Dataset Information

Environment DNA Reveals Fish Diversity in a Canyon River within the Upper Pearl River Drainage.

ABSTRACT: Investigating fish diversity in canyon rivers through conventional fish surveys is challenging due to precipitous conditions, including steep slopes, rapid water flow, and complex habitats. Additionally, intensive construction of dams has further complicated the understanding of contemporary fish diversity in these rivers. In this study, we used the environmental DNA (eDNA) technique to assess fish diversity and examine the effects of dams on fish diversity in the Mabiehe River, a canyon river in the upper reaches of the Pearl River drainage. Water samples from 15 sampling sites were collected, yielding 9,356,148 valid sequences. Utilizing the NCBI public database, a total of 60 freshwater fish species were identified, with Carassius auratus, Cyprinus carpio, and Pelteobagrus fulvidraco being the most dominant species in the Mabiehe River. We also detected one nationally protected fish species, three provincially protected fish species, and six exotic species in this river. Furthermore, eDNA analyses demonstrated that the lotic river sections harbor more species and greater diversity than dammed sections, suggesting that dams might exert significant impacts on local fish diversity. Overall, this study supports the effectiveness of the eDNA technique as a complementary tool to traditional field surveys for monitoring fish biodiversity in canyon rivers.

SUBMITTER: Luo S

PROVIDER: S-EPMC11350740 | biostudies-literature | 2024 Aug

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Environment DNA Reveals Fish Diversity in a Canyon River within the Upper Pearl River Drainage.

Luo Si S Wang Meng M Ma Weizhong W Gu Dangen D Jin Zhijun Z Yang Ruiqi R Qian Zhen Z Song Chengwen C Wang Zexin Z Jin Shiyu S

Animals : an open access journal from MDPI 20240822 16

Investigating fish diversity in canyon rivers through conventional fish surveys is challenging due to precipitous conditions, including steep slopes, rapid water flow, and complex habitats. Additionally, intensive construction of dams has further complicated the understanding of contemporary fish diversity in these rivers. In this study, we used the environmental DNA (eDNA) technique to assess fish diversity and examine the effects of dams on fish diversity in the Mabiehe River, a canyon river i ...[more]

PMID: 39199966

Similar Datasets

Project description:BACKGROUND:Repetitive species-specific sound enables the identification of the presence and behavior of soniferous species by acoustic means. Passive acoustic monitoring has been widely applied to monitor the spatial and temporal occurrence and behavior of calling species. METHODS:Underwater biological sounds in the Pearl River Estuary, China, were collected using passive acoustic monitoring, with special attention paid to fish sounds. A total of 1,408 suspected fish calls comprising 18,942 pulses were qualitatively analyzed using a customized acoustic analysis routine. RESULTS:We identified a diversity of 66 types of fish sounds. In addition to single pulse, the sounds tended to have a pulse train structure. The pulses were characterized by an approximate 8 ms duration, with a peak frequency from 500 to 2,600 Hz and a majority of the energy below 4,000 Hz. The median inter-pulsepeak interval (IPPI) of most call types was 9 or 10 ms. Most call types with median IPPIs of 9 ms and 10 ms were observed at times that were exclusive from each other, suggesting that they might be produced by different species. According to the literature, the two section signal types of 1 + 1 and 1 + N10 might belong to big-snout croaker (Johnius macrorhynus), and 1 + N19 might be produced by Belanger's croaker (J. belangerii). DISCUSSION:Categorization of the baseline ambient biological sound is an important first step in mapping the spatial and temporal patterns of soniferous fishes. The next step is the identification of the species producing each sound. The distribution pattern of soniferous fishes will be helpful for the protection and management of local fishery resources and in marine environmental impact assessment. Since the local vulnerable Indo-Pacific humpback dolphin (Sousa chinensis) mainly preys on soniferous fishes, the fine-scale distribution pattern of soniferous fishes can aid in the conservation of this species. Additionally, prey and predator relationships can be observed when a database of species-identified sounds is completed.

Project description:The Merbok River (north-west of Peninsular Malaysia) is a mangrove estuary that provides habitat for over 100 species of fish, which are economically and ecologically important. Threats such as habitat loss and overfishing are becoming a great concern for fisheries conservation and management. The identification of larval fish in this estuarine system is important to complement information on the adults. This is because the data could inform the spawning behaviour, reproductive biology, selection of nursery grounds and migration route of fish. Such information is invaluable for fisheries and aquatic environmental monitoring, and thus for their conservation and management. However, identifying fish larvae is a challenging task based only on morphology and even traditional DNA barcoding. To address this, DNA metabarcoding was utilised to detect the diversity of fish in the Merbok River. To complete the study, the fish larvae were collected at six sampling sites of the river. The extracted larval DNA was amplified for the Cytochrome Oxidase subunit 1 (COI) and 12S ribosomal RNA (12S rRNA) genes based on the metabarcoding approach using shotgun sequencing on the next-generation sequencing (NGS) Illumina MiSeq platform. Eighty-nine species from 65 genera and 41 families were detected, with Oryzias javanicus, Oryzias dancena, Lutjanus argentimaculatus and Lutjanus malabaricus among the most common species. The lower diversity observed from previous morphological studies is suggested to be mainly due to seasonal variation over the sampling period between the two methods and limited 12S rRNA sequences in current databases. The metabarcode data and a validation Sanger sequencing step using 15 species-specific primer pairs detected three species in common: Oryzias javanicus, Decapterus maruadsi and Pennahia macrocephalus. Several discrepancies observed between the two molecular approaches could be attributed to contaminants during sampling and DNA extraction, which could mask the presence of target species, especially when DNA from the contaminants is more abundant than the target organisms. In conclusion, this rapid and cost-effective identification method using DNA metabarcoding allowed the detection of numerous fish species from bulk larval samples in the Merbok River. This method can be applied to other sites and other organisms of interest.

Project description:In recent decades, hypoxic areas have rapidly expanded worldwide in estuaries and coastal zones. The Pearl River Estuary (PRE), one of China's largest estuaries, experiences frequent seasonal hypoxia due to intense human activities and eutrophication. However, the ecological effects of hypoxia in the PRE, particularly on fish communities, remain unclear. To explore these effects, we collected fish community and environmental data in July 2021 during the summer hypoxia development period. The results revealed that bottom-layer dissolved oxygen (DO) in the PRE ranged from 0.08 to 5.71 mg/L, with extensive hypoxic zones (DO ≤ 2 mg/L) observed. Hypoxia has varied effects on fish community composition, distribution, species, and functional diversity in the PRE. A total of 104 fish species were collected in this study, with approximately 30 species (28.6%) exclusively found in hypoxic areas. Species responses to hypoxia varied: species such as Sardinella zunasi, Coilia mystus, and Nuchequula nuchalis were sensitive, while Decapterus maruadsi, Siganus fuscescens, and Lagocephalus spadiceus showed higher tolerance. Within the hypoxia area, dissolved oxygen was the main limiting factor for fish community diversity. Functional diversity (FDiv) decreased with higher dissolved oxygen levels, indicating a potential shift in the functional traits and ecological roles of fish species in response to changing oxygen conditions. Further analysis demonstrated that dissolved oxygen had a significantly stronger effect on fish community structure at hypoxic sites than in the whole PRE. Moreover, other environmental variables also had significant effects on the fish community structure and interacted with dissolved oxygen in the hypoxia area. These findings suggest that maintaining sufficient dissolved oxygen levels is essential for sustaining fish communities and ecosystem health in the PRE. This study provides novel insights into the effects of hypoxia on fish communities in estuarine ecosystems and has significant implications for the ecological health and management of the PRE.

Dataset Information

Environment DNA Reveals Fish Diversity in a Canyon River within the Upper Pearl River Drainage.

Publications

Environment DNA Reveals Fish Diversity in a Canyon River within the Upper Pearl River Drainage.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets