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Wang S, Wu D, Song Y, Wang T, Fan S, Wu E, Chen N, Xia W, Xu MN, Chen Z, Wen J, Zhang Y, Mo L, Xiang L. Application of environmental DNA metabarcoding to identify fish community characteristics in subtropical river systems. Ecol Evol 2024; 14:e11214. [PMID: 38725828 PMCID: PMC11079634 DOI: 10.1002/ece3.11214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 02/28/2024] [Accepted: 03/15/2024] [Indexed: 05/12/2024] Open
Abstract
Fish are vital in river ecosystems; however, traditional investigations of fish usually cause ecological damage. Extracting DNA from aquatic environments and identifying DNA sequences offer an alternative, noninvasive approach for detecting fish species. In this study, the effects of environmental DNA (eDNA), coupled with PCR and next-generation sequencing, and electrofishing for identifying fish community composition and diversity were compared. In three subtropical rivers of southern China, fish specimens and eDNA in water were collected along the longitudinal (upstream-downstream) gradient of the rivers. Both fish population parameters, including species abundance and biomass, and eDNA OTU richness grouped 38 sampling sites into eight spatial zones with significant differences in local fish community composition. Compared with order-/family-level grouping, genus-/species-level grouping could more accurately reveal the differences between upstream zones I-III, midstream zones IV-V, and downstream zones VI-VIII. From the headwaters to the estuary, two environmental gradients significantly influenced the longitudinal distribution of the fish species, including the first gradient composed of habitat and physical water parameters and the second gradient composed of chemical water parameters. The high regression coefficient of alpha diversity between eDNA and electrofishing methods as well as the accurate identification of dominant, alien, and biomarker species in each spatial zone indicated that eDNA could characterize fish community attributes at a level similar to that of traditional approaches. Overall, our results demonstrated that eDNA metabarcoding can be used as an effective tool for revealing fish composition and diversity, which is important for using the eDNA technique in aquatic field monitoring.
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Affiliation(s)
- Sai Wang
- State Key Laboratory of Marine Resource Utilization in South China SeaHainan UniversityHaikouChina
| | - Dong‐Hai Wu
- State Key Laboratory of Marine Resource Utilization in South China SeaHainan UniversityHaikouChina
- College of Ecology and EnvironmentHainan UniversityHaikouChina
| | - Yong‐Duo Song
- State Key Laboratory of Marine Resource Utilization in South China SeaHainan UniversityHaikouChina
| | - Tuan‐Tuan Wang
- College of Ecology and EnvironmentHainan UniversityHaikouChina
- Key Laboratory of Agro‐Forestry Environmental Processes and Ecological Regulation of Hainan ProvinceHainan UniversityHaikouChina
| | - Shi‐Di Fan
- State Key Laboratory of Marine Resource Utilization in South China SeaHainan UniversityHaikouChina
| | - En‐Ni Wu
- State Key Laboratory of Marine Resource Utilization in South China SeaHainan UniversityHaikouChina
| | - Nan‐Lin Chen
- State Key Laboratory of Marine Resource Utilization in South China SeaHainan UniversityHaikouChina
| | - Wen‐Tong Xia
- State Key Laboratory of Marine Resource Utilization in South China SeaHainan UniversityHaikouChina
| | - Min N. Xu
- State Key Laboratory of Marine Resource Utilization in South China SeaHainan UniversityHaikouChina
| | - Zhong‐Bing Chen
- Department of Applied·Ecology, Faculty of Environmental SciencesCzech University of Life Sciences PraguePraha‐SuchdolCzech Republic
| | - Jing Wen
- State Key Laboratory of Marine Resource Utilization in South China SeaHainan UniversityHaikouChina
- Hainan Qingxiao Environmental Testing Co., Ltd.SanyaChina
- Hainan Qianchao Ecological Technology Co., Ltd.SanyaChina
| | - Yang Zhang
- Shenzhen Guanghuiyuan Environment Water Co., Ltd.ShenzhenChina
| | - Ling Mo
- Hainan Research Academy of Environmental SciencesHaikouChina
| | - Lei Xiang
- Department of EcologyJinan UniversityGuangzhouChina
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Wei H, Liu C, Cui X, Shen Z, Wang J. Distribution characteristics of microorganisms in sediments of Dagu River and their biological indicator function for evaluating eco-environmental quality of rural river. ENVIRONMENTAL RESEARCH 2024; 245:118032. [PMID: 38159669 DOI: 10.1016/j.envres.2023.118032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 12/20/2023] [Accepted: 12/22/2023] [Indexed: 01/03/2024]
Abstract
The microorganisms in sediments play a crucial role in biogeochemical cycle processes, and numerous studies have shown that microbial community is closely related to environmental factors. However, the usability of sediment microorganisms to evaluate the eco-environment quality of rural rivers has not been adequately explored. This study investigated the distribution characteristics and response of sediment microorganisms to environmental parameters and benthic organisms. Based on the environmental parameters and benthic community indices, the 12 stations were divided into high-polluted group A, moderate-polluted group B and low-polluted group C. Station DG01 and DG02 in group A had the highest level of As and Ni pollution and nutrient concentration, and DG09 in group A had the lowest benthic diversity. Correspondingly, group A had the lowest abundance of Proteobacteria, which has a higher requirement for the environment than Planctomycetes. Group B had the highest sulfide level (97.45 mg/kg), and bacteria (Thiobacillus, Sulfurisoma and Sulfuritalea) with genes involved in sulfur cycling were more enriched in this group. Group C had the lowest level of total nitrogen (243.36 mg/kg), and Rhodanobacteraceae in Xanthomonadales might be a key bioindicator for low nitrogen. In addition, Chlorophyta was found to be more susceptible to heavy metals, and moreover co-occurrence networks showed that microeukaryotes were more sensitive to heavy metal pollution compared to benthic animals and prokaryotes. Therefore, this study suggested that benthic microorganisms especially microeukaryotes could be used as good indicators for evaluating the eco-environmental quality of rural rivers.
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Affiliation(s)
- Hongqing Wei
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Cong Liu
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Xumeng Cui
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Zhonghua Shen
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China; Shandong Bureau Test Center of China General Administration of Metallurgical Geology, Jinan, 250013, China.
| | - Jun Wang
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China.
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Zhang J, Xu J, Tan X, Zhang Q. Nitrogen loadings affect trophic structure in stream food webs on the Tibetan Plateau, China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 844:157018. [PMID: 35772539 DOI: 10.1016/j.scitotenv.2022.157018] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 06/22/2022] [Accepted: 06/24/2022] [Indexed: 06/15/2023]
Abstract
Anthropogenic activities, such as agricultural and industrial development, have increased nutrient inputs into waterways, which affect trophic interactions and the flow of energy through food webs in the aquatic ecosystems. However, the responses of food web structure and function to specific anthropogenic stressors in the alpine stream systems remain unclear. Here, we studied the stream food webs in the Lhasa River on the Tibetan Plateau, China. We measured the isotopic ratios (δ13C and δ15N) of macroinvertebrate and fish functional feeding groups (FFGs) and their basal resources in the streams. Dietary contributions of basal resources to consumers and food web metrics including trophic length, diversity, and redundancy were used to quantify changes in stream food webs in response to anthropogenic disturbance. Dietary analysis showed that allochthonous resources contributed more than autochthonous resources to macroinvertebrate primary consumers regardless of the disturbance intensity in the adjacent land areas. Anthropogenic activities increased the δ15N values in epilithic algae and isotopic variation in basal resources and fish but reduced the trophic length and redundancy (i.e., fewer species or taxon at each trophic level) in food webs. Additionally, the total nitrogen concentration in waters was the most important environmental variable affecting trophic diversity and redundancy. Therefore, the reduction of nitrogen inputs into streams is critical for sustainable river management and biodiversity conservation in the streams on the Tibetan Plateau.
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Affiliation(s)
- Jian Zhang
- Research Center for Ecology and Environment of Qinghai-Tibetan Plateau, Tibet University, Lhasa 850000, Tibet, China; College of Science, Tibet University, Lhasa 850000, Tibet, China; Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan, Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
| | - Jilei Xu
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan, Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
| | - Xiang Tan
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan, Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China.
| | - Quanfa Zhang
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan, Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
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Wang S, Wang T, Xia W, Chen Z, Stewart SD, Yang F, Cheng G, Wang X, Wang D, Xie S. Longitudinal pattern of resource utilization by aquatic consumers along a disturbed subtropical urban river: Estimating the relative contribution of resources with stable isotope analysis. Ecol Evol 2021; 11:16763-16775. [PMID: 34938471 PMCID: PMC8668758 DOI: 10.1002/ece3.8304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 09/30/2021] [Accepted: 10/15/2021] [Indexed: 11/30/2022] Open
Abstract
The utilization of food resources by aquatic consumers reflects the structure and functioning of river food webs. In lotic water systems, where food availability and predator-prey relationships vary with gradient changes in physical conditions, understanding diet assimilation by local communities is important for ecosystem conservation. In the subtropical Liuxi River, southern China, the relative contribution of basal resources to the diet assimilation of functional feeding groups (FFGs) was determined by stable carbon (13C) and nitrogen (15N) isotope analyses. The output of Bayesian mixing models showed that diatom-dominated periphyton (epilithic biofilm), aquatic C3 plants (submerged hydrophytes), and suspended particulate organic matter (SPOM) associated with terrestrial C3 plants contributed the most to the diet assimilation of FFGs in the upper, middle, and lower reaches, respectively. The relative contribution of consumer diet assimilation was weighted by the biomass (wet weight, g/m2) of each FFG to reflect resource utilization at the assemblage level. From the upper to the lower reaches, the spatial variation in the diet assimilation of fish and invertebrate assemblages could be summarized as a longitudinal decrease in periphyton (from 57%-76% to <3%) and an increase in SPOM (from <7% to 51%-68%) with a notable midstream increase in aquatic C3 plants (23%-48%). These results indicate that instream consumers in the Liuxi River rely more on autochthonous production (e.g., periphyton and submerged hydrophytes) than on terrestrially derived allochthonous matter (e.g., terrestrial plants). The pattern of resource utilization by consumers in the mid-upper Liuxi River is consistent with findings from other open subtropical and neotropical rivers and provides evidence for the riverine productivity model. Our study indicates that protecting inherent producers in rivers (e.g., periphyton and submerged hydrophytes) and restoring their associated habitats (e.g., riffles with cobble substrate) are conducive to aquatic ecosystem management.
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Affiliation(s)
- Sai Wang
- State Key Laboratory of Marine Resource Utilization in South China SeaHainan UniversityHaikouChina
| | - Tuan‐Tuan Wang
- College of Ecology and EnvironmentHainan UniversityHaikouChina
| | - Wen‐Tong Xia
- State Key Laboratory of Marine Resource Utilization in South China SeaHainan UniversityHaikouChina
| | - Zhong‐Bing Chen
- Department of Applied Ecology, Faculty of Environmental SciencesCzech University of Life Sciences PraguePragueCzech Republic
| | | | - Feng‐Juan Yang
- China Water Resources Pearl River Planning Surveying & Designing Co., Ltd.GuangzhouChina
| | - Gong Cheng
- Shenzhen Academy of Environmental SciencesShenzhenChina
| | - Xiao‐Di Wang
- State Key Laboratory of Marine Resource Utilization in South China SeaHainan UniversityHaikouChina
| | - Ding‐Ying Wang
- State Key Laboratory of Marine Resource Utilization in South China SeaHainan UniversityHaikouChina
| | - Song‐Guang Xie
- State Key Laboratory of Marine Resource Utilization in South China SeaHainan UniversityHaikouChina
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Asadi Sharif E, Yahyavi B, Bayrami A, Rahim Pouran S, Atazadeh E, Singh R, Abdul Raman AA. Physicochemical and biological status of Aghlagan river, Iran: effects of seasonal changes and point source pollution. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:15339-15349. [PMID: 33236302 DOI: 10.1007/s11356-020-11660-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 11/12/2020] [Indexed: 06/11/2023]
Abstract
Although the macroinvertebrates have been widely used as bio-indicator for river water quality assessment in developed countries, its application is new in Iran and data on the health status of the most ecologically important rivers in Iran is scarce. The present study aimed at monitoring and assessing the ecological quality of Aghlagan river, northwest of Iran, using integrated physicochemical-biological approaches. A total of 14,423 samplings were carried out from the headwater to downstream sites at four stations (S1, 2, 3, 4) by a Surber sampler (30 cm × 30 cm) from June 2018 to April 2019. The results obtained from macroinvertebrate biotic index revealed that the genera of Gammarus (Amphipoda) and Baetis (Ephemeroptera) were the most abundant in all seasons. The PAST software was applied to analyze the diversity indices (Shannon-Weiner diversity, Evenness, and Simpson indices). Based on the cluster analysis, S3 established the least similarity to other stations. The average frequency of each macroinvertebrate species was determined by one-factor analysis of similarities (ANOSIM). In accordance with canonical correspondence analysis (CCA), temperature and phosphate were found as the dominant factors effecting the macroinvertebrate assemblage and distribution. Moreover, the results obtained from the biological indices concluded very good quality of S4 by Helsinhoff and EPT indices and fair quality using BMWP index. The data on the macrobenthos assemblage and dynamics in the Aghlagan river across a hydraulic gradient provided useful information on water management efforts that assist us to find sustainable solutions for the enhanced quality of the river by balancing environmental and human values.
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Affiliation(s)
- Ehsan Asadi Sharif
- Department of Fisheries Sciences, Faculty of Natural Resources, University of Guilan, Guilan, Rasht, Iran
| | - Behnaz Yahyavi
- Department of Biology, Faculty of Science, University of Mohaghegh Ardabili, Ardabil, Iran
| | - Abolfazl Bayrami
- Department of Biology, Faculty of Science, University of Mohaghegh Ardabili, Ardabil, Iran.
| | - Shima Rahim Pouran
- Department of Environmental and Occupational Health, Social Determinants of Health Research Centre, Ardabil University of Medical Sciences, Ardabil, Iran.
| | - Ehsan Atazadeh
- Department of Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran
| | - Ramesh Singh
- Department of Mechanical Engineering, Centre of Advanced Manufacturing and Materials Processing, Faculty of Engineering, University of Malaya, 50603, Kuala Lumpur, Malaysia
- Department of Mechanical Engineering, Faculty of Engineering, Universiti Teknologi Brunei, Tunku Highway, Gadong, BE1410, Darussalam, Brunei
| | - Abdul Aziz Abdul Raman
- Department of Chemical Engineering, Faculty of Engineering, University of Malaya, 50603, Kuala Lumpur, Malaysia
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