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Xiong W, Chen T, Du X, Hou L, Chen Y, Han JL, Zhan A. Ecological impacts of treated effluent on multitrophic biodiversity and their interactions. ENVIRONMENTAL RESEARCH 2025; 277:121585. [PMID: 40216057 DOI: 10.1016/j.envres.2025.121585] [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: 02/15/2025] [Revised: 04/06/2025] [Accepted: 04/09/2025] [Indexed: 04/15/2025]
Abstract
The reuse of water, particularly treated effluent from wastewater treatment plants (WWTPs), is a crucial and sustainable strategy for mitigating water scarcity, especially in megacities with high water demand and limited resources. However, the ecological risks associated with effluent discharge into receiving waterbodies have gained significant global attention. Understanding the dynamic effects of WWTP effluent on multi-trophic groups and their interactions is essential for assessing ecological impacts in aquatic ecosystems and informing management strategies. In this study, we examined five taxonomic groups representing different trophic levels of the freshwater food web - bacteria (decomposers), algae (primary producers), zooplankton (primary consumers), and benthic macroinvertebrates and fish (predators) - across two rivers to elucidate ecological responses to WWTP effluent from a multi-trophic perspective. Our results revealed significant but variable biological responses among these groups, depending on river conditions and trophic level. In the nutrient-rich river, primary consumers (zooplankton) were most affected, whereas in the nutrient-poor river, primary producers (algae) exhibited the strongest responses primarily derived from environmental disturbances. Notably, interactions between environmental variables and taxa were highly diverse, with trophic dynamics influenced by both bottom-up and top-down processes in the nutrient-rich river, whereas bottom-up effects dominated in the nutrient-poor river. Furthermore, niche overlap in algae-zooplankton networks was higher in the nutrient-rich river than in the nutrient-poor river. This study underscores the importance of integrating multi-trophic biodiversity profiling and trophic interaction analyses to comprehensively assess the ecological effects of WWTP effluent in receiving aquatic ecosystems with contrasting environmental contexts. Our findings highlight the importance of conservation and sustainable management practices, especially in urban aquatic ecosystems located in (semi-)arid regions that experience prolonged periods of low precipitation.
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Affiliation(s)
- Wei Xiong
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, 100049, China
| | - Ting Chen
- College of Resources Environment and Tourism, Capital Normal University, Beijing, 100048, China
| | - Xun Du
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, 100049, China
| | - Lin Hou
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, 100049, China
| | - Yiyong Chen
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Jing-Long Han
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology (Shenzhen), Shenzhen, 518055, China
| | - Aibin Zhan
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, 100049, China.
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2
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Chang C, Ren M, Wang H, Ye S, Tang X, He D, Hu E, Li M, Pan B. Riverine network size determined major driving factors of the composition and diversity of aquatic invertebrate communities in a multi-tributary mountain river basin. WATER RESEARCH 2025; 276:123257. [PMID: 39954458 DOI: 10.1016/j.watres.2025.123257] [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: 09/20/2024] [Revised: 12/18/2024] [Accepted: 02/08/2025] [Indexed: 02/17/2025]
Abstract
Revealing the spatial variation of aquatic invertebrates and their response to biotic and abiotic factors, from headwaters to estuaries, is crucial for understanding their successional patterns and protecting watershed ecosystems. This study aimed to explore the biogeographic patterns and identify the primary drivers of invertebrate community structure across river networks of varying sizes using environmental DNA (eDNA) technology. To assess the contribution of biotic and abiotic factors to invertebrate communities, we collected six categories of abiotic factors: geography, climate, hydro-morphology, human footprint index, land use, and water quality. For biotic factors, four microbial groups including archaea, bacteria, fungi, and protists were identified using eDNA techniques. Water samples were collected from a total of 187 sample sites in the upper Hanjiang River basin (China) during two seasons (Spring and Autumn), covering the transition from the headwater tributaries to the lower reaches of the main channel. The results revealed that environmental factors explained approximately 6.5 times more variation in invertebrate eDNA communities than geographic factors. Water quality and biotic factors had strong explanatory power for invertebrate eDNA diversity. Ecological succession of invertebrate eDNA communities along the river continuum showed a shift from Arthropoda-dominated communities in the headwaters to a co-dominance of Arthropoda, Rotifera, and Cnidaria downstream. The cumulative dendritic distance upstream, representing the location of each sampling site within the river network, emerged as the most predictive spatial feature. Significant differences were observed in the dominant environmental factors influencing community diversity across different river network sizes. In small river networks, invertebrate eDNA diversity was primarily influenced by biotic factors, while in medium-sized networks, it was shaped by a combination of biotic factors and water quality. In large river networks, water quality emerged as the primary driver. These findings suggest that invertebrate communities throughout the Hanjiang River basin undergo ecological succession along the river continuum, primarily shaped by environmental factors related to river network size.
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Affiliation(s)
- Chao Chang
- College of Natural Resources and Environment, Northwest A & F University, Yangling 712100, Shaanxi, China
| | - Mi Ren
- College of Natural Resources and Environment, Northwest A & F University, Yangling 712100, Shaanxi, China
| | - Han Wang
- College of Natural Resources and Environment, Northwest A & F University, Yangling 712100, Shaanxi, China
| | - Sisi Ye
- College of Natural Resources and Environment, Northwest A & F University, Yangling 712100, Shaanxi, China
| | - Xiaofeng Tang
- College of Natural Resources and Environment, Northwest A & F University, Yangling 712100, Shaanxi, China
| | - Ding He
- Department of Ocean Science and Center for Ocean Research in Hong Kong and Macau, The Hong Kong University of Science and Technology, Hong Kong SAR, China; State Key Laboratory of Geomechanics and Geotechnical Engineering, Institute of Rock and Soil Mechanics, Chinese Academy of Science, Wuhan 430071, China
| | - En Hu
- Shaanxi Provincial Academy of Environmental Science, Xi'an 710061, Shaanxi, China.
| | - Ming Li
- College of Natural Resources and Environment, Northwest A & F University, Yangling 712100, Shaanxi, China.
| | - Baozhu Pan
- State Key Laboratory of Eco-hydraulics in the Northwest Arid Region of China, Xi'an University of Technology, Xi'an, 710048, Shaanxi, China
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Sun X, Hu S, He R, Zeng J, Zhao D. Ecological restoration enhanced the stability of epiphytic microbial food webs of submerged macrophytes: Insights from predation characteristics of epiphytic predators. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 948:174547. [PMID: 38992355 DOI: 10.1016/j.scitotenv.2024.174547] [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: 04/24/2024] [Revised: 07/03/2024] [Accepted: 07/04/2024] [Indexed: 07/13/2024]
Abstract
The application of various submerged macrophytes for ecological restoration has gained increasing attention in urban lake ecosystems. The multitrophic microbial communities that colonized in various submerged macrophytes constitute microbial food webs through trophic cascade effects, which affect the biogeochemical cycles of the lake ecosystem and directly determine the effects of ecological restoration. Therefore, it is essential to reveal the diversity, composition, assembly processes, and stability of the microbial communities within epiphytic food webs of diverse submerged macrophytes under eutrophication and ecological restoration scenarios. In this study, we explored the epiphytic microbial food webs of Vallisneria natans and Hydrilla verticillata in both eutrophic and ecological restoration regions. The obtained results indicated that the two regions with different nutrient levels remarkably affected the diversity and composition of epiphytic multitrophic microbial communities of submerged macrophytes, among them, the community composition of epiphytic predators were more prone to change. Secondly, environmental filtering effects played a more important role in driving the community assembly of epiphytic predators than that of prey. Furthermore, the generality and intraguild predation of epiphytic predators were significantly improved within ecological restoration regions, which increased the stability of epiphytic microbial food webs. Additionally, compared with Hydrilla verticillata, the epiphytic microbial food webs of Vallisneria natans exhibited higher multitrophic diversity and higher network stability regardless of regions. Overall, this study focused on the role of the epiphytic microbial food webs of submerged macrophytes in ecological restoration and uncovered the potential of epiphytic predators to enhance the stability of microbial food webs, which may provide new insights into the development of ecological restoration strategies.
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Affiliation(s)
- Xiaojian Sun
- Joint International Research Laboratory of Global Change and Water Cycle, the National Key Laboratory of Water Disaster Prevention, Hohai University, Nanjing 210098, China; State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Siwen Hu
- Joint International Research Laboratory of Global Change and Water Cycle, the National Key Laboratory of Water Disaster Prevention, Hohai University, Nanjing 210098, China; State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Rujia He
- Joint International Research Laboratory of Global Change and Water Cycle, the National Key Laboratory of Water Disaster Prevention, Hohai University, Nanjing 210098, China; State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Jin Zeng
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China; Sino-Danish Centre for Education and Research, University of Chinese Academy of Sciences, Beijing 100039, China; Poyang Lake Wetland Research Station, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Jiujiang 332899, China
| | - Dayong Zhao
- Joint International Research Laboratory of Global Change and Water Cycle, the National Key Laboratory of Water Disaster Prevention, Hohai University, Nanjing 210098, China; College of Geography and Remote Sensing, Hohai University, Nanjing 210098, China.
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4
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Zhang Y, Qiu Y, Liu K, Zhong W, Yang J, Altermatt F, Zhang X. Evaluating eDNA and eRNA metabarcoding for aquatic biodiversity assessment: From bacteria to vertebrates. ENVIRONMENTAL SCIENCE AND ECOTECHNOLOGY 2024; 21:100441. [PMID: 39027464 PMCID: PMC11254946 DOI: 10.1016/j.ese.2024.100441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 06/10/2024] [Accepted: 06/10/2024] [Indexed: 07/20/2024]
Abstract
The monitoring and management of aquatic ecosystems depend on precise estimates of biodiversity. Metabarcoding analyses of environmental nucleic acids (eNAs), including environmental DNA (eDNA) and environmental RNA (eRNA), have garnered attention for their cost-effective and non-invasive biomonitoring capabilities. However, the accuracy of biodiversity estimates obtained through eNAs can vary among different organismal groups. Here we evaluate the performance of eDNA and eRNA metabarcoding across nine organismal groups, ranging from bacteria to terrestrial vertebrates, in three cross-sections of the Yangtze River, China. We observe robust complementarity between eDNA and eRNA data. The relative detectability of eNAs was notably influenced by major taxonomic groups and organismal sizes, with eDNA providing more robust signals for larger organisms. Both eDNA and eRNA exhibited similar cross-sectional and longitudinal patterns. However, the detectability of larger organisms declined in eRNA metabarcoding, possibly due to differential RNA release and decay among different organismal groups or sizes. While underscoring the potential of eDNA and eRNA in large river biomonitoring, we emphasize the need for differential interpretation of eDNA versus eRNA data. This highlights the importance of careful method selection and interpretation in biomonitoring studies.
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Affiliation(s)
- Yan Zhang
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing, 210023, China
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland
- Department of Aquatic Ecology, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - Yu Qiu
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing, 210023, China
| | - Kai Liu
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, China
| | - Wenjun Zhong
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing, 210023, China
| | - Jianghua Yang
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing, 210023, China
| | - Florian Altermatt
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland
- Department of Aquatic Ecology, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - Xiaowei Zhang
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing, 210023, China
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5
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Blackman RC, Carraro L, Keck F, Altermatt F. Measuring the state of aquatic environments using eDNA-upscaling spatial resolution of biotic indices. Philos Trans R Soc Lond B Biol Sci 2024; 379:20230121. [PMID: 38705183 PMCID: PMC11070250 DOI: 10.1098/rstb.2023.0121] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 12/10/2023] [Indexed: 05/07/2024] Open
Abstract
Aquatic macroinvertebrates, including many aquatic insect orders, are a diverse and ecologically relevant organismal group yet they are strongly affected by anthropogenic activities. As many of these taxa are highly sensitive to environmental change, they offer a particularly good early warning system for human-induced change, thus leading to their intense monitoring. In aquatic ecosystems there is a plethora of biotic monitoring or biomonitoring approaches, with more than 300 assessment methods reported for freshwater taxa alone. Ultimately, monitoring of aquatic macroinvertebrates is used to calculate ecological indices describing the state of aquatic systems. Many of the methods and indices used are not only hard to compare, but especially difficult to scale in time and space. Novel DNA-based approaches to measure the state and change of aquatic environments now offer unprecedented opportunities, also for possible integration towards commonly applicable indices. Here, we first give a perspective on DNA-based approaches in the monitoring of aquatic organisms, with a focus on aquatic insects, and how to move beyond traditional point-based biotic indices. Second, we demonstrate a proof-of-concept for spatially upscaling ecological indices based on environmental DNA, demonstrating how integration of these novel molecular approaches with hydrological models allows an accurate evaluation at the catchment scale. This article is part of the theme issue 'Towards a toolkit for global insect biodiversity monitoring'.
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Affiliation(s)
- Rosetta C. Blackman
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstr. 190, Zürich 8057, Switzerland
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, Dübendorf 8600, Switzerland
| | - Luca Carraro
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstr. 190, Zürich 8057, Switzerland
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, Dübendorf 8600, Switzerland
| | - François Keck
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstr. 190, Zürich 8057, Switzerland
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, Dübendorf 8600, Switzerland
| | - Florian Altermatt
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstr. 190, Zürich 8057, Switzerland
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, Dübendorf 8600, Switzerland
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6
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Zhang SY, Yan Q, Zhao J, Liu Y, Yao M. Distinct multitrophic biodiversity composition and community organization in a freshwater lake and a hypersaline lake on the Tibetan Plateau. iScience 2024; 27:110124. [PMID: 38957787 PMCID: PMC11217615 DOI: 10.1016/j.isci.2024.110124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 04/07/2024] [Accepted: 05/24/2024] [Indexed: 07/04/2024] Open
Abstract
Alpine lakes play pivotal roles in plateau hydrological processes but are highly sensitive to climate change, yet we lack comprehensive knowledge of their multitrophic biodiversity patterns. Here, we compared the biodiversity characteristics of diverse taxonomic groups across water depths and in surface sediments from a freshwater lake and a hypersaline lake on the northwestern Tibetan Plateau. Using multi-marker environmental DNA metabarcoding, we detected 134 cyanobacteria, 443 diatom, 1,519 invertebrate, and 28 vertebrate taxa. Each group had a substantially different community composition in the two lakes, and differences were also found between water and sediments within each lake. Cooccurrence network analysis revealed higher network complexity, lower modularity, and fewer negative cohesions in the hypersaline lake, suggesting that high salinity may destabilize ecological networks. Our results provide the first holistic view of Tibetan lake biodiversity under contrasting salinity levels and reveal structural differences in the ecological networks that may impact ecosystem resilience.
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Affiliation(s)
- Si-Yu Zhang
- School of Life Sciences, Peking University, Beijing 100871, China
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China
| | - Qi Yan
- Center for Pan-Third Pole Environment, Lanzhou University, Lanzhou 730000, China
| | - Jindong Zhao
- School of Life Sciences, Peking University, Beijing 100871, China
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China
| | - Yongqin Liu
- Center for Pan-Third Pole Environment, Lanzhou University, Lanzhou 730000, China
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 101408, China
| | - Meng Yao
- School of Life Sciences, Peking University, Beijing 100871, China
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China
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Blackman R, Couton M, Keck F, Kirschner D, Carraro L, Cereghetti E, Perrelet K, Bossart R, Brantschen J, Zhang Y, Altermatt F. Environmental DNA: The next chapter. Mol Ecol 2024; 33:e17355. [PMID: 38624076 DOI: 10.1111/mec.17355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 03/28/2024] [Accepted: 04/03/2024] [Indexed: 04/17/2024]
Abstract
Molecular tools are an indispensable part of ecology and biodiversity sciences and implemented across all biomes. About a decade ago, the use and implementation of environmental DNA (eDNA) to detect biodiversity signals extracted from environmental samples opened new avenues of research. Initial eDNA research focused on understanding population dynamics of target species. Its scope thereafter broadened, uncovering previously unrecorded biodiversity via metabarcoding in both well-studied and understudied ecosystems across all taxonomic groups. The application of eDNA rapidly became an established part of biodiversity research, and a research field by its own. Here, we revisit key expectations made in a land-mark special issue on eDNA in Molecular Ecology in 2012 to frame the development in six key areas: (1) sample collection, (2) primer development, (3) biomonitoring, (4) quantification, (5) behaviour of DNA in the environment and (6) reference database development. We pinpoint the success of eDNA, yet also discuss shortfalls and expectations not met, highlighting areas of research priority and identify the unexpected developments. In parallel, our retrospective couples a screening of the peer-reviewed literature with a survey of eDNA users including academics, end-users and commercial providers, in which we address the priority areas to focus research efforts to advance the field of eDNA. With the rapid and ever-increasing pace of new technical advances, the future of eDNA looks bright, yet successful applications and best practices must become more interdisciplinary to reach its full potential. Our retrospect gives the tools and expectations towards concretely moving the field forward.
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Affiliation(s)
- Rosetta Blackman
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland
| | - Marjorie Couton
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland
| | - François Keck
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland
| | - Dominik Kirschner
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- Department of Environmental Systems Science, Institute of Terrestrial Ecosystems, Ecosystems and Landscape Evolution, ETH Zürich, Zürich, Switzerland
- Department of Landscape Dynamics & Ecology, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | - Luca Carraro
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland
| | - Eva Cereghetti
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland
| | - Kilian Perrelet
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland
- Department of Biodiversity and Conservation Biology, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
- Department of Urban Water Management, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - Raphael Bossart
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - Jeanine Brantschen
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland
| | - Yan Zhang
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing, China
| | - Florian Altermatt
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland
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Perry WB, Seymour M, Orsini L, Jâms IB, Milner N, Edwards F, Harvey R, de Bruyn M, Bista I, Walsh K, Emmett B, Blackman R, Altermatt F, Lawson Handley L, Mächler E, Deiner K, Bik HM, Carvalho G, Colbourne J, Cosby BJ, Durance I, Creer S. An integrated spatio-temporal view of riverine biodiversity using environmental DNA metabarcoding. Nat Commun 2024; 15:4372. [PMID: 38782932 PMCID: PMC11116482 DOI: 10.1038/s41467-024-48640-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 05/09/2024] [Indexed: 05/25/2024] Open
Abstract
Anthropogenically forced changes in global freshwater biodiversity demand more efficient monitoring approaches. Consequently, environmental DNA (eDNA) analysis is enabling ecosystem-scale biodiversity assessment, yet the appropriate spatio-temporal resolution of robust biodiversity assessment remains ambiguous. Here, using intensive, spatio-temporal eDNA sampling across space (five rivers in Europe and North America, with an upper range of 20-35 km between samples), time (19 timepoints between 2017 and 2018) and environmental conditions (river flow, pH, conductivity, temperature and rainfall), we characterise the resolution at which information on diversity across the animal kingdom can be gathered from rivers using eDNA. In space, beta diversity was mainly dictated by turnover, on a scale of tens of kilometres, highlighting that diversity measures are not confounded by eDNA from upstream. Fish communities showed nested assemblages along some rivers, coinciding with habitat use. Across time, seasonal life history events, including salmon and eel migration, were detected. Finally, effects of environmental conditions were taxon-specific, reflecting habitat filtering of communities rather than effects on DNA molecules. We conclude that riverine eDNA metabarcoding can measure biodiversity at spatio-temporal scales relevant to species and community ecology, demonstrating its utility in delivering insights into river community ecology during a time of environmental change.
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Affiliation(s)
- William Bernard Perry
- Molecular Ecology and Evolution at Bangor (MEEB), School of Biological Sciences, Bangor University, Bangor, Gwynedd, LL57 2UW, UK.
- Water Research Institute, Cardiff University, Cardiff, CF10 3AX, UK.
| | | | - Luisa Orsini
- Environmental Genomics Group, School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Ifan Bryn Jâms
- Water Research Institute, Cardiff University, Cardiff, CF10 3AX, UK
| | - Nigel Milner
- Molecular Ecology and Evolution at Bangor (MEEB), School of Biological Sciences, Bangor University, Bangor, Gwynedd, LL57 2UW, UK
| | - François Edwards
- APEM Ltd, A17 Embankment Business Park, Heaton Mersey, Manchester, SK4 3GN, UK
| | - Rachel Harvey
- Centre for Ecology & Hydrology, Environment Centre Wales, Bangor, LL57 2UW, UK
| | - Mark de Bruyn
- Australian Research Centre for Human Evolution, School of Environment and Science, Griffith University, Queensland, 4111, Australia
| | - Iliana Bista
- LOEWE Centre for Translational Biodiversity Genomics, 60325, Frankfurt, Germany
- Senckenberg Research Institute, 60325, Frankfurt, Germany
- Naturalis Biodiversity Center, Darwinweg 2, 2333, Leiden, Netherlands
- Wellcome Sanger Institute, Tree of Life, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Kerry Walsh
- Environment Agency, Horizon House, Deanery Road, Bristol, BS1 5AH, UK
| | - Bridget Emmett
- Centre for Ecology & Hydrology, Environment Centre Wales, Bangor, LL57 2UW, UK
| | - Rosetta Blackman
- Department of Aquatic Ecology, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, CH-8600, Dübendorf, Switzerland
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057, Zürich, Switzerland
- Evolutionary Biology Group (@EvoHull), Department of Biological and Marine Sciences, University of Hull (UoH), Cottingham Road, Hull, HU6 7RX, UK
| | - Florian Altermatt
- Department of Aquatic Ecology, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, CH-8600, Dübendorf, Switzerland
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057, Zürich, Switzerland
| | - Lori Lawson Handley
- Evolutionary Biology Group (@EvoHull), Department of Biological and Marine Sciences, University of Hull (UoH), Cottingham Road, Hull, HU6 7RX, UK
| | - Elvira Mächler
- Department of Aquatic Ecology, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, CH-8600, Dübendorf, Switzerland
| | - Kristy Deiner
- Institute of Biogeochemistry and Pollutant Dynamics (IBP), ETH Zurich, Zurich, Switzerland
| | - Holly M Bik
- Department of Marine Sciences and Institute of Bioinformatics, University of Georgia, Georgia, USA
| | - Gary Carvalho
- Molecular Ecology and Evolution at Bangor (MEEB), School of Biological Sciences, Bangor University, Bangor, Gwynedd, LL57 2UW, UK
| | - John Colbourne
- Environmental Genomics Group, School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Bernard Jack Cosby
- Centre for Ecology & Hydrology, Environment Centre Wales, Bangor, LL57 2UW, UK
| | - Isabelle Durance
- Water Research Institute, Cardiff University, Cardiff, CF10 3AX, UK
| | - Simon Creer
- Molecular Ecology and Evolution at Bangor (MEEB), School of Biological Sciences, Bangor University, Bangor, Gwynedd, LL57 2UW, UK.
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9
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Talluto L, del Campo R, Estévez E, Altermatt F, Datry T, Singer G. Towards (better) fluvial meta-ecosystem ecology: a research perspective. NPJ BIODIVERSITY 2024; 3:3. [PMID: 39050515 PMCID: PMC11263126 DOI: 10.1038/s44185-023-00036-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 12/22/2023] [Indexed: 07/27/2024]
Abstract
Rivers are an important component of the global carbon cycle and contribute to atmospheric carbon exchange disproportionately to their total surface area. Largely, this is because rivers efficiently mobilize, transport and metabolize terrigenous organic matter (OM). Notably, our knowledge about the magnitude of globally relevant carbon fluxes strongly contrasts with our lack of understanding of the underlying processes that transform OM. Ultimately, OM processing en route to the oceans results from a diverse assemblage of consumers interacting with an equally diverse pool of resources in a spatially complex network of heterogeneous riverine habitats. To understand this interaction between consumers and OM, we must therefore account for spatial configuration, connectivity, and landscape context at scales ranging from local ecosystems to entire networks. Building such a spatially explicit framework of fluvial OM processing across scales may also help us to better predict poorly understood anthropogenic impacts on fluvial carbon cycling, for instance human-induced fragmentation and changes to flow regimes, including intermittence. Moreover, this framework must also account for the current unprecedented human-driven loss of biodiversity. This loss is at least partly due to mechanisms operating across spatial scales, such as interference with migration and habitat homogenization, and comes with largely unknown functional consequences. We advocate here for a comprehensive framework for fluvial networks connecting two spatially aware but disparate lines of research on (i) riverine metacommunities and biodiversity, and (ii) the biogeochemistry of rivers and their contribution to the global carbon cycle. We argue for a research agenda focusing on the regional scale-that is, of the entire river network-to enable a deeper mechanistic understanding of naturally arising biodiversity-ecosystem functioning coupling as a major driver of biogeochemically relevant riverine carbon fluxes.
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Affiliation(s)
- Lauren Talluto
- Department of Ecology, University of Innsbruck, Technikerstrasse 25, 6020 Innsbruck, Austria
| | - Rubén del Campo
- Department of Ecology, University of Innsbruck, Technikerstrasse 25, 6020 Innsbruck, Austria
| | - Edurne Estévez
- Department of Ecology, University of Innsbruck, Technikerstrasse 25, 6020 Innsbruck, Austria
| | - Florian Altermatt
- Department of Aquatic Ecology, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, 8600 Dübendorf, Switzerland
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Thibault Datry
- National Research Institute for Agriculture, Food and Environment (INRAE), 5 Rue de la Doua, 69100 Villeurbanne, France
| | - Gabriel Singer
- Department of Ecology, University of Innsbruck, Technikerstrasse 25, 6020 Innsbruck, Austria
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10
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Wang Z, Li F, Wu F, Guo F, Gao W, Zhang Y, Yang Z. Environmental DNA and remote sensing datasets reveal the spatial distribution of aquatic insects in a disturbed subtropical river system. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 351:119972. [PMID: 38159308 DOI: 10.1016/j.jenvman.2023.119972] [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: 08/09/2023] [Revised: 12/04/2023] [Accepted: 12/25/2023] [Indexed: 01/03/2024]
Abstract
Biodiversity datasets with high spatial resolution are critical prerequisites for river protection and management decision-making. However, traditional morphological biomonitoring is inefficient and only provides several site estimates, and there is an urgent need for new approaches to predict biodiversity on fine spatial scales throughout the entire river systems. Here, we combined the environmental DNA (eDNA) and remote sensing (RS) technologies to develop a novel approach for predicting the spatial distribution of aquatic insects with high spatial resolution in a disturbed subtropical Dongjiang River system of southeast China. First, we screened thirteen RS-based vegetation indices that significantly correlated with the eDNA-inferred richness of aquatic insects. In particular, the green normalized difference vegetation index (GNDVI) and normalized difference red-edge2 (NDRE2) were closely related to eDNA-inferred richness. Second, using the gradient boosting decision tree, our data showed that the spatial pattern of eDNA-inferred richness could achieve a high spatial resolution to 500 m reach and accurate prediction of more than 80%, and the prediction efficiency of the headwater streams (Strahler stream order = 1) was slightly higher than the downstream (Strahler stream order >1). Third, using the random forest algorithm, the spatial distribution of aquatic insects could reach a prediction rate of over 70% for the presence or absence of specific genera. Overall, this study provides a new approach to achieving high spatial resolution prediction of the distribution of aquatic insects, which supports decision-making on river diversity protection under climate changes and human impacts.
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Affiliation(s)
- Zongyang Wang
- Guangdong Provincial Key Laboratory of Water Quality Improvement and Ecological Restoration for Watersheds, School of Ecology, Environment and Resources, Guangdong University of Technology, Guangzhou, 510006, China
| | - Feilong Li
- Guangdong Provincial Key Laboratory of Water Quality Improvement and Ecological Restoration for Watersheds, School of Ecology, Environment and Resources, Guangdong University of Technology, Guangzhou, 510006, China.
| | - Feifei Wu
- Guangdong Provincial Key Laboratory of Water Quality Improvement and Ecological Restoration for Watersheds, School of Ecology, Environment and Resources, Guangdong University of Technology, Guangzhou, 510006, China
| | - Fen Guo
- Guangdong Provincial Key Laboratory of Water Quality Improvement and Ecological Restoration for Watersheds, School of Ecology, Environment and Resources, Guangdong University of Technology, Guangzhou, 510006, China
| | - Wei Gao
- Guangdong Provincial Key Laboratory of Water Quality Improvement and Ecological Restoration for Watersheds, School of Ecology, Environment and Resources, Guangdong University of Technology, Guangzhou, 510006, China
| | - Yuan Zhang
- Guangdong Provincial Key Laboratory of Water Quality Improvement and Ecological Restoration for Watersheds, School of Ecology, Environment and Resources, Guangdong University of Technology, Guangzhou, 510006, China.
| | - Zhifeng Yang
- Guangdong Provincial Key Laboratory of Water Quality Improvement and Ecological Restoration for Watersheds, School of Ecology, Environment and Resources, Guangdong University of Technology, Guangzhou, 510006, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China
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11
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Ma X, Li Y, Wang L, Niu L, Shang J, Zheng J. Hypoxia and salinity constrain the sediment microbiota-mediated N removal potential in an estuary: A multi-trophic interrelationship perspective. WATER RESEARCH 2024; 248:120872. [PMID: 38006831 DOI: 10.1016/j.watres.2023.120872] [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: 07/11/2023] [Revised: 10/27/2023] [Accepted: 11/13/2023] [Indexed: 11/27/2023]
Abstract
Reactive nitrogen (N) enrichment is a common environmental problem in estuarine ecosystems, while the microbial-mediated N removal process is complicated for other multi-environmental factors. Therefore, A systematic investigation is necessary to understand the multi-trophic microbiota-mediated N removal characteristics under various environmental factors in estuaries. Here, we studied how multiple factors affect the multi-trophic microbiota-mediated N removal potential (denitrification and anammox) and N2O emission along a river-estuary-bay continuum in southeastern China using the environmental DNA (eDNA) approach. Results suggested that hypoxia and salinity were the dominant environmental factors affecting multi-trophic microbiota-mediated N removal in the estuary. The synergistic effect of hypoxia and salinity contributed to the loss of taxonomic (MultiTaxa) and phylogenetic (MultiPhyl) diversity across multi-trophic microbiota and enhanced the interdependence among multi-trophic microbiota in the estuary. The N removal potential calculated as the activities of key N removal enzymes was also significantly constrained in the estuary (0.011), compared with the river (0.257) and bay (0.461). Structural equation modeling illustrated that metazoans were central to all sediment N removal potential regulatory pathways. The top-down forces (predation by metazoans) restrained the growth of heterotrophic bacteria, which may affect microbial N removal processes in the sediment. Furthermore, we found that the hypoxia and salinity exacerbated the N2O emission in the estuary. This study clarifies that hypoxia and salinity constrain estuarine multi-trophic microbiota-mediated N removal potential and highlights the important role of multi-trophic interactions in estuarine N removal, providing a new perspective on mitigating estuarine N accumulation.
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Affiliation(s)
- Xin Ma
- College of Hydrology and Water Resources, Hohai University, Nanjing 210098, China
| | - Yi Li
- College of Hydrology and Water Resources, Hohai University, Nanjing 210098, China; Research Institute of Mulan Ecological River, Putian 351100, China.
| | - Linqiong Wang
- College of Oceanography, Hohai University, Nanjing 210098, China
| | - Lihua Niu
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China; Research Institute of Mulan Ecological River, Putian 351100, China.
| | - Jiahui Shang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China
| | - Jinhai Zheng
- College of Harbour, Coastal and Offshore Engineering, Hohai University, Nanjing 210098, China; Research Institute of Mulan Ecological River, Putian 351100, China
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12
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Qin S, Li F, Zou Y, Xue J, Zhang Y, Yang Z. eDNA-based diversity and multitrophic network reveal the effects of land use and pollutants on the subtropical Dongjiang River systems. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 334:122157. [PMID: 37454713 DOI: 10.1016/j.envpol.2023.122157] [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: 04/28/2023] [Revised: 06/20/2023] [Accepted: 07/06/2023] [Indexed: 07/18/2023]
Abstract
Biodiversity and its constituted multitrophic network in rivers are accelerating change under human land use and pollutants. However, due to the lack of complete datasets across taxa limited by traditional morphological biomonitoring, the change patterns of biodiversity and multitrophic networks are still unclear. Here, we used the eDNA approach to capture multitrophic communities (including fish, aquatic insects, protozoa, diatom and bacteria) in the Dongjiang River, a typical subtropical river in southeast China, and analyzed the changing patterns of biodiversity and multitrophic networks in relation to land use and water pollution. First, our data showed that the eDNA approach provided a snapshot of the multitrophic communities in the Dongjiang River, and the monitored 5833 OTUs were annotated to 55 phyla, 144 classes, 329 orders, 521 families, 945 genera and 406 species. Second, the multitrophic diversity index had similar patterns on the longitudinal scale of rivers, with significant decreases from the upstream to the downstream, while individual taxonomic groups exhibited variable spatial patterns. While there were similar spatial patterns between network metrics and diversity index, the former had stronger relationships with the spatial distance. Third, the multitrophic diversity and networks were significantly negatively correlated with land use and water pollution (e.g., CODMn), and network structures often had stronger and non-linear responses. Overall, this study highlights that eDNA biomonitoring of multitrophic communities and networks can provide deeper insights into ecosystem changes and help develop more targeted management strategies.
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Affiliation(s)
- Shan Qin
- Guangdong Provincial Key Laboratory of Water Quality Improvement and Ecological Restoration for Watersheds, School of Ecology, Environment and Resources, Guangdong University of Technology, Guangzhou, 510006, China
| | - Feilong Li
- Guangdong Provincial Key Laboratory of Water Quality Improvement and Ecological Restoration for Watersheds, School of Ecology, Environment and Resources, Guangdong University of Technology, Guangzhou, 510006, China
| | - Yanting Zou
- Guangdong Provincial Key Laboratory of Water Quality Improvement and Ecological Restoration for Watersheds, School of Ecology, Environment and Resources, Guangdong University of Technology, Guangzhou, 510006, China
| | - Jingchuan Xue
- Guangdong Provincial Key Laboratory of Water Quality Improvement and Ecological Restoration for Watersheds, School of Ecology, Environment and Resources, Guangdong University of Technology, Guangzhou, 510006, China
| | - Yuan Zhang
- Guangdong Provincial Key Laboratory of Water Quality Improvement and Ecological Restoration for Watersheds, School of Ecology, Environment and Resources, Guangdong University of Technology, Guangzhou, 510006, China.
| | - Zhifeng Yang
- Guangdong Provincial Key Laboratory of Water Quality Improvement and Ecological Restoration for Watersheds, School of Ecology, Environment and Resources, Guangdong University of Technology, Guangzhou, 510006, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China
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13
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Ohlmann M, Garnier J, Vuillon L. metanetwork: A R package dedicated to handling and representing trophic metanetworks. Ecol Evol 2023; 13:e10229. [PMID: 37593755 PMCID: PMC10427773 DOI: 10.1002/ece3.10229] [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: 12/16/2022] [Revised: 05/30/2023] [Accepted: 06/14/2023] [Indexed: 08/19/2023] Open
Abstract
Trophic networks describe interactions between species at a given location and time. Due to environmental changes, anthropogenic perturbations or sampling effects, trophic networks may vary in space and time. The collection of network time series or networks in different sites thus constitutes a metanetwork. We present here the R package metanetwork, which will ease the representation, the exploration and analysis of trophic metanetwork data sets that are increasingly available. Our main methodological advance consists in suitable layout algorithm for trophic networks, which is based on trophic levels and dimension reduction in a graph diffusion kernel. In particular, it highlights relevant features of trophic networks (trophic levels, energetic channels). In addition, we developed tools to handle, compare visually and quantitatively and aggregate those networks. Static and dynamic visualisation functions have been developed to represent large networks. We apply our package workflow to several trophic network data sets.
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Affiliation(s)
- Marc Ohlmann
- Laboratoire d'Écologie Alpine, LECA, CNRSUniv. Savoie Mont Blanc, Univ. Grenoble AlpesGrenobleFrance
| | - Jimmy Garnier
- Laboratoire de Mathématiques, LAMA, CNRSUniv. Savoie Mont Blanc, Univ. Grenoble AlpesChambéryFrance
| | - Laurent Vuillon
- Laboratoire de Mathématiques, LAMA, CNRSUniv. Savoie Mont Blanc, Univ. Grenoble AlpesChambéryFrance
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14
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Carraro L, Blackman RC, Altermatt F. Modelling environmental DNA transport in rivers reveals highly resolved spatio-temporal biodiversity patterns. Sci Rep 2023; 13:8854. [PMID: 37258598 DOI: 10.1038/s41598-023-35614-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 05/21/2023] [Indexed: 06/02/2023] Open
Abstract
The ever-increasing threats to riverine ecosystems call for novel approaches for highly resolved biodiversity assessments across taxonomic groups and spatio-temporal scales. Recent advances in the joint use of environmental DNA (eDNA) data and eDNA transport models in rivers (e.g., eDITH) allow uncovering the full structure of riverine biodiversity, hence elucidating ecosystem processes and supporting conservation measures. We applied eDITH to a metabarcoding dataset covering three taxonomic groups (fish, invertebrates, bacteria) and three seasons for a catchment sampled for eDNA at 73 sites. We upscaled eDNA-based biodiversity predictions to approximately 1900 reaches, and assessed α- and β-diversity patterns across seasons and taxonomic groups over the whole network. Genus richness predicted by eDITH was generally higher than values from direct eDNA analysis. Both predicted α- and β-diversity varied depending on season and taxonomic group. Predicted fish α-diversity increased downstream in all seasons, while invertebrate and bacteria α-diversity either decreased downstream or were unrelated to network position. Spatial β-diversity mostly decreased downstream, especially for bacteria. The eDITH model yielded a more refined assessment of freshwater biodiversity as compared to raw eDNA data, both in terms of spatial coverage, diversity patterns and effect of covariates, thus providing a more complete picture of freshwater biodiversity.
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Affiliation(s)
- Luca Carraro
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, 8057, Zürich, Switzerland.
- Department of Aquatic Ecology, Swiss Federal Institute of Aquatic Science and Technology, Eawag, 8600, Dübendorf, Switzerland.
| | - Rosetta C Blackman
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, 8057, Zürich, Switzerland
- Department of Aquatic Ecology, Swiss Federal Institute of Aquatic Science and Technology, Eawag, 8600, Dübendorf, Switzerland
| | - Florian Altermatt
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, 8057, Zürich, Switzerland
- Department of Aquatic Ecology, Swiss Federal Institute of Aquatic Science and Technology, Eawag, 8600, Dübendorf, Switzerland
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15
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Li F, Zhang Y, Altermatt F, Yang J, Zhang X. Destabilizing Effects of Environmental Stressors on Aquatic Communities and Interaction Networks across a Major River Basin. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:7828-7839. [PMID: 37155929 DOI: 10.1021/acs.est.3c00456] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Human-driven environmental stressors are increasingly threatening species survival and diversity of river systems worldwide. However, it remains unclear how the stressors affect the stability changes across aquatic multiple communities. Here, we used environmental DNA (eDNA) data sets from a human-dominated river in China over 3 years and analyzed the stability changes in multiple communities under persistent anthropogenic stressors, including land use and pollutants. First, we found that persistent stressors significantly reduced multifaceted species diversity (e.g., species richness, Shannon's diversity, and Simpson's diversity) and species stability but increased species synchrony across multiple communities. Second, the structures of interaction networks inferred from an empirical meta-food web were significantly changed under persistent stressors, for example, resulting in decreased network modularity and negative/positive cohesion. Third, piecewise structural equation modeling proved that the persistent stress-induced decline in the stability of multiple communities mainly depended upon diversity-mediated pathways rather than the direct effects of stress per se; specifically, the increase of species synchrony and the decline of interaction network modularity were the main biotic drivers of stability variation. Overall, our study highlights the destabilizing effects of persistent stressors on multiple communities as well as the mechanistic dependencies, mainly through reducing species diversity, increasing species synchrony, and changing interaction networks.
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Affiliation(s)
- Feilong Li
- Guangdong Provincial Key Laboratory of Water Quality Improvement and Ecological Restoration for Watersheds, School of Ecology, Environment and Resources, Guangdong University of Technology, Guangzhou, Guangdong 510006, People's Republic of China
| | - Yan Zhang
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu 210023, People's Republic of China
| | - Florian Altermatt
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
- Department of Aquatic Ecology, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, CH-8600 Dübendorf, Switzerland
| | - Jianghua Yang
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu 210023, People's Republic of China
| | - Xiaowei Zhang
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu 210023, People's Republic of China
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16
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Lu Q, Zhang SY, Du J, Liu Q, Dong C, Zhao J, Wang Y, Yao M. Multi-group biodiversity distributions and drivers of metacommunity organization along a glacial-fluvial-limnic pathway on the Tibetan plateau. ENVIRONMENTAL RESEARCH 2023; 220:115236. [PMID: 36621545 DOI: 10.1016/j.envres.2023.115236] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 12/22/2022] [Accepted: 01/04/2023] [Indexed: 06/17/2023]
Abstract
Extensive global glacial retreats are threatening cryosphere ecosystem functioning and the associated biota in glacier-fed water systems. Understanding multi-group biodiversity distributions and compositional variation across diverse but hydrologically linked habitats under varying glacial influences will help explain the mechanisms underlying glacial community organization and ecosystem processes. However, such data are generally lacking due to the difficulty of obtaining biodiversity information across wide taxonomic ranges. Here, we used a multi-marker environmental DNA metabarcoding approach to simultaneously investigate the spatial patterns of community compositions and assembly mechanisms of four taxonomic groups (cyanobacteria, diatoms, invertebrates, and vertebrates) along the flowpaths of a tributary of Lake Nam Co on the Tibetan Plateau-from its glacier headwaters, through its downstream river and wetlands, to its estuary. We detected 869 operational taxonomic units: 119 cyanobacterial, 395 diatom, 269 invertebrate, and 86 vertebrate. Taxonomic richnesses consistently increased from upstream to downstream, and although all groups showed community similarity distance decay patterns, the trend for vertebrates was the weakest. Cyanobacteria, diatom, and invertebrate community compositions were significantly correlated with several environmental factors, while the vertebrate community was only correlated with waterway width. Variation partitioning analysis indicated that varying extents of environmental conditions and spatial factors affected community organizations for different groups. Furthermore, stochastic processes contributed prominently to the microorganisms' community assembly (Sloan's neutral model R2 = 0.77 for cyanobacteria and 0.73 for diatoms) but were less important for macroorganisms (R2 = 0.21 for invertebrates and 0.15 for vertebrates). That trend was further substantiated by modified stochasticity ratio analyses. This study provides the first holistic picture of the diverse biotic communities residing in a series of hydrologically connected glacier-influenced habitats. Our results both uncovered the distinct mechanisms that underlie the metacommunity organizations of different glacial organisms and helped comprehensively predict the ecological impacts of the world's melting glaciers.
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Affiliation(s)
- Qi Lu
- School of Life Sciences, Peking University, Beijing, 100871, China; Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, 100871, China
| | - Si-Yu Zhang
- School of Life Sciences, Peking University, Beijing, 100871, China; Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, 100871, China
| | - Jianqing Du
- Beijing Yanshan Earth Critical Zone National Research Station, University of Chinese Academy of Sciences, Beijing, 101408, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qiang Liu
- Beijing Yanshan Earth Critical Zone National Research Station, University of Chinese Academy of Sciences, Beijing, 101408, China
| | - Chunxia Dong
- School of Life Sciences, Peking University, Beijing, 100871, China
| | - Jindong Zhao
- School of Life Sciences, Peking University, Beijing, 100871, China; Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, 100871, China
| | - Yanfen Wang
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China; State Key Laboratory of Tibetan Plateau Earth System, Environment and Resources (TPESER), Chinese Academy of Sciences, Beijing, 100101, China.
| | - Meng Yao
- School of Life Sciences, Peking University, Beijing, 100871, China; Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, 100871, China.
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17
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Bai S, Zhang J, Qi X, Zeng J, Wu S, Peng X. Changes of In Situ Prokaryotic and Eukaryotic Communities in the Upper Sanya River to the Sea over a Nine-Hour Period. Microorganisms 2023; 11:microorganisms11020536. [PMID: 36838501 PMCID: PMC9964997 DOI: 10.3390/microorganisms11020536] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 02/16/2023] [Accepted: 02/17/2023] [Indexed: 02/24/2023] Open
Abstract
The transition areas of riverine, estuarine, and marine environments are particularly valuable for the research of microbial ecology, biogeochemical processes, and other physical-chemical studies. Although a large number of microbial-related studies have been conducted within such systems, the vast majority of sampling have been conducted over a large span of time and distance, which may lead to separate batches of samples receiving interference from different factors, thus increasing or decreasing the variability between samples to some extent. In this study, a new in situ filtration system was used to collect membrane samples from six different sampling sites along the Sanya River, from upstream freshwater to the sea, over a nine-hour period. We used high-throughput sequencing of 16S and 18S rRNA genes to analyze the diversity and composition of prokaryotic and eukaryotic communities. The results showed that the structures of these communities varied according to the different sampling sites. The α-diversity of the prokaryotic and eukaryotic communities both decreased gradually along the downstream course. The structural composition of prokaryotic and eukaryotic communities changed continuously with the direction of river flow; for example, the relative abundances of Rhodobacteraceae and Flavobacteriaceae increased with distance downstream, while Sporichthyaceae and Comamonadaceae decreased. Some prokaryotic taxa, such as Phycisphaeraceae and Chromobacteriaceae, were present nearly exclusively in pure freshwater environments, while some additional prokaryotic taxa, including the SAR86 clade, Clade I, AEGEAN-169 marine group, and Actinomarinaceae, were barely present in pure freshwater environments. The eukaryotic communities were mainly composed of the Chlorellales X, Chlamydomonadales X, Sphaeropleales X, Trebouxiophyceae XX, Annelida XX, and Heteroconchia. The prokaryotic and eukaryotic communities were split into abundant, common, and rare communities for NCM analysis, respectively, and the results showed that assembly of the rare community assembly was more impacted by stochastic processes and less restricted by species dispersal than that of abundant and common microbial communities for both prokaryotes and eukaryotes. Overall, this study provides a valuable reference and new perspectives on microbial ecology during the transition from freshwater rivers to estuaries and the sea.
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Affiliation(s)
- Shijie Bai
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China
- Correspondence: (S.B.); (X.P.)
| | - Jian Zhang
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China
- The State Key Laboratory of Fluid Power & Mechatronic Systems, Zhejiang University, Hangzhou 310027, China
| | - Xiaoxue Qi
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China
| | - Juntao Zeng
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shijun Wu
- The State Key Laboratory of Fluid Power & Mechatronic Systems, Zhejiang University, Hangzhou 310027, China
| | - Xiaotong Peng
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China
- Correspondence: (S.B.); (X.P.)
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18
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Li F, Guo F, Gao W, Cai Y, Zhang Y, Yang Z. Environmental DNA Biomonitoring Reveals the Interactive Effects of Dams and Nutrient Enrichment on Aquatic Multitrophic Communities. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:16952-16963. [PMID: 36383447 DOI: 10.1021/acs.est.2c06919] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Dam construction and nutrient enrichment are two pervasive stressors in rivers worldwide, which trigger a sharp decline in biodiversity and ecosystem services. However, the interactive effects of both stressors on multitrophic taxonomic groups remain largely unclear. Here, we used the multitrophic datasets captured by the environmental DNA (eDNA) approach to reveal the interactions between dams and nutrient enrichment on aquatic communities from the aspects of taxonomic α diversity, β diversity, and food webs. First, our data showed that dams and nutrient enrichment jointly shaped a unique spatial pattern of aquatic communities across the four river systems, and the dissimilarity of community structure significantly declined (i.e., structural homogenization) under both stressors. Second, dams and nutrients together explained 40-50% of the variations in aquatic communities, and dams had a stronger impact on fish, aquatic insects, and bacteria, yet nutrients had a stronger power to drive protozoa, fungi, and eukaryotic algae. Finally, we found that additive, synergistic, and antagonistic interactions of dams and nutrient enrichment were common and coexisted in river systems and led to significantly simplified aquatic food webs, with decreases in modularity (synergistic) and robustness (additive) and an increase in coherence (synergistic). Overall, our study highlights that eDNA-based datasets can provide multitrophic perspectives for fostering the understanding of the interactive effects of multiple stressors on rivers.
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Affiliation(s)
- Feilong Li
- Guangdong Provincial Key Laboratory of Water Quality Improvement and Ecological Restoration for Watersheds, School of Ecology, Environment and Resources, Guangdong University of Technology, Guangzhou510006, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou511458, China
| | - Fen Guo
- Guangdong Provincial Key Laboratory of Water Quality Improvement and Ecological Restoration for Watersheds, School of Ecology, Environment and Resources, Guangdong University of Technology, Guangzhou510006, China
| | - Wei Gao
- Guangdong Provincial Key Laboratory of Water Quality Improvement and Ecological Restoration for Watersheds, School of Ecology, Environment and Resources, Guangdong University of Technology, Guangzhou510006, China
| | - Yanpeng Cai
- Guangdong Provincial Key Laboratory of Water Quality Improvement and Ecological Restoration for Watersheds, School of Ecology, Environment and Resources, Guangdong University of Technology, Guangzhou510006, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou511458, China
| | - Yuan Zhang
- Guangdong Provincial Key Laboratory of Water Quality Improvement and Ecological Restoration for Watersheds, School of Ecology, Environment and Resources, Guangdong University of Technology, Guangzhou510006, China
| | - Zhifeng Yang
- Guangdong Provincial Key Laboratory of Water Quality Improvement and Ecological Restoration for Watersheds, School of Ecology, Environment and Resources, Guangdong University of Technology, Guangzhou510006, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou511458, China
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