236 6 Mitigation and Treatment Approaches 6.1 Conventional treatment technologies Conventional treatment technologies have been the cornerstone of water treatment for decades. These methods typically include primary, secondary, and tertiary treatment processes. Primary treatment involves the physical removal of large particles through sedimentation, while secondary treatment employs biological processes to degrade organic matter. However, these conventional methods are often insufficient for the complete removal of emerging contaminants (ECs) such as pharmaceuticals, personal care products, and endocrine-disrupting chemicals. Studies have shown that these contaminants persist through traditional treatment processes, leading to their accumulation in aquatic ecosystems and posing significant risks to human and wildlife health (Rodríguez-Narváez et al., 2017; Gogoi et al., 2018; Rasheed et al., 2019). The inefficacy of conventional methods necessitates the exploration of more advanced and integrated treatment approaches to address the challenges posed by ECs. 6.2 Emerging technologies Emerging technologies offer promising solutions for the effective removal of ECs from water bodies. Advanced oxidation processes (AOPs), membrane filtration, and adsorption techniques have shown significant potential in recent studies. AOPs, which include methods such as ozonation and photocatalysis, are effective in breaking down complex organic contaminants into less harmful substances (Bilal et al., 2019). Membrane filtration technologies, such as nanofiltration and reverse osmosis, provide high removal efficiencies for a wide range of ECs, although they can be cost-prohibitive (Talib and Randhir, 2016). Adsorption using low-cost adsorbents, such as biochar and agricultural waste, has also been identified as a viable and sustainable option for EC removal (Varsha et al., 2021; Rathi and Kumar, 2021). Additionally, biological treatment methods, including the use of microalgae and enzyme-assisted biodegradation, have shown promise in degrading and removing ECs from wastewater (Singh et al., 2021). These emerging technologies, while still under development and optimization, represent a critical advancement in the field of water treatment. 6.3 Policy and regulation Effective management of ECs in aquatic ecosystems requires robust policy and regulatory frameworks. Current regulations often fall short in addressing the complexities associated with ECs, primarily due to the lack of comprehensive health standards and guidelines for these contaminants (Gogoi et al., 2018). Policymakers need to develop and implement stringent regulations that encompass the entire lifecycle of ECs, from their production and use to their disposal and treatment. This includes setting permissible limits for EC concentrations in water bodies, promoting the use of best management practices, and encouraging the adoption of advanced treatment technologies. Additionally, public awareness and education campaigns are essential to modify human behavior and reduce the release of ECs into the environment (Talib and Randhir, 2016; Deere et al., 2021). Collaborative efforts between governments, industries, and the scientific community are crucial to establish effective policies and regulations that safeguard both environmental and public health. 7 Case Studies 7.1 Successful remediation cases Successful remediation of aquatic ecosystems contaminated by emerging pollutants has been achieved through various innovative approaches. One notable method involves the use of bioturbators, which are organisms that disturb sediment layers (Wu and Chen, 2024), thereby enhancing microbial processes that facilitate contaminant removal. A systematic review and meta-analysis have shown that bioturbators, such as polychaetes, can significantly increase the release of metals and nutrients from sediments, thus aiding in the bioremediation process. The effectiveness of this method varies depending on environmental factors such as temperature, pH, and sediment grain size, highlighting the need for context-specific applications (Pal et al., 2010). Additionally, the application of Effect-Based Methods (EBMs) in urban river stretches has proven effective in identifying and mitigating the presence of genotoxic and teratogenic pollutants. For instance, in the Tiber River, EBMs have been used to detect and address the diffuse chemical pollution caused by pharmaceuticals, pesticides, and personal care products, leading to improved water quality and ecosystem health (Carere et al., 2021).
International Journal of Aquaculture, 2024, Vol.14, No.5, 232-240 http://www.aquapublisher.com/index.php/ija 237 7.2 The aral sea recovery project The Aral Sea, once one of the largest lakes in the world, has faced severe ecological degradation due to extensive water diversion for agricultural purposes. Efforts to recover the Aral Sea have focused on reducing the inflow of pollutants and restoring natural water levels. One of the key strategies has been the implementation of advanced water treatment technologies to remove emerging contaminants from inflowing rivers. These technologies include adsorption processes, membrane filtration, and advanced oxidation processes, which have been shown to effectively remove a wide range of micropollutants, including pharmaceuticals and endocrine disruptors (Mohanavelu et al., 2021). The success of these technologies in the Aral Sea Recovery Project underscores the importance of adopting state-of-the-art treatment methods to address complex contamination issues in large aquatic ecosystems. 7.3 Cleanup of the ganges river The Ganges River, one of the most polluted rivers in the world, has been the focus of numerous cleanup initiatives aimed at reducing the levels of emerging contaminants. The river is heavily contaminated with pharmaceuticals, personal care products, and industrial chemicals, which pose significant risks to both human health and aquatic life. Recent efforts have included the deployment of integrated water quality assessment methods that combine chemical analyses with eco-genotoxicological assays. These methods have been instrumental in identifying the sources and impacts of pollution, thereby guiding targeted remediation efforts (Carere et al., 2021). Additionally, the use of biological treatment methods, such as the application of bioturbators, has shown promise in enhancing the natural attenuation of contaminants in the river sediments (Gonzalez et al., 2019). These combined approaches have led to measurable improvements in water quality and have set a precedent for future remediation projects in similarly polluted rivers around the world. 8 Concluding Remarks Emerging contaminants (ECs), including pharmaceuticals, personal care products (PPCPs), endocrine-disrupting compounds (EDCs), and other chemicals, have been detected in various aquatic environments worldwide. These contaminants pose significant risks to both human health and aquatic ecosystems due to their persistence and bioaccumulation potential. Studies have shown that current wastewater treatment plants are not adequately designed to remove these contaminants, leading to their widespread presence in surface water, groundwater, and even drinking water. The adverse effects of ECs on aquatic life, such as reproductive and developmental abnormalities, have been well-documented, highlighting the urgent need for effective mitigation strategies. Additionally, the presence of ECs in sediments and their association with microplastics further complicates their environmental impact. Future research should focus on several key areas to address the challenges posed by emerging contaminants. First, there is a need for comprehensive toxicity data to better understand the sublethal effects of ECs on aquatic organisms and ecosystems. Second, the development of advanced treatment technologies that can efficiently remove a wide range of ECs from wastewater is crucial. This includes exploring cost-effective and sustainable methods such as adsorption, nanofiltration, and advanced oxidation processes. Third, more research is needed to understand the fate and transformation of ECs in different environmental compartments, including their interactions with microplastics and other pollutants. Finally, long-term monitoring programs should be established to track the occurrence and effects of ECs in various aquatic environments, providing valuable data for risk assessment and management. To mitigate the risks associated with emerging contaminants, several policy recommendations are proposed. Regulatory agencies should establish and enforce stringent guidelines for the discharge of ECs into the environment, including setting maximum allowable concentrations for various contaminants. There is also a need for international collaboration to develop standardized methods for monitoring and assessing the environmental impact of ECs. Public awareness campaigns and educational programs can play a vital role in reducing the release of ECs by promoting responsible disposal of pharmaceuticals and personal care products. Additionally, incentives
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International Journal of Aquaculture, 2024, Vol.14, No.5, 241-248 http://www.aquapublisher.com/index.php/ija 241 Review Insight Open Access Comparative Genomics of Aquatic Organisms: Insights into Biodiversity Origins Wenli Li, Jiamin Zhang, Fan Wang Aquatic Biology Research Center, Cuixi Academy of Biotechnology, Zhuji, 311800, Zhejiang, China Corresponding author: fan.wang@cuixi.org International Journal of Aquaculture, 2024, Vol.14, No.5 doi: 10.5376/ija.2024.14.0024 Received: 26 Jun., 2024 Accepted: 08 Aug., 2024 Published: 17 Sep., 2024 Copyright © 2024 Li et al., This is an open access article published under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Preferred citation for this article: Li W.L., Zhang J.M., and Wang F., 2024, Comparative genomics of aquatic organisms: insights into biodiversity origins, International Journal of Aquaculture, 14(5): 241-248 (doi: 10.5376/ija.2024.14.0024) Abstract This study explored the origin of aquatic biodiversity through comparative genomics, and the researchers gained an in-depth understanding of the adaptive evolutionary mechanisms of species in different aquatic environments. They used genomic data to reveal the radiation adaptation of coral reef fish, the metabolic adaptability of deep-sea species, and the genomic diversity in polar ecosystems, thus providing new insights into the conservation of aquatic biodiversity. Comparative genomics can not only help understand the origin of aquatic species diversity, but also provide a scientific basis for the protection and management of fragile aquatic ecosystems, and provide a foundation for further development of genomic research on aquatic organisms, especially in understudied species and extreme environments. Keywords Aquatic biodiversity; Comparative genomics; Adaptive radiation; Metabolic adaptation; Conservation genomics 1 Introduction Aquatic ecosystems, encompassing marine, freshwater, and transitional environments, are home to a vast array of species that contribute significantly to global biodiversity. Marine habitats, which cover approximately 70% of the Earth's surface, host a diverse range of organisms adapted to various ecological niches (Kelley et al., 2016). Freshwater ecosystems, although occupying a mere 2% of the Earth's surface, exhibit high species richness and exceptional phylogenetic diversity (Román-Palacios et al., 2022). The unique properties of water, such as its physical and chemical characteristics, play a crucial role in shaping the genetic diversity and population connectivity of aquatic species (Grummer et al., 2019). Comparative genomics has emerged as a powerful tool for unraveling the evolutionary processes that drive biodiversity in aquatic environments. By comparing the genomes of different species, researchers can gain insights into the physiological and morphological adaptations that have enabled organisms to thrive in diverse habitats (Ovchinnikova and Shi, 2023). Population genomics, in particular, has provided unprecedented resolution for understanding population structuring, speciation, and adaptation in marine environments, which often have low dispersal costs and few physical barriers to gene flow (Kelley et al., 2016). Additionally, genomic and transcriptomic studies have facilitated the discovery of novel bioactive macromolecules and have advanced our understanding of the molecular mechanisms underlying survival, growth, reproduction, and homeostasis in aquatic organisms. This study provides a comprehensive overview of the role of comparative genomics in elucidating the origins of biodiversity in aquatic ecosystems, attempting to emphasize the evolutionary transitions between marine, freshwater, and terrestrial environments that shape contemporary biodiversity. We will explore the application of genomic tools in conservation, particularly in assessing the impact of environmental stressors such as climate change and human activities on aquatic species. In addition, the potential of next-generation sequencing technology and environmental DNA (eDNA) meta barcoding in advancing ecological research and biodiversity monitoring will be discussed, with the aim of emphasizing the importance of integrating genomic data and deepening our understanding of the complex adaptive processes that control aquatic biodiversity.
International Journal of Aquaculture, 2024, Vol.14, No.5, 241-248 http://www.aquapublisher.com/index.php/ija 242 2 Comparative Genomics of Coral Reef Fish 2.1 Coral reef fish as models for adaptive radiation Coral reef fish, such as clownfish and grunts, serve as excellent models for studying adaptive radiation due to their diverse ecological niches and rapid diversification. For instance, clownfish have evolved a mutualistic relationship with sea anemones, which has driven their rapid diversification. Genomic studies reveal that clownfish genomes exhibit bursts of transposable elements, accelerated coding evolution, and hybridization events, all of which have facilitated their adaptive radiation (Xu, 2024). Positive selection in genes related to social behavior and ecological divergence further underscores the role of genomic changes in their diversification (Marcionetti and Salamin, 2022). Similarly, comparative transcriptomics of sympatric species of the genus Haemulon (grunts) show positive selection in genes associated with immune response and morphological traits, indicating adaptive divergence despite overlapping habitats (Figure 1) (Bernal et al., 2019). Figure 1 Morphological differences between the three sympatric species of Haemulon(Adopted from Bernal et al., 2019) 2.2 Environmental pressures driving coral reef fish diversity Environmental pressures such as climate change and habitat variability significantly influence the diversity of coral reef fish. Coral reefs are experiencing rapid deterioration due to climate change, which imposes selective pressures on resident species. For example, seascape genomics studies on Acropora digitifera have identified genomic regions associated with heat stress resistance, highlighting the role of environmental pressures in shaping genetic diversity (Selmoni et al., 2020). Additionally, reefscape genomics leverages advances in 3D imaging to assess fine-scale patterns of genomic variation, enabling the study of spatio-temporal drivers of genetic structuring and adaptive potential in coral reef ecosystems (Bongaerts et al., 2021). These environmental pressures drive the evolution of traits that enhance survival and reproduction in changing conditions, contributing to the overall biodiversity of coral reef fish.
International Journal of Aquaculture, 2024, Vol.14, No.5, 241-248 http://www.aquapublisher.com/index.php/ija 243 2.3 Application of genomic data to coral reef conservation Genomic data is increasingly being applied to coral reef conservation efforts to better understand and mitigate the impacts of environmental changes. For instance, population genomics provides insights into the genetic structuring and adaptive potential of coral reef taxa, which is crucial for developing effective conservation strategies (Pinsky et al., 2023). The integration of genomic data with environmental and phenotypic information, as demonstrated in reefscape genomics, allows for the identification of key areas for conservation prioritization (Bongaerts et al., 2021). Moreover, the genomic characterization of coral species and their microbial symbionts reveals critical interactions that support coral health, informing strategies to enhance reef resilience (Robbins et al., 2019). These applications underscore the importance of genomics in guiding conservation efforts to preserve the biodiversity and ecological functions of coral reef ecosystems. 3 Comparative Genomics of Deep-Sea Adaptation 3.1 Genetic adaptations to extreme pressure and darkness Deep-sea organisms have evolved unique genetic adaptations to survive under extreme pressure and darkness. For instance, the Yap hadal snailfish (YHS) exhibits high levels of trimethylamine N-oxide (TMAO), a potent protein stabilizer, which is crucial for maintaining protein integrity under high hydrostatic pressure. This adaptation is supported by the presence of multiple copies of the TMAO-generating enzyme flavin-containing monooxygenase-3 gene (fmo3) in the YHS genome (Mu et al., 2021). Similarly, deep-sea Actinobacteriota have evolved higher GC content and longer intergenic spaces in their genomes, which may contribute to their survival in high-pressure environments (Roda-García et al., 2023). These genetic modifications are essential for maintaining cellular functions and structural integrity in the deep sea. 3.2 Evolutionary mechanisms underpinning metabolic adaptations Metabolic adaptations are critical for deep-sea organisms to thrive in environments with limited food supply and low temperatures. The deep-sea fish Coryphaenoides rupestris shows genotypic segregation by depth, with distinct genotypes at functional loci that may be linked to different metabolic requirements at varying depths (Gaither et al., 2018). Additionally, Arctic Charr (Salvelinus alpinus) morphs adapted to deep-water habitats exhibit genomic divergence in genes associated with cardiac function, membrane transport, and DNA repair, which are vital for coping with the metabolic demands of deep-water environments (Kess et al., 2021). These evolutionary mechanisms highlight the importance of metabolic flexibility in deep-sea adaptation. 3.3 Genomic data in deep-sea conservation efforts Genomic data play a crucial role in the conservation of deep-sea species by providing insights into their evolutionary history and adaptive mechanisms. For example, the annotated genome assembly of the deep-sea fish Coryphaenoides rupestris can inform conservation strategies by identifying loci under disruptive selection that are crucial for survival at different depths (Kelley et al., 2016). Furthermore, the genomic analysis of marine vertebrates, including deep-sea species, can help assess the impact of fisheries and climate change on their populations, thereby guiding conservation efforts (Yuan et al., 2021). Understanding the genetic basis of adaptation in deep-sea organisms is essential for developing effective conservation strategies to protect these unique and vulnerable ecosystems. 4 Technological Advances in Comparative Genomics 4.1 Next-generation sequencing for case studies 4.1.1 Sequencing coral reef fish genomes Next-generation sequencing (NGS) has revolutionized the study of coral reef fish genomes, enabling researchers to uncover the genetic diversity and evolutionary history of these species. For instance, the development of universal PCR primers for metabarcoding environmental DNA (eDNA) from fishes has allowed for the detection of over 230 subtropical marine species, demonstrating the efficiency and sensitivity of NGS in biodiversity monitoring (Miya et al., 2015). Additionally, genome-wide sequencing approaches have provided new opportunities to understand both neutral and adaptive contributions to the genetic diversity of coral reef organisms, despite the challenges associated with aquatic environments (Bongaerts et al., 2021).
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