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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: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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Meng J, Xu F, Yang H, Li X, Zhao P. Exploring microbiome and plankton responses and interactions in the mangrove ecosystem through eDNA and network analysis. Sci Total Environ 2024; 930:172581. [PMID: 38641112 DOI: 10.1016/j.scitotenv.2024.172581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 04/11/2024] [Accepted: 04/17/2024] [Indexed: 04/21/2024]
Abstract
The comprehensive analysis of multiple biological communities is essential for assessing diversities within mangrove ecosystems, yet such studies are infrequent. Environmental DNA (eDNA) facilitates the simultaneous exploration of organisms across various levels within a single ecosystem. In this investigation, 16S rRNA, cytochrome C oxidase I (COI), and Mito-fish primers were employed to characterize the microbiome, eukaryotic plankton, and fish communities, along with their intricate interactions, across 24 samples from three Chinese mangrove reservoirs. The resulting dataset encompasses 3779 taxonomic groups (genus level), spanning from the microbiome to vertebrates. Diversity analysis unveiled a higher level of stability in the microbiome community compared to plankton, underscoring the superior site-specificity of plankton. The association analysis revealed that biodiversity was primarily affected by temperature, turbidity, and fluorescent dissolved organic matter (fDOM). Notably, the physicochemical factors, turbidity, and fDOM had a more pronounced impact on the microbiome than on plankton, explaining their distinct sensitivities to site-specific conditions. Network analysis constructed 15 biological interaction subnetworks representing various community connections. The most connected genera in each subnetwork, highly responsive to different environmental factors, could serve as potential indicators of distinct ecosystem states. In summary, our findings represent the first comparison of the response sensitivities of different communities and the construction of their interaction networks in mangrove environments. These results contribute valuable insights into marine ecosystem dynamics and the role of environmental factors in shaping biodiversity.
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Affiliation(s)
- Jie Meng
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Fei Xu
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China; Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Wuhan, China
| | - Haijie Yang
- School of Marine Science and Engineering, Hainan University, Haikou 570228, China; State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou 570228, China
| | - Xiaoxu Li
- School of Marine Science and Engineering, Hainan University, Haikou 570228, China; State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou 570228, China
| | - Peng Zhao
- School of Marine Science and Engineering, Hainan University, Haikou 570228, China; State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou 570228, China.
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Hu H, Liu L, Wei XY, Duan JJ, Deng JY, Pei DS. Revolutionizing aquatic eco-environmental monitoring: Utilizing the RPA-Cas-FQ detection platform for zooplankton. Sci Total Environ 2024; 929:172414. [PMID: 38631624 DOI: 10.1016/j.scitotenv.2024.172414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 03/15/2024] [Accepted: 04/10/2024] [Indexed: 04/19/2024]
Abstract
The integration of recombinase polymerase amplification (RPA) with CRISPR/Cas technology has revolutionized molecular diagnostics and pathogen detection due to its unparalleled sensitivity and trans-cleavage ability. However, its potential in the ecological and environmental monitoring scenarios for aquatic ecosystems remains largely unexplored, particularly in accurate qualitative/quantitative detection, and its actual performance in handling complex real environmental samples. Using zooplankton as a model, we have successfully optimized the RPA-CRISPR/Cas12a fluorescence detection platform (RPA-Cas-FQ), providing several crucial "technical tips". Our findings indicate the sensitivity of CRISPR/Cas12a alone is 5 × 109 copies/reaction, which can be dramatically increased to 5 copies/reaction when combined with RPA. The optimized RPA-Cas-FQ enables reliable qualitative and semi-quantitative detection within 50 min, and exhibits a good linear relationship between fluorescence intensity and DNA concentration (R2 = 0.956-0.974***). Additionally, we developed a rapid and straightforward identification procedure for single zooplankton by incorporating heat-lysis and DNA-barcode techniques. We evaluated the platform's effectiveness using real environmental DNA (eDNA) samples from the Three Gorges Reservoir, confirming its practicality. The eDNA-RPA-Cas-FQ demonstrated strong consistency (Kappa = 0.43***) with eDNA-Metabarcoding in detecting species presence/absence in the reservoir. Furthermore, the two semi-quantitative eDNA technologies showed a strong positive correlation (R2 = 0.58-0.87***). This platform also has the potential to monitor environmental pollutants by selecting appropriate indicator species. The novel insights and methodologies presented in this study represent a significant advancement in meeting the complex needs of aquatic ecosystem protection and monitoring.
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Affiliation(s)
- Huan Hu
- Chongqing Jiaotong University, Chongqing 400074, China; Chongqing Institute of Green and Intelligent Technology, Chongqing School of University of Chinese Academy of Sciences, Chinese Academy of Sciences, Chongqing 400714, China
| | - Li Liu
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Xing-Yi Wei
- Chongqing Jiaotong University, Chongqing 400074, China; Chongqing Institute of Green and Intelligent Technology, Chongqing School of University of Chinese Academy of Sciences, Chinese Academy of Sciences, Chongqing 400714, China
| | - Jin-Jing Duan
- Chongqing Miankai Biotechnology Research Institute Co., Ltd., Chongqing 400025, China; School of Public Health, Chongqing Medical University, Chongqing 400016, China
| | - Jiao-Yun Deng
- School of Public Health, Chongqing Medical University, Chongqing 400016, China
| | - De-Sheng Pei
- School of Public Health, Chongqing Medical University, Chongqing 400016, China.
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Tian S, Shi L, Ren Y, van der Mei HC, Busscher HJ. A normalized parameter for comparison of biofilm dispersants in vitro. Biofilm 2024; 7:100188. [PMID: 38495770 PMCID: PMC10943042 DOI: 10.1016/j.bioflm.2024.100188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 02/12/2024] [Accepted: 02/28/2024] [Indexed: 03/19/2024] Open
Abstract
Dispersal of infectious biofilms increases bacterial concentrations in blood. To prevent sepsis, the strength of a dispersant should be limited to allow the immune system to remove dispersed bacteria from blood, preferably without antibiotic administration. Biofilm bacteria are held together by extracellular polymeric substances that can be degraded by dispersants. Currently, comparison of the strength of dispersants is not possible by lack of a suitable comparison parameter. Here, a biofilm dispersal parameter is proposed that accounts for differences in initial biofilm properties, dispersant concentration and exposure time by using PBS as a control and normalizing outcomes with respect to concentration and time. The parameter yielded near-identical values based on dispersant-induced reductions in biomass or biofilm colony-forming-units and appeared strain-dependent across pathogens. The parameter as proposed is largely independent of experimental methods and conditions and suitable for comparing different dispersants with respect to different causative strains in particular types of infection.
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Affiliation(s)
- Shuang Tian
- University of Groningen and University Medical Center Groningen, Department of Biomedical Engineering, Antonius Deusinglaan 1, 9713, AV, Groningen, the Netherlands
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Functional polymer Materials of Ministry of Education, Institute of Polymer Chemistry, College of Chemistry, Nankai University, Tianjin, 300071, PR China
| | - Linqi Shi
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Functional polymer Materials of Ministry of Education, Institute of Polymer Chemistry, College of Chemistry, Nankai University, Tianjin, 300071, PR China
| | - Yijin Ren
- University of Groningen and University Medical Center Groningen, Department of Orthodontics, Hanzeplein 1, 9700, RB, Groningen, the Netherlands
| | - Henny C. van der Mei
- University of Groningen and University Medical Center Groningen, Department of Biomedical Engineering, Antonius Deusinglaan 1, 9713, AV, Groningen, the Netherlands
| | - Henk J. Busscher
- University of Groningen and University Medical Center Groningen, Department of Biomedical Engineering, Antonius Deusinglaan 1, 9713, AV, Groningen, the Netherlands
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Yoshida T, Yamazaki A, Kawato M, Fujiwara Y. Rapid, contamination-less, and efficient environmental DNA filtration system. MethodsX 2024; 12:102621. [PMID: 38439931 PMCID: PMC10909735 DOI: 10.1016/j.mex.2024.102621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 02/19/2024] [Indexed: 03/06/2024] Open
Abstract
Due to the sporadic distribution and trace amount of environmental DNA (eDNA) in deep-sea water, in the context of biodiversity monitoring, large volumes of filtration and multiple filtration replicates are required for eDNA metabarcoding. To address issues tied to the use of multiple filtration devices and large filtration volumes (e.g., contamination, time consumption, etc.), we have developed two systems for simple, rapid, and contamination-less filtration simultaneously that allow for the processing of multiple sample replicates from large volumes of water. First, the water from a Niskin bottle was filtered directly using a solenoid pump. Second, the pumped deep-sea water, using the siphon effect, was directly filtered by a filtration device driven by water pressure. This system can process 24 replicates simultaneously without the need for expensive equipment and active driving force. Compared with conventional filtering methods, e.g., peristaltic pumps, the proposed systems reduce filtration time, minimizing contamination, and enabling the simultaneous acquisition of multiple replicates. Overall, the systems presented here provide an effective approach for eDNA metabarcoding analysis, particularly for the filtration of large volumes of water containing small amounts of eDNA, such as deep-sea water. •The present systems reduce filtration time and contamination without water having to be transferred.•Simultaneous multiple replicates improve the efficiency and reliability of biodiversity assessments.
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Affiliation(s)
- Takao Yoshida
- Marine Biodiversity and Environmental Assessment Research Center (BioEnv), Research Institute for Global Change (RIGC), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Aya Yamazaki
- Marine Biodiversity and Environmental Assessment Research Center (BioEnv), Research Institute for Global Change (RIGC), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Masaru Kawato
- Marine Biodiversity and Environmental Assessment Research Center (BioEnv), Research Institute for Global Change (RIGC), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Yoshihiro Fujiwara
- Marine Biodiversity and Environmental Assessment Research Center (BioEnv), Research Institute for Global Change (RIGC), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
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Parikh A, Pansu J, Stow A, Warne MSJ, Chivas C, Greenfield P, Boyer F, Simpson S, Smith R, Gruythuysen J, Carlin G, Caulfield N, Viard F, Chariton AA. Environmental DNA highlights the influence of salinity and agricultural run-off on coastal fish assemblages in the Great Barrier Reef region. Environ Pollut 2024; 349:123954. [PMID: 38604307 DOI: 10.1016/j.envpol.2024.123954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 03/14/2024] [Accepted: 04/09/2024] [Indexed: 04/13/2024]
Abstract
Agricultural run-off in Australia's Mackay-Whitsunday region is a major source of nutrient and pesticide pollution to coastal and inshore ecosystems of the Great Barrier Reef. While the effects of run-off are well documented for the region's coral and seagrass habitats, the ecological impacts on estuaries, the direct recipients of run-off, are less known. This is particularly true for fish communities, which are shaped by the physico-chemical properties of coastal waterways that vary greatly in tropical regions. To address this knowledge gap, we used environmental DNA (eDNA) metabarcoding to examine fish assemblages at four locations (three estuaries and a harbour) subjected to varying levels of agricultural run-off during a wet and dry season. Pesticide and nutrient concentrations were markedly elevated during the sampled wet season with the influx of freshwater and agricultural run-off. Fish taxa richness significantly decreased in all three estuaries (F = 164.73, P = <0.001), along with pronounced changes in community composition (F = 46.68, P = 0.001) associated with environmental variables (largely salinity: 27.48% contribution to total variance). In contrast, the nearby Mackay Harbour exhibited a far more stable community structure, with no marked changes in fish assemblages observed between the sampled seasons. Among the four sampled locations, variation in fish community composition was more pronounced within the wet season (F = 2.5, P = 0.001). Notably, variation in the wet season was significantly correlated with agricultural contaminants (phosphorus: 6.25%, pesticides: 5.22%) alongside environmental variables (salinity: 5.61%, DOC: 5.57%). Historically contaminated and relatively unimpacted estuaries each demonstrated distinct fish communities, reflecting their associated catchment use. Our findings emphasise that while seasonal effects play a key role in shaping the community structure of fish in this region, agricultural contaminants are also important contributors in estuarine systems.
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Affiliation(s)
- Aashi Parikh
- School of Natural Sciences, Wallumattagal (North Ryde) Campus, Macquarie University, NSW, 2113, Australia.
| | - Johan Pansu
- School of Natural Sciences, Wallumattagal (North Ryde) Campus, Macquarie University, NSW, 2113, Australia; CSIRO Environment, Lucas Heights, NSW, 2234, Australia; ISEM, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, 34095, France; Univ Lyon, Université Claude Bernard Lyon 1, CNRS, ENTPE, UMR 5023 LEHNA, F-69622, Villeurbanne, France.
| | - Adam Stow
- School of Natural Sciences, Wallumattagal (North Ryde) Campus, Macquarie University, NSW, 2113, Australia.
| | - Michael St J Warne
- Reef Catchments Science Partnership, Mackay, QLD, 4740, Australia; School of Earth and Environmental Sciences, University of Queensland, QLD, 4067, Australia; Centre for Agroecology, Water and Resilience, Coventry University, West Midlands, United Kingdom; Queensland Department of Environment and Science, Brisbane, QLD, 4179, Australia.
| | - Christine Chivas
- School of Natural Sciences, Wallumattagal (North Ryde) Campus, Macquarie University, NSW, 2113, Australia.
| | - Paul Greenfield
- School of Natural Sciences, Wallumattagal (North Ryde) Campus, Macquarie University, NSW, 2113, Australia; CSIRO Energy, Lindfield, NSW, 2070, Australia.
| | - Frédéric Boyer
- Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, Grenoble, 38000, France.
| | | | - Rachael Smith
- Office of the Great Barrier Reef, Queensland Department of Environment and Science, Brisbane, QLD, 4179, Australia.
| | - Jacob Gruythuysen
- Science Division, Queensland Department of Environment and Science, Brisbane, QLD, 4179, Australia.
| | - Geoffrey Carlin
- CSIRO Environment, Dutton Park, Queensland, 4102, Australia.
| | - Natalie Caulfield
- School of Natural Sciences, Wallumattagal (North Ryde) Campus, Macquarie University, NSW, 2113, Australia.
| | - Frédérique Viard
- ISEM, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, 34095, France.
| | - Anthony A Chariton
- School of Natural Sciences, Wallumattagal (North Ryde) Campus, Macquarie University, NSW, 2113, Australia.
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Li X, Xu Q, Xia R, Zhang N, Wang S, Ding S, Gao X, Jia X, Shang G, Chen X. Stochastic process is main factor to affect plateau river fish community assembly. Environ Res 2024; 254:119083. [PMID: 38735377 DOI: 10.1016/j.envres.2024.119083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 05/03/2024] [Accepted: 05/04/2024] [Indexed: 05/14/2024]
Abstract
Plateau river ecosystems are often highly vulnerable and responsive to environmental change. The driving mechanism of fish diversity and community assembly in plateau rivers under changing environments presents a significant complexity to the interdisciplinary study of ecology and environment. This study integrated molecular biological techniques and mathematical models to identify the mechanisms influencing spatial heterogeneity of freshwater fish diversity and driving fish community assembly in plateau rivers. By utilizing environmental-DNA metabarcoding and the null model, this study revealed the impact of the stochastic process on fish diversity variations and community assembly in the Huangshui Plateau River of the Yellow River Basin (YRB) in China. This research identified 30 operational taxonomic units (OTUs), which correspond to 20 different fish species. The findings of this study revealed that the fish α-diversity in the upstream region of Xining is significantly higher than in the middle-lower reach (Shannon index: P = 0.017 and Simpson: P = 0.035). This pattern was not found to be related to any other environmental factors besides altitude (P = 0.023) that we measured. Further, the study indicated that the assembly of fish communities in the Huangshui River primarily depends on stochastic ecological processes. These findings suggested that elevation was not the primary factor impacting the biodiversity patterns of fish in plateau rivers. In plateau rivers, spatial heterogeneity of fish community on elevation is mainly determined by stochastic processes under habitat fragmentation, rather than any other physicochemical environmental factors. The limitations of connectivity in the downstream channel of the river could be taken the mainly responsibility for stochastic processes of fish community in Huangshui River. Incorporating ecological processes in the eDNA approach holds great potential for future monitoring and evaluation of fish biodiversity and community assembly in plateau rivers.
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Affiliation(s)
- Xiaoxuan Li
- State Environmental Protection Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China; State Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Chinese Research Academy of Environmental Science, Beijing, China
| | - Qigong Xu
- State Environmental Protection Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China; State Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Chinese Research Academy of Environmental Science, Beijing, China
| | - Rui Xia
- State Environmental Protection Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China; State Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Chinese Research Academy of Environmental Science, Beijing, China.
| | - Nan Zhang
- College of Water Science, Beijing Normal University, Beijing, China
| | - Shuping Wang
- State Environmental Protection Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China; State Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Chinese Research Academy of Environmental Science, Beijing, China
| | - Sen Ding
- State Environmental Protection Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China; State Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Chinese Research Academy of Environmental Science, Beijing, China
| | - Xin Gao
- State Environmental Protection Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China; State Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Chinese Research Academy of Environmental Science, Beijing, China
| | - Xiaobo Jia
- State Environmental Protection Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China; State Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Chinese Research Academy of Environmental Science, Beijing, China
| | - Guangxia Shang
- State Environmental Protection Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China; State Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Chinese Research Academy of Environmental Science, Beijing, China
| | - Xiaofei Chen
- State Environmental Protection Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China; State Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Chinese Research Academy of Environmental Science, Beijing, China
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Pawlowski J, Cermakova K, Cordier T, Frontalini F, Apothéloz-Perret-Gentil L, Merzi T. Assessing the potential of nematode metabarcoding for benthic monitoring of offshore oil platforms. Sci Total Environ 2024; 933:173092. [PMID: 38729369 DOI: 10.1016/j.scitotenv.2024.173092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 04/11/2024] [Accepted: 05/07/2024] [Indexed: 05/12/2024]
Abstract
Environmental DNA metabarcoding is gaining momentum as a time and cost-effective tool for biomonitoring and environmental impact assessment. Yet, its use as a replacement for the conventional marine benthic monitoring based on morphological analysis of macrofauna is still challenging. Here we propose to study the meiofauna, which is much better represented in sediment DNA samples. We focus on nematodes, which are the most numerous and diverse group of meiofauna. Our aim is to assess the potential of nematode metabarcoding to monitor impacts associated with offshore oil platform activities. To achieve this goal, we used nematode-optimized marker (18S V1V2-Nema) and universal eukaryotic marker (18S V9) region to analyse 252 sediment DNA samples collected near three offshore oil platforms in the North Sea. For both markers, we analysed changes in alpha and beta diversity in relation to distance from the platforms and environmental variables. We also defined three impact classes based on selected environmental variables that are associated with oil extraction activities and used random forest classifiers to compare the predictive performance of both datasets. Our results show that alpha- and beta-diversity of nematodes varies with the increasing distance from the platforms. The variables directly related to platform activity, such as Ba and THC, strongly influence the nematode community. The nematode metabarcoding data provide more robust predictive models than eukaryotic data. Furthermore, the nematode community appears more stable in time and space, as illustrated by the overlap of nematode datasets obtained from the same platform three years apart. A significative negative correlation between distance and Shannon diversity also advocates for higher performance of the V1V2-Nema over the V9. Overall, these results suggest that the sensitivity of nematodes is higher compared to the eukaryotic community. Hence, nematode metabarcoding has the potential to become an effective tool for benthic monitoring in marine environment.
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Affiliation(s)
- J Pawlowski
- Institute of Oceanology, Polish Academy of Sciences, Sopot, Poland; ID-Gene ecodiagnostics, Plan-les-Ouates, Switzerland.
| | - K Cermakova
- ID-Gene ecodiagnostics, Plan-les-Ouates, Switzerland
| | - T Cordier
- NORCE Climate and Environment, NORCE Norwegian Research Centre AS, Norway
| | - F Frontalini
- Department of Pure and Applied Sciences, University of Urbino "Carlo Bo", Urbino, Italy
| | | | - T Merzi
- TotalEnergies OneTech, Centre Scientifique et Technique Jean Feger, Pau, France
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Lopes AA, Vendrell-Fernández S, Deschamps J, Georgeault S, Cokelaer T, Briandet R, Ghigo JM. Bile-induced biofilm formation in Bacteroides thetaiotaomicron requires magnesium efflux by an RND pump. mBio 2024; 15:e0348823. [PMID: 38534200 PMCID: PMC11078008 DOI: 10.1128/mbio.03488-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Accepted: 03/06/2024] [Indexed: 03/28/2024] Open
Abstract
Bacteroides thetaiotaomicron is a prominent member of the human gut microbiota contributing to nutrient exchange, gut function, and maturation of the host's immune system. This obligate anaerobe symbiont can adopt a biofilm lifestyle, and it was recently shown that B. thetaiotaomicron biofilm formation is promoted by the presence of bile. This process also requires a B. thetaiotaomicron extracellular DNase, which is not, however, regulated by bile. Here, we showed that bile induces the expression of several Resistance-Nodulation-Division (RND) efflux pumps and that inhibiting their activity with a global competitive efflux inhibitor impaired bile-dependent biofilm formation. We then showed that, among the bile-induced RND-efflux pumps, only the tripartite BT3337-BT3338-BT3339 pump, re-named BipABC [for Bile Induced Pump A (BT3337), B (BT3338), and C (BT3339)], is required for biofilm formation. We demonstrated that BipABC is involved in the efflux of magnesium to the biofilm extracellular matrix, which leads to a decrease of extracellular DNA concentration. The release of magnesium in the biofilm matrix also impacts biofilm structure, potentially by modifying the electrostatic repulsion forces within the matrix, reducing interbacterial distance and allowing bacteria to interact more closely and form denser biofilms. Our study therefore, identified a new molecular determinant of B. thetaiotaomicron biofilm formation in response to bile salts and provides a better understanding on how an intestinal chemical cue regulates biofilm formation in a major gut symbiont.IMPORTANCEBacteroides thetaiotaomicron is a prominent member of the human gut microbiota able to degrade dietary and host polysaccharides, altogether contributing to nutrient exchange, gut function, and maturation of the host's immune system. This obligate anaerobe symbiont can adopt a biofilm community lifestyle, providing protection against environmental factors that might, in turn, protect the host from dysbiosis and dysbiosis-related diseases. It was recently shown that B. thetaiotaomicron exposure to intestinal bile promotes biofilm formation. Here, we reveal that a specific B. thetaiotaomicron membrane efflux pump is induced in response to bile, leading to the release of magnesium ions, potentially reducing electrostatic repulsion forces between components of the biofilm matrix. This leads to a reduction of interbacterial distance and strengthens the biofilm structure. Our study, therefore, provides a better understanding of how bile promotes biofilm formation in a major gut symbiont, potentially promoting microbiota resilience to stress and dysbiosis events.
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Affiliation(s)
- Anne-Aurélie Lopes
- Institut Pasteur, Université Paris-Cité, UMR CNRS 6047, Genetics of Biofilms Laboratory, Department of Microbiology, Paris, France
- Pediatric Emergency, AP-HP, Necker-Enfants-Malades University Hospital, Paris, France
| | - Sol Vendrell-Fernández
- Institut Pasteur, Université Paris-Cité, UMR CNRS 6047, Genetics of Biofilms Laboratory, Department of Microbiology, Paris, France
| | - Julien Deschamps
- INRAE, AgroParisTech, Université Paris-Saclay Institut Micalis, Paris, France
| | - Sonia Georgeault
- Plateforme IBiSA des Microscopies, Université et CHRU de Tours, Tours, France
| | - Thomas Cokelaer
- Institut Pasteur, Université Paris Cité, Plate-forme Technologique Biomics, Center for Technological Resources and Research, Paris, France
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, Center for Technological Resources and Research, Paris, France
| | - Romain Briandet
- INRAE, AgroParisTech, Université Paris-Saclay Institut Micalis, Paris, France
| | - Jean-Marc Ghigo
- Institut Pasteur, Université Paris-Cité, UMR CNRS 6047, Genetics of Biofilms Laboratory, Department of Microbiology, Paris, France
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10
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Green ME, Hardesty BD, Deagle BE, Wilcox C. Environmental DNA as a tool to reconstruct catch composition for longline fisheries vessels. Sci Rep 2024; 14:10188. [PMID: 38702492 PMCID: PMC11068744 DOI: 10.1038/s41598-024-60917-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 04/29/2024] [Indexed: 05/06/2024] Open
Abstract
Global wild-capture fisheries are a large and diverse sector requiring various tools for fisheries-dependant data collection and effective Monitoring, Control and Surveillance (MCS). Here we present a novel protocol to collect eDNA from brine tanks onboard commercial longline vessels to reconstruct catch composition. We collected samples from nine vessels operating out of the Eastern Tuna Billfish Fishery, Australia, validating eDNA results with reliable catch data consisting of seven target and bycatch species. Environmental DNA was highly effective for detecting species retained on vessels without contamination or false positives. For four vessels, logbook data and eDNA were consistent with detections of all species. The remaining vessels detected all species except for rare catches of short-billed spearfish (Tetrapturus angustirostris). Similarities between rank abundance distributions of catch and eDNA reads were observed with logbook data mirrored when eDNA sequences were organised into rank order abundance. The method was effective at identifying highly abundant taxa retained in brine tanks- tuna (Thunnus spp.), swordfish (Xiphias gladius), marlin (Kajijia audax), and Atlantic Pomfret (Brama brama). Further research is required to validate how eDNA and other molecular monitoring tools can be scaled and applied to provide solutions for monitoring challenges in the fisheries sector.
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Affiliation(s)
- M E Green
- Institute for Marine and Antactic Studies, University of Tasmania, Private Bag 49, Hobart, TAS, 7001, Australia.
- Centre for Marine Socioecology, University of Tasmania, Private Bag 49, Hobart, TAS, 7001, Australia.
| | - B D Hardesty
- CSIRO Environment, Castray Esplanade, Hobart, TAS, 7001, Australia
| | - B E Deagle
- CSIRO Australian National Fish Collection, Castray Esplanade, Hobart, TAS, 7001, Australia
| | - C Wilcox
- Wilco Analytics, 93 Carlton Beach Road, Dodges Ferry, TAS, 7173, Australia
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11
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Wilcox TM, Kronenberger JA, Young MK, Mason DH, Franklin TW, Schwartz MK. The unknown unknown: A framework for assessing environmental DNA assay specificity against unsampled taxa. Mol Ecol Resour 2024; 24:e13932. [PMID: 38263813 DOI: 10.1111/1755-0998.13932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 12/21/2023] [Accepted: 01/15/2024] [Indexed: 01/25/2024]
Abstract
Taxon-specific quantitative PCR (qPCR) assays are commonly used for environmental DNA sampling-based inference of animal presence. These assays require thorough validation to ensure that amplification truly indicates detection of the target taxon, but a thorough validation is difficult when there are potentially many non-target taxa, some of which may have incomplete taxonomies. Here, we use a previously published, quantitative model of cross-amplification risk to describe a framework for assessing qPCR assay specificity when there is missing information and it is not possible to assess assay specificity for each individual non-target confamilial. In this framework, we predict assay specificity against unsampled taxa (non-target taxa without sequence data available) using the sequence information that is available for other confamilials. We demonstrate this framework using four case study assays for: (1) An endemic, freshwater arthropod (meltwater stonefly; Lednia tumana), (2) a globally distributed, marine ascidian (Didemnum perlucidum), (3) a continentally distributed freshwater crustacean (virile crayfish; Faxonius virilis, deanae and nais species complex) and (4) a globally distributed freshwater teleost (common carp; Cyprinus carpio and its close relative C. rubrofuscus). We tested the robustness of our approach to missing information by simulating application of our framework for all possible subsamples of 20-all non-target taxa. Our results suggest that the modelling framework results in estimates which are largely concordant with observed levels of cross-amplification risk using all available sequence data, even when there are high levels of data missingness. We explore potential limitations and extensions of this approach for assessing assay specificity and provide users with an R Markdown template for generating reproducible reports to support their own assay validation efforts.
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Affiliation(s)
- Taylor M Wilcox
- USDA Forest Service, Rocky Mountain Research Station, National Genomics Center for Wildlife and Fish Conservation, Forestry Sciences Laboratory, Missoula, Montana, USA
| | - John A Kronenberger
- USDA Forest Service, Rocky Mountain Research Station, National Genomics Center for Wildlife and Fish Conservation, Forestry Sciences Laboratory, Missoula, Montana, USA
| | - Michael K Young
- USDA Forest Service, Rocky Mountain Research Station, National Genomics Center for Wildlife and Fish Conservation, Forestry Sciences Laboratory, Missoula, Montana, USA
| | - Daniel H Mason
- USDA Forest Service, Rocky Mountain Research Station, National Genomics Center for Wildlife and Fish Conservation, Forestry Sciences Laboratory, Missoula, Montana, USA
| | - Thomas W Franklin
- USDA Forest Service, Rocky Mountain Research Station, National Genomics Center for Wildlife and Fish Conservation, Forestry Sciences Laboratory, Missoula, Montana, USA
| | - Michael K Schwartz
- USDA Forest Service, Rocky Mountain Research Station, National Genomics Center for Wildlife and Fish Conservation, Forestry Sciences Laboratory, Missoula, Montana, USA
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12
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Schlegel M, Treindl AD, Panziera J, Zengerer V, Zani D, Brännhage J, Gross A. A case study on the application of spore sampling for the monitoring of macrofungi. Mol Ecol Resour 2024; 24:e13941. [PMID: 38409666 DOI: 10.1111/1755-0998.13941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 12/13/2023] [Accepted: 02/09/2024] [Indexed: 02/28/2024]
Abstract
Fungi play a vital role in ecosystem functioning, yet significant knowledge gaps persist in understanding their diversity and distribution leading to uncertainties about their threat status and extinction risk. This is partly owed to the difficulty of monitoring fungi using traditional fruiting body surveys. The present study evaluates airborne environmental DNA (eDNA) sampling as a monitoring tool with a focus on grassland macrofungi. We applied active and passive air sampling methods, complemented by extensive field surveys of waxcap and clavarioid fungi-species groups of high relevance for conservation. Twenty-nine species were recorded during the field surveys, 19 of which were also detectable by ITS2 metabarcoding of the collected samples. An additional 12 species from the studied genera were identified exclusively in air eDNA. We found that the patterns of species detection and read abundance in air samples reflected the abundance and occurrence of fruiting bodies on the field. Dispersal kernels fitted for the three dominant species predicted rapidly decreasing spore concentrations with increasing distance from fruitbodies. Airborne assemblages were dominated by a high diversity of common species, while rare and threatened red-listed species were under-represented, which underscores the difficulty in detecting rare species, not only in conventional surveys. Considering the benefits and drawbacks of air sampling and fruitbody surveys, we conclude that air sampling serves as a cost- and time-efficient tool to characterize local macrofungal communities, providing the potential to facilitate and improve future fungal monitoring efforts.
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Affiliation(s)
- Markus Schlegel
- Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | | | - Jenny Panziera
- Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | | | - Deborah Zani
- Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | - Jonas Brännhage
- Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | - Andrin Gross
- Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
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13
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Fantinato C, Gill P, Fonneløp AE. Investigative use of human environmental DNA in forensic genetics. Forensic Sci Int Genet 2024; 70:103021. [PMID: 38335776 DOI: 10.1016/j.fsigen.2024.103021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 01/19/2024] [Accepted: 01/25/2024] [Indexed: 02/12/2024]
Abstract
Individuals leave behind traces of their DNA wherever they go. DNA can be transferred to surfaces and items upon touch, can be released into the air, and may be deposited in indoor dust. The mere presence of individuals in a location is sufficient to facilitate either direct or indirect DNA transfer into the surrounding environment. In this study, we analyzed samples recovered from commonly touched surfaces such as light switches and door handles in an office environment. We evaluated two different methods to isolate DNA and co-extract DNA and RNA from the samples. DNA profiles were compared to the references of the inhabitants of the different locations and were analyzed taking into consideration the type of sampled surface, sampling location and information about the activities in a room during the sampling day. Results from DNA samples collected from surfaces were also compared to those from air and dust samples collected in parallel from the same areas. We characterized the amount and composition of DNA found on various surfaces and showed that surface DNA sampling can be used to detect occupants of a location. The results also indicate that combining information from environmental samples collected from different DNA sources can improve our understanding of DNA transfer events in an indoor setting. This study further demonstrates the potential of human environmental DNA as an investigative tool in forensic genetics.
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Affiliation(s)
- Chiara Fantinato
- Forensic Genetics Research Group, Department of Forensic Sciences, Oslo University Hospital, Oslo, Norway; Department of Forensic Medicine, Institute of Clinical Medicine, University of Oslo, Oslo, Norway.
| | - Peter Gill
- Forensic Genetics Research Group, Department of Forensic Sciences, Oslo University Hospital, Oslo, Norway; Department of Forensic Medicine, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Ane Elida Fonneløp
- Forensic Genetics Research Group, Department of Forensic Sciences, Oslo University Hospital, Oslo, Norway; Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
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14
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Zan R, Stirling R, Blackburn A, Walsh C, Werner D. Activated carbon amendment of sand in the base of a permeable pavement reduces total nitrogen and nitrate leaching. Sci Total Environ 2024; 931:172831. [PMID: 38685424 DOI: 10.1016/j.scitotenv.2024.172831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 04/25/2024] [Accepted: 04/26/2024] [Indexed: 05/02/2024]
Abstract
Urban runoff from impermeable surfaces contains various pollutants. Stormwater samples were collected for one year from car parks on the campus of Newcastle University, located in northeast England, to monitor seasonal variation in stormwater properties and leachate quality following stormwater percolation through pilot-scale, outdoor permeable pavements. The pilot study compared an innovative 'pollution munching' permeable pavement with 2 % activated carbon (AC) amendment in the sand base with a conventional, un-amended sand base permeable pavement. Faecal coliforms were detected in stormwater at an average value of 3.75 ± 0.79 log10 CFUs per 100 mL. The permeable pavements without and with AC had mean log removal values of 0.81 ± 0.35 and 0.70 ± 0.35 for these faecal bacteria. The absence of genetic markers for human host associated Bacteroides (HF183) in eleven out of twelve stormwater samples showed that the faecal bacteria were mainly from animal sources. 16S rRNA gene sequencing results confirmed the presence of nitrifying bacteria from the genera Nitrosomonas, Nitrobacter, Nitrosococcus, Nitrospira, and Nitrosospira in stormwater. Nitrification and nitrate leaching was more notable for the conventional permeable pavement and may pose a groundwater pollution risk. Two percent AC amendment of the sand base reduced nitrate and total nitrogen leaching significantly compared with the conventional permeable pavement, by 57 ± 15 % and 40 ± 20 %, respectively. The AC amendment also resulted in significantly reduced Cu and DOC leaching, and lesser accumulation of PAHs by passive samplers embedded in the permeable pavement base. Hydraulic tests showed that the AC amended base layer still met the design specifications for permeable pavements, making it a promising proposition for pollution reduction in Sustainable Drainage Systems (SuDS).
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Affiliation(s)
- Rixia Zan
- School of Engineering, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom
| | - Ross Stirling
- School of Engineering, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom; UKCRIC National Green Infrastructure Facility, Newcastle upon Tyne NE4 5TG, United Kingdom
| | - Adrian Blackburn
- School of Engineering, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom
| | - Claire Walsh
- School of Engineering, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom; UKCRIC National Green Infrastructure Facility, Newcastle upon Tyne NE4 5TG, United Kingdom
| | - David Werner
- School of Engineering, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom.
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15
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Muenzel D, Bani A, De Brauwer M, Stewart E, Djakiman C, Halwi, Purnama R, Yusuf S, Santoso P, Hukom FD, Struebig M, Jompa J, Limmon G, Dumbrell A, Beger M. Combining environmental DNA and visual surveys can inform conservation planning for coral reefs. Proc Natl Acad Sci U S A 2024; 121:e2307214121. [PMID: 38621123 PMCID: PMC11047114 DOI: 10.1073/pnas.2307214121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 11/14/2023] [Indexed: 04/17/2024] Open
Abstract
Environmental DNA (eDNA) metabarcoding has the potential to revolutionize conservation planning by providing spatially and taxonomically comprehensive data on biodiversity and ecosystem conditions, but its utility to inform the design of protected areas remains untested. Here, we quantify whether and how identifying conservation priority areas within coral reef ecosystems differs when biodiversity information is collected via eDNA analyses or traditional visual census records. We focus on 147 coral reefs in Indonesia's hyper-diverse Wallacea region and show large discrepancies in the allocation and spatial design of conservation priority areas when coral reef species were surveyed with underwater visual techniques (fishes, corals, and algae) or eDNA metabarcoding (eukaryotes and metazoans). Specifically, incidental protection occurred for 55% of eDNA species when targets were set for species detected by visual surveys and 71% vice versa. This finding is supported by generally low overlap in detection between visual census and eDNA methods at species level, with more overlap at higher taxonomic ranks. Incomplete taxonomic reference databases for the highly diverse Wallacea reefs, and the complementary detection of species by the two methods, underscore the current need to combine different biodiversity data sources to maximize species representation in conservation planning.
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Affiliation(s)
- Dominic Muenzel
- School of Biology, Faculty of Biological Sciences, University of Leeds, LeedsLS2 9JT, United Kingdom
- Durrell Institute of Conservation and Ecology, School of Anthropology and Conservation, University of Kent, CanterburyCT2 7NR, United Kingdom
| | - Alessia Bani
- School of Biology, Faculty of Biological Sciences, University of Leeds, LeedsLS2 9JT, United Kingdom
- School of Life Sciences, University of Essex, ColchesterCO4 3SQ, United Kingdom
- College of Science and Engineering, School of Built and Natural Environment,University of Derby, DerbyDE22 1 GB, United Kingdom
| | - Maarten De Brauwer
- School of Biology, Faculty of Biological Sciences, University of Leeds, LeedsLS2 9JT, United Kingdom
- Commonwealth Scientific and Industrial Research Organisation Oceans & Atmosphere, Battery Point, Hobart, TAS7004, Australia
| | - Eleanor Stewart
- Durrell Institute of Conservation and Ecology, School of Anthropology and Conservation, University of Kent, CanterburyCT2 7NR, United Kingdom
| | - Cilun Djakiman
- School of Biology, Faculty of Biological Sciences, University of Leeds, LeedsLS2 9JT, United Kingdom
- Maritime and Marine Science Center of Excellence, Pattimura University, Ambon85XW+H66, Indonesia
| | - Halwi
- Graduate School, Universitas Hasanuddin, Makassar90245, Indonesia
| | - Ray Purnama
- Maritime and Marine Science Center of Excellence, Pattimura University, Ambon85XW+H66, Indonesia
| | - Syafyuddin Yusuf
- Faculty of Marine Science and Fisheries, Universitas Hasanuddin, Makassar90245, Indonesia
| | - Prakas Santoso
- Department of Marine Science and Technology, Institut Pertanian Bogor, Bogor16680, Indonesia
| | - Frensly D. Hukom
- Research Centre for Oceanography, Badan Riset dan Inovasi Nasional, Jakarta14430, Indonesia
- The Center for Collaborative Research on Aquatic Ecosystem in Eastern Indonesia, Pattimura University, Ambon97234, Indonesia
| | - Matthew Struebig
- Durrell Institute of Conservation and Ecology, School of Anthropology and Conservation, University of Kent, CanterburyCT2 7NR, United Kingdom
| | - Jamaluddin Jompa
- Faculty of Marine Science and Fisheries, Universitas Hasanuddin, Makassar90245, Indonesia
| | - Gino Limmon
- Maritime and Marine Science Center of Excellence, Pattimura University, Ambon85XW+H66, Indonesia
- The Center for Collaborative Research on Aquatic Ecosystem in Eastern Indonesia, Pattimura University, Ambon97234, Indonesia
| | - Alex Dumbrell
- School of Life Sciences, University of Essex, ColchesterCO4 3SQ, United Kingdom
| | - Maria Beger
- School of Biology, Faculty of Biological Sciences, University of Leeds, LeedsLS2 9JT, United Kingdom
- Centre for Biodiversity and Conservation Science, School of Biological Sciences, University of Queensland, Brisbane, QLD4072, Australia
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16
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Honka J, Kvist L, Olli S, Laaksonen T, Aspi J. Optimised PCR assays for detecting elusive waterfowl from environmental DNA. Ecol Evol 2024; 14:e11224. [PMID: 38571801 PMCID: PMC10985361 DOI: 10.1002/ece3.11224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 03/07/2024] [Accepted: 03/15/2024] [Indexed: 04/05/2024] Open
Abstract
For many aquatic and semiaquatic mammal, amphibian and fish species, environmental DNA (eDNA) methods are employed to detect species distribution and to monitor their presence, but eDNA is much less employed for avian species. Here, we developed primers for the detection of true geese and swan species using eDNA and optimised a PCR protocol for eDNA. We selected taiga bean goose (Anser fabalis fabalis) as our focal (sub)species and sampled water from lakes, from which the presence of taiga bean goose was visually confirmed. To test, if taiga bean goose DNA could be detected among DNA of other goose species, we similarly sampled eDNA from a zoo pond housing several Anatidae species. We were able to detect taiga bean goose DNA in all but one of the tested lakes, including the zoo pond. The primers developed are not species-specific, but rather specific to the genus Anser, due to the close relatedness of Anser species, which prevented the development of species-specific primers and the use of, for example, quantitative PCR. We also developed eDNA primers for Branta species and Cygnus species and tested these primers using the same samples. Canada goose (B. canadensis) and barnacle goose (B. leucopsis) DNA were only detected in the zoo pond (in which they were present), as the sampled natural lakes fall outside the range of these species. We detected whooper swan (C. cygnus) DNA in three lakes and the zoo pond (in which the species was present). The eDNA method presented here provides a potential means to monitor elusive goose species and to study the co-occurrence of large waterfowl.
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Affiliation(s)
- Johanna Honka
- Ecology and Genetics Research UnitUniversity of OuluOuluFinland
| | - Laura Kvist
- Ecology and Genetics Research UnitUniversity of OuluOuluFinland
| | - Suvi Olli
- Ecology and Genetics Research UnitUniversity of OuluOuluFinland
| | - Toni Laaksonen
- Department of BiologyUniversity of TurkuTurkuFinland
- Natural Resources Institute Finland (Luke)HelsinkiFinland
| | - Jouni Aspi
- Ecology and Genetics Research UnitUniversity of OuluOuluFinland
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17
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Mertz NE, Paterson RA, Finstad B, Brandsegg H, Andersskog IPØ, Fossøy F. Molecular quantification of parasitic sea louse larvae depends on species and life stage. J Fish Dis 2024; 47:e13908. [PMID: 38146073 DOI: 10.1111/jfd.13908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 11/30/2023] [Accepted: 12/08/2023] [Indexed: 12/27/2023]
Abstract
Sea lice cause substantial economic and environmental harm to Norway's aquaculture industry and wild salmonid populations. Rapid, accurate quantification of lice larval densities in coastal waters remains the greatest bottleneck for providing empirical data on infestation risk within wild salmon habitats and aquaculture production regions. We evaluated the capability of droplet digital PCR (ddPCR) as an absolute quantification method for the planktonic stages of two parasitic louse species, Lepeophtheirus salmonis (Krøyer) and Caligus elongatus (von Nordman). Results demonstrated linear relationships between the DNA quantity measured and the number of spiked larvae for both species and life stages. However, L. salmonis contained a significantly greater number of DNA copies than C. elongatus individuals and for C. elongatus, nauplii displayed a significantly higher number of DNA copies than copepodids. Our results suggest that ddPCR can effectively enumerate louse larvae, but interpreting ddPCR results differ between the two louse species. Obtaining larval abundance estimates from marine plankton samples will depend on the nauplii to copepodid ratio for C. elongatus, but not for L. salmonis.
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Affiliation(s)
- Nathan E Mertz
- Department of Biology, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
- Norwegian Institute for Nature Research (NINA), Trondheim, Norway
| | | | - Bengt Finstad
- Department of Biology, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
- Norwegian Institute for Nature Research (NINA), Trondheim, Norway
| | - Hege Brandsegg
- Norwegian Institute for Nature Research (NINA), Trondheim, Norway
| | | | - Frode Fossøy
- Norwegian Institute for Nature Research (NINA), Trondheim, Norway
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18
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Han X, Chen J, Wu L, Zhang G, Fan X, Yan T, Zhu L, Guan Y, Zhou L, Hou T, Xue X, Li X, Wang M, Xing H, Xiong X, Wang Z. Species distribution modeling combined with environmental DNA analysis to explore distribution of invasive alien mosquitofish (Gambusia affinis) in China. Environ Sci Pollut Res Int 2024; 31:25978-25990. [PMID: 38492140 DOI: 10.1007/s11356-024-32935-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 03/11/2024] [Indexed: 03/18/2024]
Abstract
China has become one of the most serious countries suffering from biological invasions in the world. In the context of global climate change, invasive alien species (IAS) are likely to invade a wider area, posing greater ecological and economic threats in China. Western mosquitofish (Gambusia affinis), which is known as one of the 100 most invasive alien species, has distributed widely in southern China and is gradually spreading to the north, causing serious ecological damage and economic losses. However, its distribution in China is still unclear. Hence, there is an urgent need for a more convenient way to detect and monitor the distribution of G. affinis to put forward specific management. Therefore, we detected the distribution of G. affinis in China under current and future climate change by combing Maxent modeling prediction and eDNA verification, which is a more time-saving and reliable method to estimate the distribution of species. The Maxent modeling showed that G. affinis has a broad habitat suitability in China (especially in southern China) and would continue to spread in the future with ongoing climate change. However, eDNA monitoring showed that occurrences can already be detected in regions that Maxent still categorized as unsuitable. Besides temperature, precipitation and human influence were the most important environmental factors affecting the distribution of G. affinis in China. In addition, by environmental DNA analysis, we verified the presence of G. affinis predicted by Maxent in the Qinling Mountains where the presence of G. affinis had not been previously recorded.
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Affiliation(s)
- Xu Han
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Jinxiao Chen
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Lang Wu
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Guo Zhang
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Xiaoteng Fan
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Tao Yan
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Long Zhu
- College of Marine Science and Fisheries, Jiangsu Ocean University, Lianyungang, 222005, Jiangsu, China
| | - Yongjing Guan
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Linjun Zhou
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Tingting Hou
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Xue Xue
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Xiangju Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Mingrong Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Haoran Xing
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Xiaofan Xiong
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Zaizhao Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China.
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19
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Yabuki A, Hoshino T, Nakamura T, Mizuno K. The copy number of the eukaryotic rRNA gene can be counted comprehensively. Microbiologyopen 2024; 13:e1399. [PMID: 38436548 PMCID: PMC10910464 DOI: 10.1002/mbo3.1399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 01/16/2024] [Accepted: 01/30/2024] [Indexed: 03/05/2024] Open
Abstract
Gene sequence has been widely used in molecular ecology. For instance, the ribosomal RNA (rRNA) gene has been widely used as a biological marker to understand microbial communities. The variety of the detected rRNA gene sequences reflects the diversity of the microorganisms existing in the analyzed sample. Their biomass can also be estimated by applying quantitative sequencing with information on rRNA gene copy numbers in genomes; however, information on rRNA gene copy numbers is still limited. Especially, the copy number in microbial eukaryotes is much less understood than that of prokaryotes, possibly because of the large and complex structure of eukaryotic genomes. In this study, we report an alternative approach that is more appropriate than the existing method of quantitative sequencing and demonstrate that the copy number of eukaryotic rRNA can be measured efficiently and comprehensively. By applying this approach widely, information on the eukaryotic rRNA copy number can be determined, and their community structures can be depicted and compared more efficiently.
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Affiliation(s)
- Akinori Yabuki
- Research Institute for Global ChangeJapan Agency for Marine‐Earth Science and TechnologyYokosukaKanagawaJapan
- Advanced Institute for Marine Ecosystem Change (WPI‐AIMEC)YokosukaKanagawaJapan
| | - Tatsuhiko Hoshino
- Advanced Institute for Marine Ecosystem Change (WPI‐AIMEC)YokosukaKanagawaJapan
- Institute for Extra‐cutting‐edge Science and Technology Avant‐garde ResearchJapan Agency for Marine‐Earth Science and TechnologyNankokuKochiJapan
| | - Tamiko Nakamura
- Research Institute for Global ChangeJapan Agency for Marine‐Earth Science and TechnologyYokosukaKanagawaJapan
| | - Keiko Mizuno
- Research Institute for Global ChangeJapan Agency for Marine‐Earth Science and TechnologyYokosukaKanagawaJapan
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Ibabe A, Menéndez-Teleña D, Soto-López V, Ardura A, Arias A, Bartolomé M, Borrell YJ, Fernandez S, Machado-Schiaffino G, Mateo JL, Dopico E, Garcia-Vazquez E. New dockside eDNA based protocol to detect the seaweed Asparagopsis armata evaluated by stakeholders. Mar Pollut Bull 2024; 201:116259. [PMID: 38492267 DOI: 10.1016/j.marpolbul.2024.116259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 03/10/2024] [Accepted: 03/11/2024] [Indexed: 03/18/2024]
Abstract
Early detection of invasive species is crucial to deal effectively with biological invasions in ports, which are hotspots of species introductions. In this study, a simplified end-time PCR methodology conducted on eDNA from water samples was developed for rapid detection of the invasive seaweed Asparagopsis armata (four hours from water collection to result visualization). It was tested dockside in four international Spanish ports in presence of stakeholders, whose feedback was obtained to explore the real applicability of this biotechnology. Although biological invasions were not a main concern for them, results indicate a unanimous approval of the methodology by the stakeholders, having detected the presence of A. armata in three of the ports. Stakeholders suggested further developments for easier application of the tool and multiple species detection, to be adopted for the control of invasive species in ports.
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Affiliation(s)
- Aitor Ibabe
- Department of Functional Biology, C/Julian Claveria s/n, 33006 Oviedo, Spain
| | - Deva Menéndez-Teleña
- Department of Nautical Science and Technology, Escuela S. Marina Civil de Gijon 1ª Planta, Campus de Gijon s/n, 33203 Gijon, Spain
| | - Verónica Soto-López
- Department of Nautical Science and Technology, Escuela S. Marina Civil de Gijon 1ª Planta, Campus de Gijon s/n, 33203 Gijon, Spain
| | - Alba Ardura
- Department of Functional Biology, C/Julian Claveria s/n, 33006 Oviedo, Spain
| | - Andrés Arias
- Department of Biology of Organisms and Systems, C/Catedrático Rodrigo Uría s/n, 33071 Oviedo, Spain
| | - Marlene Bartolomé
- Department of Nautical Science and Technology, Escuela S. Marina Civil de Gijon 1ª Planta, Campus de Gijon s/n, 33203 Gijon, Spain
| | - Yaisel J Borrell
- Department of Functional Biology, C/Julian Claveria s/n, 33006 Oviedo, Spain
| | - Sara Fernandez
- Department of Functional Biology, C/Julian Claveria s/n, 33006 Oviedo, Spain
| | | | - Juan L Mateo
- Department of Informatics, Edificio Departamental 1, Campus de Gijon s/n, 33204 Gijon, Spain
| | - Eduardo Dopico
- Department of Education Sciences, Campus de Llamaquique, C/Aniceto Sela s/n, 33005 Oviedo, Spain
| | - Eva Garcia-Vazquez
- Department of Functional Biology, C/Julian Claveria s/n, 33006 Oviedo, Spain.
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21
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Yang C, Du Y, Zeng X, Ni G. Development and Testing of Species-Specific Primers for Detecting the Presence of the Northern Pacific Sea Star (Asterias amurensis) from Environmental DNA. Mar Biotechnol (NY) 2024; 26:215-222. [PMID: 38341825 DOI: 10.1007/s10126-024-10292-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 01/25/2024] [Indexed: 02/13/2024]
Abstract
The starfish Asterias amurensis, a well-known predator of molluscan species in intertidal ecosystems, has caused substantial ecological and economic losses in North China such as offshore Qingdao. Effective monitoring and prevention measures are urged to minimize its negative impacts. Compared with traditional biomonitoring methods, environmental DNA technology has emerged as a powerful and cost-efficient tool for inferring species' presence and abundance. In this study, we developed a pair of species-specific primers (i.e., Ast-F and Ast-R) for the A. amurensis mitochondrial COI gene and tested its utility in amplifying and quantifying the DNA fragments from environmental samples under both laboratory and field conditions. The results of controlled water tank experiments demonstrated that the amount of eDNA released by A. amurensis was positively related to its biomass; after the removal of the starfish, the eDNA degraded significantly in 24 h and remained detectable for 8 days. The number of eDNA copies enriched tended to increase with smaller pore size of filter membrane and larger volume of filtered water. For field tests, we confirmed the validation of our approach in six locations in Qingdao by filtering 1000 ml water per sample with a 0.45-µm pore size filtration. All the amplification products generated a single and bright band via gel electrophoresis, and the quantitative PCR results unveiled significant differences in eDNA copies. This study provided an eDNA-based approach for investigating the distribution and biomass of A. amurensis, which may help to formulate early warning and management strategies in coastal Qingdao and other regions.
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Affiliation(s)
- Chenhu Yang
- Ministry of Education Key Laboratory of Mariculture, Ocean University of China, Qingdao, 266003, China
| | - Yanzhen Du
- Ministry of Education Key Laboratory of Mariculture, Ocean University of China, Qingdao, 266003, China
| | - Xiaoqi Zeng
- Ministry of Education Key Laboratory of Mariculture, Ocean University of China, Qingdao, 266003, China
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Gang Ni
- Ministry of Education Key Laboratory of Mariculture, Ocean University of China, Qingdao, 266003, China.
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22
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Chen Y, Bin Q, Liu H, Xie Y, Wang S, Lu J, Ou W, Zhang M, Wang L, Yu K. A novel biosensing strategy on the dynamic and on-site detection of Vibrio coralliilyticus eDNA for coral health warnings. Bioelectrochemistry 2024; 158:108697. [PMID: 38554560 DOI: 10.1016/j.bioelechem.2024.108697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Revised: 03/20/2024] [Accepted: 03/27/2024] [Indexed: 04/01/2024]
Abstract
Heat stress and coral diseases are the predominant factors causing the degradation of coral reef ecosystems. Over recent years, Vibrio coralliilyticus was identified as a temperature-dependent pathogen causing tissue lysis in Pocillopora damicornis and one of the primary pathogens causing bleaching and mortality in other corals. Yet current detection techniques for V. coralliilyticus rely primarily on qPCR and ddPCR, which cannot meet the requirements for non-invasive and real-time detection. Herein, we developed an effective electrochemical biosensor modified by an Au-MoS2/rGO (AMG) nanocomposites and a specific capture probe to dynamically detect V. coralliilyticus environment DNA (eDNA) in aquarium experiments, with a lower limit of detection (0.28 fM) for synthetic DNA and a lower limit of quantification (9.8 fg/µL, ∼0.86 copies/µL) for genomic DNA. Its reliability and accuracy were verified by comparison with the ddPCR method (P > 0.05). Notably, coral tissue started to lyse at only 29 °C when the concentration of V. coralliilyticus increased abruptly to 880 copies/µL, indicating the biosensor could reflect the types of pathogen and health risks of corals under heat stress. Overall, the novel and reliable electrochemical biosensing technology provides an efficient strategy for the on-site monitoring and early warning of coral health in the context of global warming.
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Affiliation(s)
- Yingzhan Chen
- School of Resources, Environment and Materials, School of Marine Sciences, School of Chemistry and Chemical Engineering, School of Life Science and Technology, Guangxi University, Nanning 530004, China; Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Guangxi University, Nanning 530004, China
| | - Qi Bin
- School of Resources, Environment and Materials, School of Marine Sciences, School of Chemistry and Chemical Engineering, School of Life Science and Technology, Guangxi University, Nanning 530004, China; Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Guangxi University, Nanning 530004, China
| | - Hongjie Liu
- School of Resources, Environment and Materials, School of Marine Sciences, School of Chemistry and Chemical Engineering, School of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Yuanyu Xie
- School of Resources, Environment and Materials, School of Marine Sciences, School of Chemistry and Chemical Engineering, School of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Shaopeng Wang
- School of Resources, Environment and Materials, School of Marine Sciences, School of Chemistry and Chemical Engineering, School of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Jie Lu
- School of Resources, Environment and Materials, School of Marine Sciences, School of Chemistry and Chemical Engineering, School of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Wenchao Ou
- School of Resources, Environment and Materials, School of Marine Sciences, School of Chemistry and Chemical Engineering, School of Life Science and Technology, Guangxi University, Nanning 530004, China; Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Guangxi University, Nanning 530004, China
| | - Man Zhang
- School of Resources, Environment and Materials, School of Marine Sciences, School of Chemistry and Chemical Engineering, School of Life Science and Technology, Guangxi University, Nanning 530004, China; Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Guangxi University, Nanning 530004, China.
| | - Liwei Wang
- School of Resources, Environment and Materials, School of Marine Sciences, School of Chemistry and Chemical Engineering, School of Life Science and Technology, Guangxi University, Nanning 530004, China; Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Guangxi University, Nanning 530004, China.
| | - Kefu Yu
- School of Resources, Environment and Materials, School of Marine Sciences, School of Chemistry and Chemical Engineering, School of Life Science and Technology, Guangxi University, Nanning 530004, China; Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Guangxi University, Nanning 530004, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
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23
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Filippova N, Zvyagina E, Rudykina EA, Ishmanov TF, Filippov IV, Bulyonkova TM, Dobrynina AS. DNA-based occurrence dataset on peatland fungal communities studied by metabarcoding in north-western Siberia. Biodivers Data J 2024; 12:e119851. [PMID: 38586530 PMCID: PMC10998959 DOI: 10.3897/bdj.12.e119851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 03/19/2024] [Indexed: 04/09/2024] Open
Abstract
Background The paper represents the first DNA-based occurrence dataset on peatland fungal communities published for north-western Siberia, the first for Russia and complements several existing datasets on metabarcoding of peat soils globally. New information The aim of the present publication is to describe the first DNA-based occurrence dataset on fungal communities in peat soils and other substrates studied by the eDNA approach in the Mukhrino raised bog, located in a large paludified area of north-western Siberia. A comparison of the species diversity of larger fungi identified by the conventional approach and by eDNA showed a high proportion of shared taxa. Other groups (mainly Ascomycota), described by metabarcoding, revealed high diversity compared with conventional observation. Overall, the species richness identified in one peatland locality (the Mukhrino Bog) was comparable in number of species to the global estimation of fungal diversity in peatlands, previously reported in literature.
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Affiliation(s)
- Nina Filippova
- Yugra State University, Khanty-Mansiysk, RussiaYugra State UniversityKhanty-MansiyskRussia
| | - Elena Zvyagina
- Yugra State University, Khanty-Mansiysk, RussiaYugra State UniversityKhanty-MansiyskRussia
- Moscow State University, Moscow, RussiaMoscow State UniversityMoscowRussia
| | - Elena A. Rudykina
- Yugra State University, Khanty-Mansiysk, RussiaYugra State UniversityKhanty-MansiyskRussia
| | - Tagir F. Ishmanov
- Yugra State University, Khanty-Mansiysk, RussiaYugra State UniversityKhanty-MansiyskRussia
| | - Ilya V. Filippov
- Yugra State University, Khanty-Mansiysk, RussiaYugra State UniversityKhanty-MansiyskRussia
| | | | - Alevtina S. Dobrynina
- Yugra State University, Khanty-Mansiysk, RussiaYugra State UniversityKhanty-MansiyskRussia
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24
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Lu S, Zeng H, Xiong F, Yao M, He S. Advances in environmental DNA monitoring: standardization, automation, and emerging technologies in aquatic ecosystems. Sci China Life Sci 2024:10.1007/s11427-023-2493-5. [PMID: 38512561 DOI: 10.1007/s11427-023-2493-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 10/30/2023] [Indexed: 03/23/2024]
Abstract
Environmental DNA (eDNA) monitoring, a rapidly advancing technique for assessing biodiversity and ecosystem health, offers a noninvasive approach for detecting and quantifying species from various environmental samples. In this review, a comprehensive overview of current eDNA collection and detection technologies is provided, emphasizing the necessity for standardization and automation in aquatic ecological monitoring. Furthermore, the intricacies of water bodies, from streams to the deep sea, and the associated challenges they pose for eDNA capture and analysis are explored. The paper delineates three primary eDNA survey methods, namely, bringing back water, bringing back filters, and bringing back data, each with specific advantages and constraints in terms of labor, transport, and data acquisition. Additionally, innovations in eDNA sampling equipment, including autonomous drones, subsurface samplers, and in-situ filtration devices, and their applications in monitoring diverse taxa are discussed. Moreover, recent advancements in species-specific detection and eDNA metabarcoding are addressed, highlighting the integration of novel techniques such as CRISPR-Cas and nanopore sequencing that enable precise and rapid detection of biodiversity. The implications of environmental RNA and epigenetic modifications are considered for future applications in providing nuanced ecological data. Lastly, the review stresses the critical role of standardization and automation in enhancing data consistency and comparability for robust long-term biomonitoring. We propose that the amalgamation of these technologies represents a paradigm shift in ecological monitoring, aligning with the urgent call for biodiversity conservation and sustainable management of aquatic ecosystems.
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Affiliation(s)
- Suxiang Lu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Honghui Zeng
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Fan Xiong
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Meng Yao
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, 100871, China.
- School of Life Sciences, Peking University, Beijing, 100871, China.
| | - Shunping He
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
- Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China.
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China.
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25
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Shah S, Damare SR, Mascarenhas-Pereira MBL, Patil J, Parab S, Nair S, Ghosh A. An insight into the prokaryotic diversity from a polymetallic nodule-rich region in the Central Indian Ocean Basin using next generation sequencing approach. Front Microbiol 2024; 15:1295149. [PMID: 38567074 PMCID: PMC10985493 DOI: 10.3389/fmicb.2024.1295149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 02/28/2024] [Indexed: 04/04/2024] Open
Abstract
Deep sea is a vast, dark, and difficult-to-access terrain and is now looked upon as a unique niche harboring diverse microorganism. We used a metataxonomic approach to decipher the microbial diversity present in the water column (surface to near bottom), water overlaying the sediments, and the deep-sea sediments (up to 35 cm) from the Indian Contract Region (ICR) in the Central Indian Ocean Basin (CIOB). Samples were collected from #IRZ (Impact Reference Zone), #PRZ (Potential Reference Zone), and #BC20 (Control site, outside potential mining area) with an average water depth of 5,200 m. 16S rRNA (V3-V4 region) amplicon sequencing on the MiSeq platform resulted in 942,851 ASVs across 65 water and sediment samples. Higher prokaryotic diversity was observed below 200 m in the water column to the seafloor. Proteobacteria was the most dominant bacterial phylum among all the water samples while Firmicutes, Actinobacteria and, Bacteroidota dominated the sediments. Sediment (below 10 cm) was co-dominated by Firmicutes. Thermoplasmata was the dominant archaeal group in the water column while Crenarchaeota was in the sediments. BC20 was less diverse than IRZ and PRZ. Deep Sea microorganisms could play a vital role in the mineralization processes, nutrient cycling, and also different biogeochemical cycles.
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Affiliation(s)
- Shruti Shah
- Biological Oceanography Division, CSIR-National Institute of Oceanography, Panaji, India
- School of Earth, Ocean, and Atmospheric Sciences, Goa University, Taleigão, India
| | - Samir R. Damare
- Biological Oceanography Division, CSIR-National Institute of Oceanography, Panaji, India
| | | | - Jayesh Patil
- Geological Oceanography Division, CSIR-National Institute of Oceanography, Panaji, India
| | - Sneha Parab
- Geological Oceanography Division, CSIR-National Institute of Oceanography, Panaji, India
| | - Sushil Nair
- Geological Oceanography Division, CSIR-National Institute of Oceanography, Panaji, India
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26
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Damasceno FL, Alves Martins MV, Frontalini F, Pawlowski J, Cermakova K, Angeles IB, Costa Santos LG, Filho JGM, Francescangeli F, Senez-Mello TM, Castelo WFL, Rebouças RC, Duleba W, Mello E Sousa SHD, Laut L, Antonioli L. Assessment of the ecological quality status of the Sepetiba Bay (SE Brazil): When metabarcoding meets morphology on foraminifera. Mar Environ Res 2024; 195:106340. [PMID: 38232436 DOI: 10.1016/j.marenvres.2024.106340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 12/22/2023] [Accepted: 01/01/2024] [Indexed: 01/19/2024]
Abstract
In recent years, the region surrounding Sepetiba Bay (SB; SE Brazil) has become a hub of intense urban expansion and economic exploitation in response to ore transport and industrial and port activities. As a result, contaminants have been introduced into the bay, leading to an overall worsening of the environmental quality. The present work applies for the first time a foraminiferal morphology-based approach (M) and eDNA-based metabarcoding sequencing (G), along with geochemical data to assess the ecological quality status (EcoQS) in the SB. Principal component analysis shows that the eDNA and morphospecies diversity as well as most of the taxa relative abundance decline in response to the environmental stress (ES) gradient related to total organic carbon (TOC) and metal pollution. Based on ecological indices, Exp(H'bc) (G), Exp(H'bc) (M), foraminifera ATZI marine biotic index (Foram-AMBI), Foram Stress Index (FSI), and geochemical indices (TOC and Potential Ecological Risk Index), the lowest values of EcoQS (i.e., bad to moderate) are inferred in the innermost part of the SB. Despite minor discrepancies among the six EcoQS indices, an agreement has been found for 63% of the stations. To improve the agreement between the ecological indices, it is necessary to fill the gap in species ecology; information on the ecology of many species is still unknown. This work reinforces the importance of molecular analysis and morphological methods in environmental impact studies and confirms the reliability of foraminiferal metabarcoding in EcoQS assessment. This is the first study evaluating the EcoQS in the South Atlantic by using combined foraminiferal eDNA metabarcoding with morphological data.
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Affiliation(s)
- Fabrício Leandro Damasceno
- Universidade do Estado do Rio de Janeiro, UERJ, Av. São Francisco Xavier, 524, Maracanã, CEP: 20550-013 Rio de Janeiro, RJ, Brazil.
| | - Maria Virgínia Alves Martins
- Universidade do Estado do Rio de Janeiro, UERJ, Av. São Francisco Xavier, 524, Maracanã, CEP: 20550-013 Rio de Janeiro, RJ, Brazil; Universidade de Aveiro, GeoBioTec, Departamento de Geociências, Campus de Santiago, 3810-193 Aveiro, Portugal.
| | - Fabrizio Frontalini
- Department of Pure and Applied Sciences, Università degli Studi di Urbino "Carlo Bo", 61029, Urbino, Italy.
| | - Jan Pawlowski
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland; ID-Gene ecodiagnostics, Chemin du Pont-du-Centenaire 109, 1228 Plan-les-Ouates, Switzerland; Institute of Oceanology, Polish Academy of Sciences, 81-712 Sopot, Poland.
| | - Kristina Cermakova
- ID-Gene ecodiagnostics, Chemin du Pont-du-Centenaire 109, 1228 Plan-les-Ouates, Switzerland.
| | - Inès Barrenechea Angeles
- Department of Geosciences, The Arctic University of Norway, Dramsvegen 201, N-9037, Tromsø, Norway.
| | | | | | - Fabio Francescangeli
- Department of Geosciences, University of Fribourg, Chemin du Musée 6, 1700 Fribourg/Freiburg, Switzerland.
| | - Thaise M Senez-Mello
- Universidade do Estado do Rio de Janeiro, UERJ, Av. São Francisco Xavier, 524, Maracanã, CEP: 20550-013 Rio de Janeiro, RJ, Brazil; Federal Fluminense University (UFF), Rio de Janeiro, Brazil.
| | - Wellen Fernanda Louzada Castelo
- Universidade do Estado do Rio de Janeiro, UERJ, Av. São Francisco Xavier, 524, Maracanã, CEP: 20550-013 Rio de Janeiro, RJ, Brazil.
| | - Renata Cardia Rebouças
- Universidade do Estado do Rio de Janeiro, UERJ, Av. São Francisco Xavier, 524, Maracanã, CEP: 20550-013 Rio de Janeiro, RJ, Brazil.
| | - Wania Duleba
- Escola de Artes, Ciências e Humanidades da Universidade de São Paulo. Rua Arlindo Bettio, 1000, Vila Guaraciaba, São Paulo - SP, Brazil.
| | - Silvia Helena de Mello E Sousa
- Instituto Oceanográfico, Universidade de São Paulo (IOUSP). Address: Pça. do Oceanográfico, 191, Butantã, São Paulo, Brazil.
| | - Lazaro Laut
- Universidade Federal do Estado do Rio de Janeiro - UNIRIO, Av. Pasteur 458, s. 500, Urca, Rio de Janeiro, Brazil.
| | - Luzia Antonioli
- Universidade do Estado do Rio de Janeiro, UERJ, Av. São Francisco Xavier, 524, Maracanã, CEP: 20550-013 Rio de Janeiro, RJ, Brazil.
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Fukumori K, Kondo NI, Kohzu A, Tsuchiya K, Ito H, Kadoya T. Vertical eDNA distribution of cold-water fishes in response to environmental variables in stratified lake. Ecol Evol 2024; 14:e11091. [PMID: 38500853 PMCID: PMC10945234 DOI: 10.1002/ece3.11091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 01/22/2024] [Accepted: 02/16/2024] [Indexed: 03/20/2024] Open
Abstract
In summer, the survival zones of cold-water species are predicted to narrow by both increasing water temperatures from the surface and by expanding hypoxic zones from the lake bottom. To examine how the abundance of cold-water fishes changes along environmental gradients, we assessed the vertical environmental DNA (eDNA) distributions of three salmonid species which may have different water temperature tolerances during both stratification and turnover periods using quantitative PCR (qPCR). In addition, we examined on the vertical distribution of diverse fish fauna using an eDNA metabarcoding assay. The results suggested that the kokanee salmon (Oncorhynchus nerka) eDNA were abundant in deep, cold waters. On the other hand, rainbow trout (O. mykiss) eDNA were distributed uniformly throughout the water column, suggesting that they may have high water-temperature tolerance compared with kokanee salmon. The eDNA concentrations of masu salmon (O. masou) were below the detection limit (i.e., <10 copies μL-1) at all stations and depths and hence could not be quantified during stratification. Together with the finding that the eDNA distributions of other prey fish species were also constrained vertically in species-specific ways, our results suggest that climate change will result in substantial changes in the vertical distributions of lake fish species and thus affect their populations and interactions.
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Affiliation(s)
- Kayoko Fukumori
- Biodiversity DivisionNational Institute for Environmental Studies (NIES)IbarakiJapan
| | - Natsuko I. Kondo
- Biodiversity DivisionNational Institute for Environmental Studies (NIES)IbarakiJapan
| | - Ayato Kohzu
- Regional Environment Conservation DivisionNational Institute for Environmental Studies (NIES)IbarakiJapan
| | - Kenji Tsuchiya
- Regional Environment Conservation DivisionNational Institute for Environmental Studies (NIES)IbarakiJapan
| | - Hiroshi Ito
- Biodiversity DivisionNational Institute for Environmental Studies (NIES)IbarakiJapan
| | - Taku Kadoya
- Biodiversity DivisionNational Institute for Environmental Studies (NIES)IbarakiJapan
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28
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Cagri Ozturk R, Feyzioglu AM, Capkin E, Yildiz I, Altinok I. Effects of environmental parameters on spatial and temporal distribution of marine microbial communities in the southern Black Sea. Mar Environ Res 2024; 195:106344. [PMID: 38232435 DOI: 10.1016/j.marenvres.2024.106344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 12/27/2023] [Accepted: 01/07/2024] [Indexed: 01/19/2024]
Abstract
The Black Sea is a unique environment with strong and permanent vertical stratification, with a thin layer of oxic zone above and a permanent anoxic zone below. Few high-throughput genomic surveys have been conducted to examine microbiota in the Black Sea. Yet, there is no study on the seasonal and vertical variation in microbial community compositions, driving forces and mechanisms of community assembly. In this study, seasonal, vertical, and spatial microbial assemblages were studied in terms of diversity, abundance, and community structure using 16S rRNA metabarcoding. 16S rRNA metabarcoding confirmed seasonal changes in microbial communities and the presence of distinct microbial groups among different water layers. Taxa belonging to Cyanobiaceae contributed a large fraction of the total biomass and were the most abundant autotrophic bacteria found across the whole water column, including hydrogen sulfide-containing anoxic zone. Temperature, salinity, water density, conductivity, light, chlorophyll-a, O2, NO3, NH3, PO4, Si, and H2S had a significant influence on the vertical bacterial community assemblages. The copper mine discharge system at 180 m did not affect microbial community structure and composition. Temperature seemed to be a primary factor in the variance between shallow depths. In conclusion, the lack of light, low dissolved oxygen levels, and low temperature do not restrict microbial diversity, as proven by the higher diversity observed in deeper zones. Wastewater in Black Sea region may be discharged into the Black Sea to depth of 180 m or deeper without impacting microbial ecology.
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Affiliation(s)
- Rafet Cagri Ozturk
- Department of Fisheries Technology Engineering, Faculty of Marine Sciences, Karadeniz Technical University, 61530, Trabzon, Türkiye; Aquatic Animal Health and Molecular Genetics (AQUANETIC) Lab, Department of Chemistry C Block, 61080, Ortahisar, Trabzon, Türkiye.
| | - Ali Muzaffer Feyzioglu
- Department of Marine Science and Technology, Faculty of Marine Science, Karadeniz Technical University, 61530, Trabzon, Türkiye.
| | - Erol Capkin
- Department of Fisheries Technology Engineering, Faculty of Marine Sciences, Karadeniz Technical University, 61530, Trabzon, Türkiye.
| | - Ilknur Yildiz
- Institute of Marine Sciences and Technology, Karadeniz Technical University, 61080, Trabzon, Türkiye.
| | - Ilhan Altinok
- Department of Fisheries Technology Engineering, Faculty of Marine Sciences, Karadeniz Technical University, 61530, Trabzon, Türkiye; Aquatic Animal Health and Molecular Genetics (AQUANETIC) Lab, Department of Chemistry C Block, 61080, Ortahisar, Trabzon, Türkiye; Institute of Marine Sciences and Technology, Karadeniz Technical University, 61080, Trabzon, Türkiye.
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Rishan ST, Kline RJ, Rahman MS. Exploitation of environmental DNA ( eDNA) for ecotoxicological research: A critical review on eDNA metabarcoding in assessing marine pollution. Chemosphere 2024; 351:141238. [PMID: 38242519 DOI: 10.1016/j.chemosphere.2024.141238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 01/05/2024] [Accepted: 01/15/2024] [Indexed: 01/21/2024]
Abstract
The rise in worldwide population has led to a noticeable spike in the production, consumption, and transportation of energy and food, contributing to elevated environmental pollution. Marine pollution is a significant global environmental issue with ongoing challenges, including plastic waste, oil spills, chemical pollutants, and nutrient runoff, threatening marine ecosystems, biodiversity, and human health. Pollution detection and assessment are crucial to understanding the state of marine ecosystems. Conventional approaches to pollution evaluation usually represent laborious and prolonged physical and chemical assessments, constraining their efficacy and expansion. The latest advances in environmental DNA (eDNA) are valuable methods for the detection and surveillance of pollution in the environment, offering enhanced sensibility, efficacy, and involvement. Molecular approaches allow genetic information extraction from natural resources like water, soil, or air. The application of eDNA enables an expanded evaluation of the environmental condition by detecting both identified and unidentified organisms and contaminants. eDNA methods are valuable for assessing community compositions, providing indirect insights into the intensity and quality of marine pollution through their effects on ecological communities. While eDNA itself is not direct evidence of pollution, its analysis offers a sensitive tool for monitoring changes in biodiversity, serving as an indicator of environmental health and allowing for the indirect estimation of the impact and extent of marine pollution on ecosystems. This review explores the potential of eDNA metabarcoding techniques for detecting and identifying marine pollutants. This review also provides evidence for the efficacy of eDNA assessment in identifying a diverse array of marine pollution caused by oil spills, harmful algal blooms, heavy metals, ballast water, and microplastics. In this report, scientists can expand their knowledge and incorporate eDNA methodologies into ecotoxicological research.
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Affiliation(s)
- Sakib Tahmid Rishan
- Biochemistry and Molecular Biology Program, School of Integrative Biological and Chemical Sciences, University of Texas Rio Grande Valley, Brownsville, Texas, USA
| | - Richard J Kline
- Biochemistry and Molecular Biology Program, School of Integrative Biological and Chemical Sciences, University of Texas Rio Grande Valley, Brownsville, Texas, USA; School of Earth, Environmental, and Marine Sciences, University of Texas Rio Grande Valley, Brownsville, Texas, USA
| | - Md Saydur Rahman
- Biochemistry and Molecular Biology Program, School of Integrative Biological and Chemical Sciences, University of Texas Rio Grande Valley, Brownsville, Texas, USA; School of Earth, Environmental, and Marine Sciences, University of Texas Rio Grande Valley, Brownsville, Texas, USA.
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Shi L, Zhang D, Yang M, Li F, Zhao J, He Z, Bai Y. New discovery of extremely high adsorption of environmental DNA on cuttlefish bone pyrolysis derivative via large pore structure and carbon film. Waste Manag 2024; 175:286-293. [PMID: 38237404 DOI: 10.1016/j.wasman.2024.01.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 01/02/2024] [Accepted: 01/09/2024] [Indexed: 01/29/2024]
Abstract
Environmental DNA (eDNA) carrying antibiotic resistance gene (ARG) has attracted a great deal of attention because of its threat to the ecology and human health. Traditional porous adsorbents, such as microporous biochar and natural mineral, are low-effective in removing eDNA from sewage. This study used cuttlefish-bone (CB), a fishery waste, as an anticipated material to adsorb a model compound of eDNA from herring sperm (hsDNA). An interesting result was firstly observed that extremely high DNA adsorption on cuttlefish-bone pyrolysis derivative (CCB) was up to 88.7 mg/g, 3-10 folds higher than that of most other adsorbents in the existing literatures, which was attributed to the carbon film and large pores. To achieve an adsorption rate of 75 %, hsDNA adsorption took 96 h on CB but only 24 h on CCB, which was attributed to the fluent channel of CCB. The ligand exchange, Ca2+ bridge and π-π interaction were identified as dominated adsorption mechanisms, based on FTIR and phosphate competition experiments. This study exploited a high-efficient, environmentally friendly, and low-cost adsorbent for treating ARG-contaminated soil and water.
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Affiliation(s)
- Lin Shi
- Shandong Provincial Key Laboratory of Water and Soil Conservation and Environmental Protection, College of Resources and Environment, Linyi University, Linyi, 276005, China.
| | - Di Zhang
- Shandong Provincial Key Laboratory of Water and Soil Conservation and Environmental Protection, College of Resources and Environment, Linyi University, Linyi, 276005, China; Yunnan Provincial Key Laboratory of Soil Carbon Sequestration and Pollution Control, Faculty of Environmental Science and Engineering, Kunming University of Science and Technology, Kunming, 650500, China.
| | - Mingyi Yang
- Yunnan Provincial Key Laboratory of Soil Carbon Sequestration and Pollution Control, Faculty of Environmental Science and Engineering, Kunming University of Science and Technology, Kunming, 650500, China.
| | - Fangfang Li
- Yunnan Provincial Key Laboratory of Soil Carbon Sequestration and Pollution Control, Faculty of Environmental Science and Engineering, Kunming University of Science and Technology, Kunming, 650500, China.
| | - Jinfeng Zhao
- Shandong Provincial Key Laboratory of Water and Soil Conservation and Environmental Protection, College of Resources and Environment, Linyi University, Linyi, 276005, China.
| | - Zhaohui He
- Yunnan Provincial Key Laboratory of Soil Carbon Sequestration and Pollution Control, Faculty of Environmental Science and Engineering, Kunming University of Science and Technology, Kunming, 650500, China.
| | - Yangwei Bai
- Chinese Research Academy of Environmental Sciences, Beijing, 100012, China.
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Goray M, Taylor D, Bibbo E, Patel D, Fantinato C, Fonneløp AE, Gill P, van Oorschot RAH. Up in the air: Presence and collection of DNA from air and air conditioner units. Electrophoresis 2024. [PMID: 38416600 DOI: 10.1002/elps.202300227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 01/23/2024] [Accepted: 02/19/2024] [Indexed: 03/01/2024]
Abstract
Biological material is routinely collected at crime scenes and from exhibits and is a key type of evidence during criminal investigations. Touch or trace DNA samples from surfaces and objects deemed to have been contacted are frequently collected. However, a person of interest may not leave any traces on contacted surfaces, for example, if wearing gloves. A novel means of sampling human DNA from air offers additional avenues for DNA collection. In the present study, we report on the results of a pilot study into the prevalence and persistence of human DNA in the air. The first aspect of the pilot study investigates air conditioner units that circulate air around a room, by sampling units located in four offices and four houses at different time frames post-cleaning. The second aspect investigates the ability to collect human DNA from the air in rooms, with and without people, for different periods of time and with different types of collection filters. Results of this pilot study show that human DNA can be collected on air conditioner unit surfaces and from the air, with air samples representing the more recent occupation while air conditioner units showing historic use of the room.
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Affiliation(s)
- Mariya Goray
- College of Science and Engineering, Flinders University, Adelaide, South Australia, Australia
| | - Duncan Taylor
- College of Science and Engineering, Flinders University, Adelaide, South Australia, Australia
- Forensic Science SA, Adelaide, South Australia, Australia
| | - Emily Bibbo
- College of Science and Engineering, Flinders University, Adelaide, South Australia, Australia
| | - Dhruvi Patel
- College of Science and Engineering, Flinders University, Adelaide, South Australia, Australia
| | - Chiara Fantinato
- Forensic Genetics Research Group, Department of Forensic Sciences, Oslo University Hospital, Oslo, Norway
- Department of Forensic Medicine, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Ane Elida Fonneløp
- Forensic Genetics Research Group, Department of Forensic Sciences, Oslo University Hospital, Oslo, Norway
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Peter Gill
- Forensic Genetics Research Group, Department of Forensic Sciences, Oslo University Hospital, Oslo, Norway
- Department of Forensic Medicine, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Roland A H van Oorschot
- Victoria Police Forensic Services Department, Office of Chief Forensic Scientist, Macleod, Victoria, Australia
- School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, Victoria, Australia
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Wilkinson SP, Gault AA, Welsh SA, Smith JP, David BO, Hicks AS, Fake DR, Suren AM, Shaffer MR, Jarman SN, Bunce M. TICI: a taxon-independent community index for eDNA-based ecological health assessment. PeerJ 2024; 12:e16963. [PMID: 38426140 PMCID: PMC10903356 DOI: 10.7717/peerj.16963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 01/26/2024] [Indexed: 03/02/2024] Open
Abstract
Global biodiversity is declining at an ever-increasing rate. Yet effective policies to mitigate or reverse these declines require ecosystem condition data that are rarely available. Morphology-based bioassessment methods are difficult to scale, limited in scope, suffer prohibitive costs, require skilled taxonomists, and can be applied inconsistently between practitioners. Environmental DNA (eDNA) metabarcoding offers a powerful, reproducible and scalable solution that can survey across the tree-of-life with relatively low cost and minimal expertise for sample collection. However, there remains a need to condense the complex, multidimensional community information into simple, interpretable metrics of ecological health for environmental management purposes. We developed a riverine taxon-independent community index (TICI) that objectively assigns indicator values to amplicon sequence variants (ASVs), and significantly improves the statistical power and utility of eDNA-based bioassessments. The TICI model training step uses the Chessman iterative learning algorithm to assign health indicator scores to a large number of ASVs that are commonly encountered across a wide geographic range. New sites can then be evaluated for ecological health by averaging the indicator value of the ASVs present at the site. We trained a TICI model on an eDNA dataset from 53 well-studied riverine monitoring sites across New Zealand, each sampled with a high level of biological replication (n = 16). Eight short-amplicon metabarcoding assays were used to generate data from a broad taxonomic range, including bacteria, microeukaryotes, fungi, plants, and animals. Site-specific TICI scores were strongly correlated with historical stream condition scores from macroinvertebrate assessments (macroinvertebrate community index or MCI; R2 = 0.82), and TICI variation between sample replicates was minimal (CV = 0.013). Taken together, this demonstrates the potential for taxon-independent eDNA analysis to provide a reliable, robust and low-cost assessment of ecological health that is accessible to environmental managers, decision makers, and the wider community.
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Affiliation(s)
- Shaun P. Wilkinson
- Wilderlab NZ Ltd., Wellington, New Zealand
- School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia
| | | | | | - Joshua P. Smith
- School of Science, The University of Waikato, Hamilton, Waikato, New Zealand
- Waikato Regional Council, Hamilton, Waikato, New Zealand
| | - Bruno O. David
- Waikato Regional Council, Hamilton, Waikato, New Zealand
| | - Andy S. Hicks
- Ministry for the Environment, Wellington, New Zealand
- Hawke’s Bay Regional Council, Napier, Hawke’s Bay, New Zealand
| | - Daniel R. Fake
- Hawke’s Bay Regional Council, Napier, Hawke’s Bay, New Zealand
| | - Alastair M. Suren
- Bay of Plenty Regional Council, Tauranga, Bay of Plenty, New Zealand
| | - Megan R. Shaffer
- School of Marine and Environmental Affairs, University of Washington, Seattle, WA, United States of America
| | - Simon N. Jarman
- School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia
| | - Michael Bunce
- School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia
- Department of Conservation, Wellington, New Zealand
- School of Biomedical Sciences, University of Otago, Dunedin, Otago, New Zealand
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Olinger LK, McClenaghan B, Hajibabaei M, Fahner N, Berghuis L, Rajabi H, Erwin P, Lane CS, Pawlik JR. Looking for the sponge loop: analyses of detritus on a Caribbean forereef using stable isotope and eDNA metabarcoding techniques. PeerJ 2024; 12:e16970. [PMID: 38410802 PMCID: PMC10896084 DOI: 10.7717/peerj.16970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 01/29/2024] [Indexed: 02/28/2024] Open
Abstract
Coral reefs are biodiverse ecosystems that rely on trophodynamic transfers from primary producers to consumers through the detrital pathway. The sponge loop hypothesis proposes that sponges consume dissolved organic carbon (DOC) and produce large quantities of detritus on coral reefs, with this turn-over approaching the daily gross primary production of the reef ecosystem. In this study, we collected samples of detritus in the epilithic algal matrix (EAM) and samples from potential sources of detritus over two seasons from the forereef at Carrie Bow Cay, Belize. We chose this location to maximize the likelihood of finding support for the sponge loop hypothesis because Caribbean reefs have higher sponge abundances than other tropical reefs worldwide and the Mesoamerican barrier reef is an archetypal coral reef ecosystem. We used stable isotope analyses and eDNA metabarcoding to determine the composition of the detritus. We determined that the EAM detritus was derived from a variety of benthic and pelagic sources, with primary producers (micro- and macroalgae) as major contributors and metazoans (Arthropoda, Porifera, Cnidaria, Mollusca) as minor contributors. None of the sponge species that reportedly produce detritus were present in EAM detritus. The cnidarian signature in EAM detritus was dominated by octocorals, with a scarcity of hard corals. The composition of detritus also varied seasonally. The negligible contribution of sponges to reef detritus contrasts with the detrital pathway originally proposed in the sponge loop hypothesis. The findings indicate a mix of pelagic and benthic sources in the calmer summer and primarily benthic sources in the more turbulent spring.
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Affiliation(s)
- Lauren K. Olinger
- Center for Marine and Environmental Studies, University of the Virgin Islands, St Thomas, Virgin Islands, U.S. Virgin Islands, United States of America
- Department of Biology and Marine Biology, University of North Carolina Wilmington, Wilmington, NC, United States of America
| | | | - Mehrdad Hajibabaei
- eDNAtec Inc., Newfoundland and Labrador, St. John’s, Canada
- Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
| | - Nicole Fahner
- eDNAtec Inc., Newfoundland and Labrador, St. John’s, Canada
| | | | - Hoda Rajabi
- eDNAtec Inc., Newfoundland and Labrador, St. John’s, Canada
| | - Patrick Erwin
- Department of Biology and Marine Biology, University of North Carolina Wilmington, Wilmington, NC, United States of America
| | - Chad S. Lane
- Department of Earth and Ocean Sciences, University of North Carolina Wilmington, Wilmington, NC, United States of America
| | - Joseph R. Pawlik
- Department of Biology and Marine Biology, University of North Carolina Wilmington, Wilmington, NC, United States of America
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Tegart LJ, Schiro G, Dickinson JL, Green BJ, Barberán A, Marthick JR, Bissett A, Johnston FH, Jones PJ. Decrypting seasonal patterns of key pollen taxa in cool temperate Australia: A multi-barcode metabarcoding analysis. Environ Res 2024; 243:117808. [PMID: 38043901 DOI: 10.1016/j.envres.2023.117808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 11/23/2023] [Accepted: 11/27/2023] [Indexed: 12/05/2023]
Abstract
Pollen allergies pose a considerable global public health concern. Allergy risk can vary significantly within plant families, yet some key pollen allergens can only be identified to family level by current optical methods. Pollen information with greater taxonomic resolution is therefore required to best support allergy prevention and self-management. We used environmental DNA (eDNA) metabarcoding to deepen taxonomic insights into the seasonal composition of airborne pollen in cool temperate Australia, a region with high rates of allergic respiratory disease. In Hobart, Tasmania, we collected routine weekly air samples from December 2018 until October 2020 and sequenced the internal transcribed spacer 2 (ITS2) and chloroplastic tRNA-Leucine tRNA-Phenylalanine intergenic spacer (trnL-trnF) regions in order to address the following questions: a) What is the genus-level diversity of known and potential aeroallergens in Hobart, in particular, in the families Poaceae, Cupressaceae and Myrtaceae? b) How do the atmospheric concentrations of these taxa change over time, and c) Does trnL-trnF enhance resolution of biodiversity when used in addition to ITS2? Our results suggest that individuals in the region are exposed to temperate grasses including Poa and Bromus in the peak grass pollen season, however low levels of exposure to the subtropical grass Cynodon may occur in autumn and winter. Within Cupressaceae, both metabarcodes showed that exposure is predominantly to pollen from the introduced genera Cupressus and Juniperus. Only ITS2 detected the native genus, Callitris. Both metabarcodes detected Eucalyptus as the major Myrtaceae genus, with trnL-trnF exhibiting primer bias for this family. These findings help refine our understanding of allergy triggers in Tasmania and highlight the utility of multiple metabarcodes in aerobiome studies.
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Affiliation(s)
- Lachlan J Tegart
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS, 7000, Australia.
| | - Gabriele Schiro
- Department of Environmental Science, University of Arizona, Tucson, AZ, 85721, United States.
| | - Joanne L Dickinson
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS, 7000, Australia.
| | - Brett J Green
- Office of the Director, Health Effects Laboratory Division, Centers for Disease Control and Prevention, National Institute for Occupational Safety and Health, Morgantown, WV, 26505, United States.
| | - Albert Barberán
- Department of Environmental Science, University of Arizona, Tucson, AZ, 85721, United States.
| | - James R Marthick
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS, 7000, Australia.
| | - Andrew Bissett
- Commonwealth Scientific and Industrial Research Organisation, Hobart, TAS, Australia.
| | - Fay H Johnston
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS, 7000, Australia; Public Health Services, Department of Health, Hobart, TAS, 7000, Australia.
| | - Penelope J Jones
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS, 7000, Australia.
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Schuijt LM, van Drimmelen CKE, Buijse LL, van Smeden J, Wu D, Boerwinkel MC, Belgers DJM, Matser AM, Roessink I, Beentjes KK, Trimbos KB, Smidt H, Van den Brink PJ. Assessing ecological responses to exposure to the antibiotic sulfamethoxazole in freshwater mesocosms. Environ Pollut 2024; 343:123199. [PMID: 38128712 DOI: 10.1016/j.envpol.2023.123199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 12/16/2023] [Accepted: 12/18/2023] [Indexed: 12/23/2023]
Abstract
Antibiotics are a contaminant class of worldwide concern as they are frequently detected in aquatic ecosystems. To better understand the impacts of antibiotics on aquatic ecosystems, we conducted an outdoor mesocosm experiment in which aquatic communities were exposed to different concentrations of the antibiotic sulfamethoxazole (0, 0.15, 1.5, 15 and 150 μg/L). These concentrations include mean (0.15 μg/L) and maximum detected concentrations (15 and 150 μg/L) in aquatic ecosystems worldwide. Sulfamethoxazole was applied once a week for eight consecutive weeks to 1530 L outdoor mesocosms in the Netherlands, followed by an eight-week recovery period. We evaluated phytoplankton-, bacterial- and invertebrate responses during and after sulfamethoxazole exposure and assessed impacts on organic matter decomposition. Contrary to our expectations, consistent treatment-related effects on algal and bacterial communities could not be demonstrated. In addition, sulfamethoxazole did not significantly affect zooplankton and macroinvertebrate communities. However, some effects on specific taxa were observed, with an increase in Mesostoma flatworm abundance (NOEC of <0.15 μg/L). In addition, eDNA analyses indicated negative impacts on the insects Odonata at a sulfamethoxazole concentration of 15 μg/L. Overall, environmentally relevant sulfamethoxazole concentration did not result in direct or indirect impairment of entire aquatic communities and ecological processes in our mesocosms. However, several specific macroinvertebrate taxa demonstrated significant (in)direct effects from sulfamethoxazole. Comparison of the results with the literature showed inconsistent results between studies using comparable, environmentally relevant, concentrations. Therefore, our study highlights the importance of testing the ecological impacts of pharmaceuticals (such as sulfamethoxazole) across multiple trophic levels spanning multiple aquatic communities, to fully understand its potential ecological threats.
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Affiliation(s)
- Lara M Schuijt
- Aquatic Ecology and Water Quality Management Group, Wageningen University & Research, Wageningen, the Netherlands; Wageningen Environmental Research, Wageningen University & Research, Wageningen, the Netherlands
| | - Chantal K E van Drimmelen
- Aquatic Ecology and Water Quality Management Group, Wageningen University & Research, Wageningen, the Netherlands; Hamburg University of Applied Science, Ulmenliet 20, D-21033, Hamburg, Germany
| | - Laura L Buijse
- Wageningen Environmental Research, Wageningen University & Research, Wageningen, the Netherlands
| | - Jasper van Smeden
- Wageningen Environmental Research, Wageningen University & Research, Wageningen, the Netherlands
| | - Dailing Wu
- Aquatic Ecology and Water Quality Management Group, Wageningen University & Research, Wageningen, the Netherlands
| | - Marie-Claire Boerwinkel
- Wageningen Environmental Research, Wageningen University & Research, Wageningen, the Netherlands
| | - Dick J M Belgers
- Wageningen Environmental Research, Wageningen University & Research, Wageningen, the Netherlands
| | - Arrienne M Matser
- Wageningen Environmental Research, Wageningen University & Research, Wageningen, the Netherlands
| | - Ivo Roessink
- Wageningen Environmental Research, Wageningen University & Research, Wageningen, the Netherlands
| | | | - Krijn B Trimbos
- Institute of Environmental Sciences, Leiden University, Leiden, the Netherlands
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University and & Research, Wageningen, the Netherlands
| | - Paul J Van den Brink
- Aquatic Ecology and Water Quality Management Group, Wageningen University & Research, Wageningen, the Netherlands.
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Siriarchawatana P, Harnpicharnchai P, Phithakrotchanakoon C, Kitikhun S, Mayteeworakoon S, Chunhametha S, Eurwilaichitr L, Ingsriswang S. Elucidating potential bioindicators from insights in the diversity and assembly processes of prokaryotic and eukaryotic communities in the Mekong River. Environ Res 2024; 243:117800. [PMID: 38056615 DOI: 10.1016/j.envres.2023.117800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 11/23/2023] [Accepted: 11/25/2023] [Indexed: 12/08/2023]
Abstract
Drivers for spatio-temporal distribution patterns of overall planktonic prokaryotes and eukaryotes in riverine ecosystems are generally not fully understood. This study employed amplicon metabarcoding to investigate the distributions and assembly mechanisms of bacterial and eukaryotic communities in the Mekong River. The prevailing bacteria taxa were found to be Betaproteobacteria, Actinobacteria, and Bacteroidetes, while the dominant eukaryotic organisms were cryptophytes, chlorophytes, and diatoms. The community assemblages were influenced by a combination of stochastic and deterministic processes. Drift (DR) and dispersal limitation (DL), signifying the stochastic mechanism, were the main processes shaping the overall prokaryotic and eukaryotic communities. However, homogeneous selection (HoS), indicating deterministic mechanism, played a major role in the assembly process of core prokaryotic communities, especially in the wet season. In contrast, the core eukaryotic communities including Opisthokonta, Sar, and Chlorophyta were dominated by stochastic processes. The significance of HoS within prokaryotic communities was also found to exhibit a decreasing trend from the upstream sampling sites (Chiang Saen and Chiang Khan, Nong Khai) towards the downstream sites (Mukdahan, and Khong Chiam) of the Mekong River. The environmental gradients resulting from the site-specific variations and the gradual decrease in elevation along the river may have a potential influence on the role of HoS in community assembly. Crucial environmental factors that shape the phylogenetic structure within distinct bins of the core prokaryotic communities including water depth, temperature, chloride, sodium, and sulphate were identified, as inferred by their correlation with the beta Net Relatedness Index (betaNRI) during the wet season. Overall, these findings enhance understanding of the complex mechanisms governing the spatio-temporal dynamics of prokaryotic and eukaryotic communities in the Mekong River. Finally, insights gained from this study could provide information on further use of specific core bacteria as microbial-based bioindicators that are effective for the assessment and conservation of the Mekong River ecosystem.
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Affiliation(s)
- Paopit Siriarchawatana
- Thailand Bioresource Research Center (TBRC), National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathumthani, Thailand
| | - Piyanun Harnpicharnchai
- Thailand Bioresource Research Center (TBRC), National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathumthani, Thailand
| | - Chitwadee Phithakrotchanakoon
- Thailand Bioresource Research Center (TBRC), National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathumthani, Thailand
| | - Supattra Kitikhun
- Thailand Bioresource Research Center (TBRC), National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathumthani, Thailand
| | - Sermsiri Mayteeworakoon
- Thailand Bioresource Research Center (TBRC), National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathumthani, Thailand
| | - Suwanee Chunhametha
- Thailand Bioresource Research Center (TBRC), National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathumthani, Thailand
| | - Lily Eurwilaichitr
- National Energy Technology Center (ENTEC), National Science and Technology Development Agency (NSTDA), Pathumthani, Thailand
| | - Supawadee Ingsriswang
- Thailand Bioresource Research Center (TBRC), National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathumthani, Thailand.
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37
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Weber S, Stothut M, Mahla L, Kripp A, Hirschler L, Lenz N, Junker A, Künzel S, Krehenwinkel H. Plant-derived environmental DNA complements diversity estimates from traditional arthropod monitoring methods but outperforms them detecting plant-arthropod interactions. Mol Ecol Resour 2024; 24:e13900. [PMID: 38010630 DOI: 10.1111/1755-0998.13900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Revised: 09/29/2023] [Accepted: 10/26/2023] [Indexed: 11/29/2023]
Abstract
Our limited knowledge about the ecological drivers of global arthropod decline highlights the urgent need for more effective biodiversity monitoring approaches. Monitoring of arthropods is commonly performed using passive trapping devices, which reliably recover diverse communities, but provide little ecological information on the sampled taxa. Especially the manifold interactions of arthropods with plants are barely understood. A promising strategy to overcome this shortfall is environmental DNA (eDNA) metabarcoding from plant material on which arthropods leave DNA traces through direct or indirect interactions. However, the accuracy of this approach has not been sufficiently tested. In four experiments, we exhaustively test the comparative performance of plant-derived eDNA from surface washes of plants and homogenized plant material against traditional monitoring approaches. We show that the recovered communities of plant-derived eDNA and traditional approaches only partly overlap, with eDNA recovering various additional taxa. This suggests eDNA as a useful complementary tool to traditional monitoring. Despite the differences in recovered taxa, estimates of community α- and β-diversity between both approaches are well correlated, highlighting the utility of eDNA as a broad scale tool for community monitoring. Last, eDNA outperforms traditional approaches in the recovery of plant-specific arthropod communities. Unlike traditional monitoring, eDNA revealed fine-scale community differentiation between individual plants and even within plant compartments. Especially specialized herbivores are better recovered with eDNA. Our results highlight the value of plant-derived eDNA analysis for large-scale biodiversity assessments that include information about community-level interactions.
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Affiliation(s)
- Sven Weber
- Department of Biogeography, Trier University, Trier, Germany
| | - Manuel Stothut
- Department of Biogeography, Trier University, Trier, Germany
| | - Lisa Mahla
- Department of Biogeography, Trier University, Trier, Germany
| | - Alanah Kripp
- iES Landau, Institute for Environmental Sciences, University of Kaiserslautern-Landau, Landau in der Pfalz, Germany
| | - Lena Hirschler
- Department of Biogeography, Trier University, Trier, Germany
| | - Nina Lenz
- Department of Biogeography, Trier University, Trier, Germany
| | - Anneke Junker
- Department of Biogeography, Trier University, Trier, Germany
| | - Sven Künzel
- Max Planck Institute for Evolutionary Biology, Plön, Germany
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Sun X, Guo N, Gao J, Xiao N. Using eDNA to survey amphibians: Methods, applications, and challenges. Biotechnol Bioeng 2024; 121:456-471. [PMID: 37986625 DOI: 10.1002/bit.28592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 10/23/2023] [Accepted: 10/24/2023] [Indexed: 11/22/2023]
Abstract
In recent years, environmental DNA (eDNA) has received attention from biologists due to its sensitivity, convenience, labor and material efficiency, and lack of damage to organisms. The extensive application of eDNA has opened avenues for the monitoring and biodiversity assessment of amphibians, which are frequently small and difficult to observe in the field, in areas such as biodiversity survey assessment and detection of specific, rare and threatened, or alien invasive species. However, the accuracy of eDNA can be influenced by factors such as ambient temperature, pH, and false positives or false negatives, which makes eDNA an adjunctive tool rather than a replacement for traditional surveys. This review provides a concise overview of the eDNA method and its workflow, summarizes the differences between applying eDNA for detecting amphibians and other organisms, reviews the research progress in eDNA technology for amphibian monitoring, identifies factors influencing detection efficiency, and discusses the challenges and prospects of eDNA. It aims to serve as a reference for future research on the application of eDNA in amphibian detection.
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Affiliation(s)
- Xiaoxuan Sun
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China
| | - Ningning Guo
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China
| | - Jianan Gao
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China
- Collage of Forestry, Shanxi Agricultural University, Jinzhong, China
| | - Nengwen Xiao
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China
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ullah S, Huda N, Wahab RA, Hamid AAA, Nasir MHM, Mohamad MAN, Ahmad HF, Oyewusi HA, Huyop F. Baseline amplicon sequencing data for the ITS2 region in the green honey of Banggi Island, Sabah. Data Brief 2024; 52:110044. [PMID: 38328502 PMCID: PMC10847015 DOI: 10.1016/j.dib.2024.110044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 01/03/2024] [Accepted: 01/05/2024] [Indexed: 02/09/2024] Open
Abstract
Green honey, was discovered on Banggi Island, Sabah, showing high in essential amino acids and chlorophyll derivatives. Despite its lucrative market potential owing to its distinctive color, uncertainties persist regarding its nature. This study leverages amplicon sequencing by targeting micro- and macro-organisms present in honey environmental DNA (eDNA) using Internal Transcribed Spacer 2 (ITS2) region, enabling the identification of floral and microorganism sources that represent the honey's composition. The investigation into green honey from Banggi Island concerns the prevalence of honey adulteration and authenticity for economic gain. Adulteration methods, such as the addition of sugar syrups, compromise honey purity. Using a sequencing approach would help in determining the geographic origin and verifying the authenticity of the honey. The study aims to identify plant species or microorganisms in honey's eDNA. To authenticate honey, we utilized ITS2 with Illumina sequencing, exploring the diversity of green honey samples. Raw sequence reads obtained for the green honey sample revealed 1,438,627 raw reads, with a GC average of 49.22 %. A total of 44 amplicon sequence variances (ASVs) were identified, including three genera: Zygosaccharomyces with two species, Fraxinus with three species, and the genus Ficaria with only one species. Their respective relative abundances were 98.55%, 0.94%, and 0.51%. Zygosaccharomyces rouxii and Zygosaccharomyces mellis were identified as the pre-dominant yeast species in honey, while the Fraxinus and Ficaria genus represent common plant species in Sabah, particularly in Banggi Island. The dominance of Zygosaccharomyces species aligns with their known prevalence in honey, affirming the reliability of our findings. The presence of Fraxinus and Ficaria in the honey sample correlates with its abundance in the local environment. This amplicon sequencing approach not only contributes to our understanding of green honey composition but also serves as a valuable resource for authenticating honey origin in Malaysia, particularly for green honey from Banggi Island, Sabah. Our study pioneers the application of ITS2 amplicon sequencing for green honey amplicon sequencing, providing valuable insights into its composition and origin. This methodology, with a focus on eDNA, contributes to the authentication and quality determination of honey in Malaysia, addressing the pressing concerns of adulteration and variability in production practices.
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Affiliation(s)
- Saeed ullah
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, 81310 Johor Bahru, Malaysia
| | - Nurul Huda
- Faculty of Sustainable Agriculture, Universiti Malaysia Sabah, 90509 Sandakan, Sabah, Malaysia
| | - Roswanira Ab. Wahab
- Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, 81310 Johor Bahru, Malaysia
| | - Azzmer Azzar Abdul Hamid
- Research Unit for Bioinformatics and Computational Biology (RUBIC), Kulliyyah of Science, International Islamic University Malaysia, Bandar Indera Mahkota, 25200 Kuantan, Pahang, Malaysia
| | - Mohd Hamzah Mohd Nasir
- Research Unit for Bioinformatics and Computational Biology (RUBIC), Kulliyyah of Science, International Islamic University Malaysia, Bandar Indera Mahkota, 25200 Kuantan, Pahang, Malaysia
| | - Mohd Azrul Naim Mohamad
- Research Unit for Bioinformatics and Computational Biology (RUBIC), Kulliyyah of Science, International Islamic University Malaysia, Bandar Indera Mahkota, 25200 Kuantan, Pahang, Malaysia
| | - Hajar Fauzan Ahmad
- Faculty of Industrial Sciences and Technology, Universiti Malaysia Pahang Al Sultan Abdullah, 26300 Gambang, Pahang, Malaysia
| | - Habeebat Adekilekun Oyewusi
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, 81310 Johor Bahru, Malaysia
- Department of Biochemistry, School of Science and Computer Studies, Federal Polytechnic Ado Ekiti, Ado Ekiti PMB 5351, Ekiti State, Nigeria
| | - Fahrul Huyop
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, 81310 Johor Bahru, Malaysia
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Gallucci S. DNA at the center of mammalian innate immune recognition of bacterial biofilms. Trends Immunol 2024; 45:103-112. [PMID: 38281884 PMCID: PMC11032746 DOI: 10.1016/j.it.2023.12.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 12/20/2023] [Accepted: 12/20/2023] [Indexed: 01/30/2024]
Abstract
Historically, the study of innate immune detection of bacterial infections has focused on the recognition of pathogen-associated molecular patterns (PAMPs) from bacteria growing as single cells in planktonic phase. However, over the past two decades, studies have highlighted an adaptive advantage of bacteria: the formation of biofilms. These structures are complex fortresses that stand against a hostile environment, including antibiotics and immune responses. Extracellular DNA (eDNA) is a crucial component of the matrix of most known biofilms. In this opinion article, I propose that eDNA is a universal PAMP that the immune system uses to recognize biofilms. Outstanding questions concern the discrimination between biofilm-associated eDNA and DNA from planktonic bacteria, the innate receptors involved, and the immune response to biofilms.
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Affiliation(s)
- Stefania Gallucci
- Laboratory of Dendritic Cell Biology, Division of Innate Immunity, Department of Medicine, UMass Chan Medical School, Worcester, MA, USA.
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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. J Environ Manage 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] [What about the content of this article? (0)] [Affiliation(s)] [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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Saenz-Agudelo P, Ramirez P, Beldade R, Campoy AN, Garmendia V, Search FV, Fernández M, Wieters EA, Navarrete SA, Landaeta MF, Pérez-Matus A. Environmental DNA reveals temporal variation in mesophotic reefs of the Humboldt upwelling ecosystems of central Chile: Toward a baseline for biodiversity monitoring of unexplored marine habitats. Ecol Evol 2024; 14:e10999. [PMID: 38390005 PMCID: PMC10881902 DOI: 10.1002/ece3.10999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 01/12/2024] [Accepted: 01/26/2024] [Indexed: 02/24/2024] Open
Abstract
Temperate mesophotic reef ecosystems (TMREs) are among the least known marine habitats. Information on their diversity and ecology is geographically and temporally scarce, especially in highly productive large upwelling ecosystems. Lack of information remains an obstacle to understanding the importance of TMREs as habitats, biodiversity reservoirs and their connections with better-studied shallow reefs. Here, we use environmental DNA (eDNA) from water samples to characterize the community composition of TMREs on the central Chilean coast, generating the first baseline for monitoring the biodiversity of these habitats. We analyzed samples from two depths (30 and 60 m) over four seasons (spring, summer, autumn, and winter) and at two locations approximately 16 km apart. We used a panel of three metabarcodes, two that target all eukaryotes (18S rRNA and mitochondrial COI) and one specifically targeting fishes (16S rRNA). All panels combined encompassed eDNA assigned to 42 phyla, 90 classes, 237 orders, and 402 families. The highest family richness was found for the phyla Arthropoda, Bacillariophyta, and Chordata. Overall, family richness was similar between depths but decreased during summer, a pattern consistent at both locations. Our results indicate that the structure (composition) of the mesophotic communities varied predominantly with seasons. We analyzed further the better-resolved fish assemblage and compared eDNA with other visual methods at the same locations and depths. We recovered eDNA from 19 genera of fish, six of these have also been observed on towed underwater videos, while 13 were unique to eDNA. We discuss the potential drivers of seasonal differences in community composition and richness. Our results suggest that eDNA can provide valuable insights for monitoring TMRE communities but highlight the necessity of completing reference DNA databases available for this region.
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Affiliation(s)
- Pablo Saenz-Agudelo
- Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile Valdivia Chile
- Millennium Nucleus for Ecology and Conservation of Temperate Marine Ecosystems, NUTME Las Cruces Chile
| | - Paula Ramirez
- Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile Valdivia Chile
- Millennium Nucleus for Ecology and Conservation of Temperate Marine Ecosystems, NUTME Las Cruces Chile
| | - Ricardo Beldade
- Millennium Nucleus for Ecology and Conservation of Temperate Marine Ecosystems, NUTME Las Cruces Chile
- Estación Costera de Investigaciones Marinas Pontificia Universidad Católica Las Cruces Chile
| | - Ana N Campoy
- Center of Marine Sciences (CCMAR-CIMAR) University of the Algarve Faro Portugal
| | - Vladimir Garmendia
- Millennium Nucleus for Ecology and Conservation of Temperate Marine Ecosystems, NUTME Las Cruces Chile
- Estación Costera de Investigaciones Marinas Pontificia Universidad Católica Las Cruces Chile
| | - Francesca V Search
- Millennium Nucleus for Ecology and Conservation of Temperate Marine Ecosystems, NUTME Las Cruces Chile
| | - Miriam Fernández
- Millennium Nucleus for Ecology and Conservation of Temperate Marine Ecosystems, NUTME Las Cruces Chile
- Estación Costera de Investigaciones Marinas Pontificia Universidad Católica Las Cruces Chile
| | - Evie A Wieters
- Millennium Nucleus for Ecology and Conservation of Temperate Marine Ecosystems, NUTME Las Cruces Chile
- Estación Costera de Investigaciones Marinas Pontificia Universidad Católica Las Cruces Chile
| | - Sergio A Navarrete
- Millennium Nucleus for Ecology and Conservation of Temperate Marine Ecosystems, NUTME Las Cruces Chile
- Estación Costera de Investigaciones Marinas Pontificia Universidad Católica Las Cruces Chile
- Center for Applied Ecology and Sustainability (CAPES) and Coastal Socio-Ecological Millennium Institute (SECOS) Pontificia Universidad Católica de Chile Santiago Chile
- Center for Oceanographic Research COASTAL-COASTAL Universidad de Concepción Concepción Chile
| | - Mauricio F Landaeta
- Millennium Nucleus for Ecology and Conservation of Temperate Marine Ecosystems, NUTME Las Cruces Chile
- Laboratorio de Ictiología e Interacciones Biofísicas (LABITI) Instituto de Biología, Facultad de Ciencias, Universidad de Valparaíso Valparaíso Chile
| | - Alejandro Pérez-Matus
- Millennium Nucleus for Ecology and Conservation of Temperate Marine Ecosystems, NUTME Las Cruces Chile
- Estación Costera de Investigaciones Marinas Pontificia Universidad Católica Las Cruces Chile
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Schuijt LM, van Smeden J, van Drimmelen CKE, Buijse LL, Wu D, Boerwinkel MC, Belgers DJM, Matser AM, Roessink I, Heikamp-de Jong I, Beentjes KK, Trimbos KB, Smidt H, Van den Brink PJ. Effects of antidepressant exposure on aquatic communities assessed by a combination of morphological identification, functional measurements, environmental DNA metabarcoding and bioassays. Chemosphere 2024; 349:140706. [PMID: 37992907 DOI: 10.1016/j.chemosphere.2023.140706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 10/30/2023] [Accepted: 11/11/2023] [Indexed: 11/24/2023]
Abstract
The antidepressant fluoxetine is frequently detected in aquatic ecosystems, yet the effects on aquatic communities and ecosystems are still largely unknown. Therefore the aim of this study is to assess the effects of the long-term application of fluoxetine on key components of aquatic ecosystems including macroinvertebrate-, zooplankton-, phytoplankton- and microbial communities and organic matter decomposition by using traditional and non-traditional assessment methods. For this, we exposed 18 outdoor mesocosms (water volume of 1530 L and 10 cm of sediment) to five different concentrations of fluoxetine (0.2, 2, 20 and 200 μg/L) for eight weeks, followed by an eight-week recovery period. We quantified population and community effects by morphological identification, environmental DNA metabarcoding, in vitro and in vivo bioassays and measured organic matter decomposition as a measure of ecosystem functioning. We found effects of fluoxetine on bacterial, algal, zooplankton and macroinvertebrate communities and decomposition rates, mainly for the highest (200 μg/L) treatment. Treatment-related decreases in abundances were found for damselfly larvae (NOEC of 0.2 μg/L) and Sphaeriidae bivalves (NOEC of 20 μg/L), whereas Asellus aquaticus increased in abundance (NOEC <0.2 μg/L). Fluoxetine decreased photosynthetic activity and primary production of the suspended algae community. eDNA assessment provided additional insights by revealing that the algae belonging to the class Cryptophyceae and certain cyanobacteria taxa were the most negatively responding taxa to fluoxetine. Our results, together with results of others, suggest that fluoxetine can alter community structure and ecosystem functioning and that some impacts of fluoxetine on certain taxa can already be observed at environmentally realistic concentrations.
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Affiliation(s)
- Lara M Schuijt
- Aquatic Ecology and Water quality management group, Wageningen University and Research, Wageningen, the Netherlands; Wageningen Environmental Research, Wageningen University and Research, Wageningen, the Netherlands
| | - Jasper van Smeden
- Wageningen Environmental Research, Wageningen University and Research, Wageningen, the Netherlands
| | - Chantal K E van Drimmelen
- Aquatic Ecology and Water quality management group, Wageningen University and Research, Wageningen, the Netherlands
| | - Laura L Buijse
- Wageningen Environmental Research, Wageningen University and Research, Wageningen, the Netherlands
| | - Dailing Wu
- Aquatic Ecology and Water quality management group, Wageningen University and Research, Wageningen, the Netherlands
| | - Marie-Claire Boerwinkel
- Wageningen Environmental Research, Wageningen University and Research, Wageningen, the Netherlands
| | - Dick J M Belgers
- Wageningen Environmental Research, Wageningen University and Research, Wageningen, the Netherlands
| | - Arrienne M Matser
- Wageningen Environmental Research, Wageningen University and Research, Wageningen, the Netherlands
| | - Ivo Roessink
- Wageningen Environmental Research, Wageningen University and Research, Wageningen, the Netherlands
| | - Ineke Heikamp-de Jong
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, the Netherlands
| | | | - Krijn B Trimbos
- Institute of Environmental Sciences, Leiden University, Leiden, the Netherlands
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, the Netherlands
| | - Paul J Van den Brink
- Aquatic Ecology and Water quality management group, Wageningen University and Research, Wageningen, the Netherlands.
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Porco D, Purnomo CA, Glesener L, Proess R, Lippert S, Jans K, Colling G, Schneider S, Stassen R, Frantz AC. eDNA-based monitoring of Batrachochytrium dendrobatidis and Batrachochytrium salamandrivorans with ddPCR in Luxembourg ponds: taking signals below the Limit of Detection (LOD) into account. BMC Ecol Evol 2024; 24:4. [PMID: 38178008 PMCID: PMC10768104 DOI: 10.1186/s12862-023-02189-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 12/09/2023] [Indexed: 01/06/2024] Open
Abstract
BACKGROUND Batrachochytrium dendrobatidis (Bd) and Batrachochytrium salamandrivorans (Bsal) are two pathogenic fungi that are a significant threat to amphibian communities worldwide. European populations are strongly impacted and the monitoring of the presence and spread of these pathogens is crucial for efficient decision-making in conservation management. RESULTS Here we proposed an environmental DNA (eDNA) monitoring of these two pathogenic agents through droplet digital PCR (ddPCR) based on water samples from 24 ponds in Luxembourg. In addition, amphibians were swabbed in eight of the targeted ponds in order to compare the two approaches at site-level detection. This study allowed the development of a new method taking below-Limit of Detection (LOD) results into account thanks to the statistical comparison of the frequencies of false positives in no template controls (NTC) and below-LOD results in technical replicates. In the eDNA-based approach, the use of this method led to an increase in Bd and Bsal detection of 28 and 50% respectively. In swabbing, this resulted in 8% more positive results for Bd. In some samples, the use of technical replicates allowed to recover above-LOD signals and increase Bd detection by 35 and 33% respectively for eDNA and swabbing, and Bsal detection by 25% for eDNA. CONCLUSIONS These results confirmed the usefulness of technical replicates to overcome high levels of stochasticity in very low concentration samples even for a highly sensitive technique such as ddPCR. In addition, it showed that below-LOD signals could be consistently recovered and the corresponding amplification events assigned either to positive or negative detection via the method developed here. This methodology might be particularly worth pursuing in pathogenic agents' detection as false negatives could have important adverse consequences. In total, 15 ponds were found positive for Bd and four for Bsal. This study reports the first record of Bsal in Luxembourg.
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Affiliation(s)
- David Porco
- Musée national d'histoire naturelle du Luxembourg, 25, rue Münster, Luxembourg, L-2160, Luxembourg.
- Fondation Faune Flore, 24, rue Münster, Luxembourg, L-2160, Luxembourg.
| | - Chanistya Ayu Purnomo
- Musée national d'histoire naturelle du Luxembourg, 25, rue Münster, Luxembourg, L-2160, Luxembourg
| | - Liza Glesener
- Naturschutzsyndikat SICONA, 12, rue de Capellen, L-8393 Olm, Luxembourg, Luxembourg
| | - Roland Proess
- Umweltplanungsbüro Ecotop, 45, Schlassuecht, L-7435 Hollenfels, Luxembourg, Luxembourg
| | - Stéphanie Lippert
- Musée national d'histoire naturelle du Luxembourg, 25, rue Münster, Luxembourg, L-2160, Luxembourg
| | - Kevin Jans
- Natur&ëmwelt Fondation Hëllef fir d'Natur, 5, Route de Luxembourg, L-1899, Kockelscheuer, Luxembourg
| | - Guy Colling
- Musée national d'histoire naturelle du Luxembourg, 25, rue Münster, Luxembourg, L-2160, Luxembourg
- Fondation Faune Flore, 24, rue Münster, Luxembourg, L-2160, Luxembourg
| | - Simone Schneider
- Musée national d'histoire naturelle du Luxembourg, 25, rue Münster, Luxembourg, L-2160, Luxembourg
- Naturschutzsyndikat SICONA, 12, rue de Capellen, L-8393 Olm, Luxembourg, Luxembourg
| | - Raf Stassen
- Biota.lu, 9a, Rue Principale, L-6990, Hostert, Luxembourg
| | - Alain C Frantz
- Musée national d'histoire naturelle du Luxembourg, 25, rue Münster, Luxembourg, L-2160, Luxembourg
- Fondation Faune Flore, 24, rue Münster, Luxembourg, L-2160, Luxembourg
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Wang L, Bin Q, Liu H, Zhang Y, Wang S, Luo S, Chen Z, Zhang M, Yu K. New insights into the on-site monitoring of probiotics eDNA using biosensing technology for heat-stress relieving in coral reefs. Biosens Bioelectron 2024; 243:115790. [PMID: 37906999 DOI: 10.1016/j.bios.2023.115790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 10/24/2023] [Indexed: 11/02/2023]
Abstract
Coral probiotics can improve the tolerance of corals to heat stress, thus mitigating the process of coral thermal bleaching. Sensitive and specific detection of coral probiotics at low abundances is highly desirable but remains challenging, especially for rapid and on-site detection of coral probiotics. Since the electrochemical biosensor has been recently used in the field of environmental DNA (eDNA) detection, herein, an efficient electrochemical biosensor was developed based on CoS2/CoSe2-NC HNCs electrode material with a specific DNA probe for the C. marina detection. After optimization, the lower limit of detection (LOD) values of such biosensors for the target DNA and genomic DNA were 1.58 fM and 6.5 pM, respectively. On this basis, a portable device was constructed for the practical detection of C. marina eDNA, and its reliability and accuracy were verified by comparison with the ddPCR method (P > 0.05). For each analysis, the average cost was only ∼ $1.08 and could be completed within 100 min with reliable sensitivity and specificity. Overall, the biosensor could reflect the protective effect of probiotics on coral heat stress, and the proposed technique will put new insights into the rapid and on-site detection of coral probiotics to assist corals against global warming.
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Affiliation(s)
- Liwei Wang
- School of Marine Sciences, School of Resources, Environment and Materials, School of Chemistry and Chemical Engineering, Guangxi University, Nanning, 530004, China; Coral Reef Research Center of China, Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Nanning, 530004, China; Guangxi, Key Laboratory of Processing for Non-ferrous Metallic and Featured Materials, Nanning, 530004, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China
| | - Qi Bin
- School of Marine Sciences, School of Resources, Environment and Materials, School of Chemistry and Chemical Engineering, Guangxi University, Nanning, 530004, China
| | - Hongjie Liu
- School of Marine Sciences, School of Resources, Environment and Materials, School of Chemistry and Chemical Engineering, Guangxi University, Nanning, 530004, China
| | - Yibo Zhang
- School of Marine Sciences, School of Resources, Environment and Materials, School of Chemistry and Chemical Engineering, Guangxi University, Nanning, 530004, China
| | - Shaopeng Wang
- School of Marine Sciences, School of Resources, Environment and Materials, School of Chemistry and Chemical Engineering, Guangxi University, Nanning, 530004, China
| | - Songlin Luo
- School of Marine Sciences, School of Resources, Environment and Materials, School of Chemistry and Chemical Engineering, Guangxi University, Nanning, 530004, China
| | - Zhenghua Chen
- School of Marine Sciences, School of Resources, Environment and Materials, School of Chemistry and Chemical Engineering, Guangxi University, Nanning, 530004, China; Coral Reef Research Center of China, Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Nanning, 530004, China
| | - Man Zhang
- School of Marine Sciences, School of Resources, Environment and Materials, School of Chemistry and Chemical Engineering, Guangxi University, Nanning, 530004, China; Coral Reef Research Center of China, Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Nanning, 530004, China.
| | - Kefu Yu
- School of Marine Sciences, School of Resources, Environment and Materials, School of Chemistry and Chemical Engineering, Guangxi University, Nanning, 530004, China; Coral Reef Research Center of China, Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Nanning, 530004, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China.
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46
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Fountain-Jones NM, Giraud T, Zinger L, Bik H, Creer S, Videvall E. Molecular ecology of microbiomes in the wild: Common pitfalls, methodological advances and future directions. Mol Ecol 2024; 33:e17223. [PMID: 38014746 DOI: 10.1111/mec.17223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 11/12/2023] [Accepted: 11/15/2023] [Indexed: 11/29/2023]
Abstract
The study of microbiomes across organisms and environments has become a prominent focus in molecular ecology. This perspective article explores common challenges, methodological advancements, and future directions in the field. Key research areas include understanding the drivers of microbiome community assembly, linking microbiome composition to host genetics, exploring microbial functions, transience and spatial partitioning, and disentangling non-bacterial components of the microbiome. Methodological advancements, such as quantifying absolute abundances, sequencing complete genomes, and utilizing novel statistical approaches, are also useful tools for understanding complex microbial diversity patterns. Our aims are to encourage robust practices in microbiome studies and inspire researchers to explore the next frontier of this rapidly changing field.
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Affiliation(s)
| | - Tatiana Giraud
- Laboratoire Ecologie Systématique et Evolution, UMR 8079, Bâtiment 680, Université Paris-Saclay, CNRS, AgroParisTech, Gif-sur-Yvette, France
| | - Lucie Zinger
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, PSL Université Paris, Paris, France
- Laboratoire Evolution et Diversité Biologique (EDB), UMR5174, CNRS, Institut de Recherche pour le Développement (IRD), Université Toulouse 3 Paul Sabatier, Toulouse, France
| | - Holly Bik
- Department of Marine Sciences and Institute of Bioinformatics, University of Georgia, Athens, Georgia, USA
| | - Simon Creer
- School of Environmental and Natural Sciences, Bangor University, Bangor, UK
| | - Elin Videvall
- Department of Ecology, Evolution and Organismal Biology, Brown University, Providence, Rhode Island, USA
- Institute at Brown for Environment and Society, Brown University, Providence, Rhode Island, USA
- Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
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47
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Marques V, Loot G, Blanchet S, Miaud C, Planes S, Peyran C, Arnal V, Calvet C, Pioch S, Manel S. Optimizing detectability of the endangered fan mussel using eDNA and ddPCR. Ecol Evol 2024; 14:e10807. [PMID: 38288365 PMCID: PMC10822771 DOI: 10.1002/ece3.10807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 11/22/2023] [Accepted: 11/24/2023] [Indexed: 01/31/2024] Open
Abstract
Spatial and temporal monitoring of species threatened with extinction is of critical importance for conservation and ecosystem management. In the Mediterranean coast, the fan mussel (Pinna nobilis) is listed as critically endangered after suffering from a mass mortality event since 2016, leading to 100% mortality in most marine populations. Conventional monitoring for this macroinvertebrate is done using scuba, which is challenging in dense meadows or with low visibility. Here we developed an environmental DNA assay targeting the fan mussel and assessed the influence of several environmental parameters on the species detectability in situ. We developed and tested an eDNA molecular marker and collected 48 water samples in two sites at the Thau lagoon (France) with distinct fan mussel density, depths and during two seasons (summer and autumn). Our marker can amplify fan mussel DNA but lacks specificity since it also amplifies a conspecific species (Pinna rudis). We successfully amplified fan mussel DNA from in situ samples with 46 positive samples (out of 48) using ddPCR, although the DNA concentrations measured were low over almost all samples. Deeper sampling depth slightly increased DNA concentrations, but no seasonal effect was found. We highlight a putative spawning event on a single summer day with much higher DNA concentration compared to all other samples. We present an eDNA molecular assay able to detect the endangered fan mussel and provide guidelines to optimize the sampling protocol to maximize detectability. Effective and non-invasive monitoring tools for endangered species are promising to monitor remaining populations and have the potential of ecological restoration or habitat recolonization following a mass mortality event.
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Affiliation(s)
- Virginie Marques
- CEFE, Univ Montpellier, CNRS, EPHE‐PSL University, IRD, Univ Paul Valéry Montpellier 3MontpellierFrance
- Ecosystems and Landscape Evolution, Institute of Terrestrial Ecosystems, Department of Environmental System ScienceETH ZürichZürichSwitzerland
- Land Change ScienceSwiss Federal Research Institute WSLBirmensdorfSwitzerland
| | - Géraldine Loot
- EDB, Laboratoire Ecologie et Evolution (UMR 5174)Université de Toulouse, UPS, CNRS, IRDToulouseFrance
| | - Simon Blanchet
- SETE, Station d'Écologie Théorique et Expérimentale (UAR2029), Centre National pour la Recherche ScientifiqueMoulisFrance
| | - Claude Miaud
- CEFE, Univ Montpellier, CNRS, EPHE‐PSL University, IRD, Univ Paul Valéry Montpellier 3MontpellierFrance
| | - Serge Planes
- PSL Research University: EPHE – UPVD – CNRS, UAR 3278 CRIOBEPerpignanFrance
| | - Claire Peyran
- PSL Research University: EPHE – UPVD – CNRS, UAR 3278 CRIOBEPerpignanFrance
| | - Véronique Arnal
- CEFE, Univ Montpellier, CNRS, EPHE‐PSL University, IRD, Univ Paul Valéry Montpellier 3MontpellierFrance
| | - Coralie Calvet
- AgroParisTechParisFrance
- Montpellier Research in Management (MRM)Univ Montpellier, Univ Paul Valéry Montpellier 3, Univ Perpignan Via DomitiaMontpellierFrance
| | - Sylvain Pioch
- AgroParisTechParisFrance
- Montpellier Research in Management (MRM)Univ Montpellier, Univ Paul Valéry Montpellier 3, Univ Perpignan Via DomitiaMontpellierFrance
| | - Stéphanie Manel
- CEFE, Univ Montpellier, CNRS, EPHE‐PSL University, IRDMontpellierFrance
- Institut Universitaire de FranceParisFrance
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48
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Li Z, Li F, Qin S, Guo F, Wang S, Zhang Y. Environmental DNA biomonitoring reveals the human impacts on native and non-native fish communities in subtropical river systems. J Environ Manage 2024; 349:119595. [PMID: 37979384 DOI: 10.1016/j.jenvman.2023.119595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Revised: 10/30/2023] [Accepted: 11/10/2023] [Indexed: 11/20/2023]
Abstract
Subtropical rivers are one of the hotspots of global biodiversity, facing increased risks of fish diversity changes and species extinction. However, until now, human impacts on native and non-native fish communities in subtropical rivers still lack sufficient effort. Here, we used the environmental DNA (eDNA) approach to investigate fish communities in the Dongjiang River of southeast China, a typical subtropical river, and explored the effects of regional land use and local water pollution on fish taxonomic and functional diversity. Our data showed that 90 species or genera of native fish and 15 species or genera of non-native fish were detected by the eDNA approach, and there was over 85% overlap between eDNA datasets and historical records. The taxonomic and functional diversity of all, native and non-native fish communities showed consistent spatial patterns, that is, the upstream of the tributary was significantly higher than that of the mainstream and downstream. Land use and water pollution such as COD and TP were the determinants in shaping the spatial structure of fish communities, and water pollution explained 31.56%, 29.88%, and 27.80% of the structural variation in all, native and non-native fish communities, respectively. The Shannon diversity and functional richness of native fish showed a significant downward trend driven by COD (pShannon = 0.0374; pfunctional = 0.0215) and land use (pShannon = 0.0159; pfunctional = 0.0441), but they did not have significant impacts on non-native fish communities. Overall, this study emphasizes the inconsistent response of native and non-native fish communities to human impacts in subtropical rivers, and managers need to develop strategies tailored to specific fish species to effectively protect water security and rivers.
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Affiliation(s)
- Zhen 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
| | - 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.
| | - 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
| | - 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
| | - Shuping Wang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, 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
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49
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Gwiazdowski R. Principles for Constructing DNA Barcode Reference Libraries. Methods Mol Biol 2024; 2744:491-502. [PMID: 38683337 DOI: 10.1007/978-1-0716-3581-0_29] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2024]
Abstract
All DNA barcode methods rely on reference sequences linked to well-curated voucher specimens. Definitions for and locations of DNA barcode reference libraries are not standardized, and vary throughout the literature. Standardizing, and centralizing reference specimens would provide an unambiguous source, analogous to reference genomes, to reproduce identifications and improve a library. This chapter proposes a working definition of a DNA barcode reference library, consistent with DNA barcode data standards, along with principles and methods to consider when producing or using such a library. These methods allow explicit traceback to sequence-sources which elevate the value of voucher specimens, and create a potential for community curation.
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Affiliation(s)
- Rodger Gwiazdowski
- Department of Environmental Conservation, University of Massachusetts, Amherst, MA, USA.
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50
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Cunningham SW, Tessler M, Johnson-Rosemond J, Whittaker IS, Brugler MR. Environmental DNA Isolation, Validation, and Preservation Methods. Methods Mol Biol 2024; 2744:171-180. [PMID: 38683318 DOI: 10.1007/978-1-0716-3581-0_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2024]
Abstract
Environmental DNA (eDNA) workflows contain many familiar molecular-lab techniques, but also employ several unique methodologies. When working with eDNA, it is essential to avoid contamination from the point of collection through preservation and select a meaningful negative control. As eDNA can be obtained from a variety of samples and habitats (e.g., soil, water, air, or tissue), protocols will vary depending on usage. Samples may require additional steps to dilute, block, or remove inhibitors or physically break up samples or filters. Thereafter, standard DNA isolation techniques (kit-based or phenol:chloroform:isoamyl [PCI]) are employed. Once DNA is extracted, it is typically quantified using a fluorometer. Yields vary greatly, but are important to know prior to amplification of the gene(s) of interest. Long-term storage of both the sampled material and the extracted DNA is encouraged, as it provides a backup for spilled/contaminated samples, lost data, reanalysis, and future studies using newer technology. Storage in a freezer is often ideal; however, some storage buffers (e.g., Longmires) require that filters or swabs are kept at room temperature to prevent precipitation of buffer-related solutes. These baseline methods for eDNA isolation, validation, and preservation are detailed in this protocol chapter. In addition, we outline a cost-effective, homebrew extraction protocol optimized to extract eDNA.
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Affiliation(s)
- Seth W Cunningham
- Department of Biological Sciences, Fordham University, Bronx, NY, USA.
- Institute for Comparative Genomics, American Museum of Natural History, New York, NY, USA.
| | - Michael Tessler
- Institute for Comparative Genomics, American Museum of Natural History, New York, NY, USA
- Division of Invertebrate Zoology, American Museum of Natural History, New York, NY, USA
- Department of Biology, St. Francis College, Brooklyn, NY, USA
| | | | - Iesha S Whittaker
- Department of Natural Sciences, University of South Carolina Beaufort, Beaufort, SC, USA
| | - Mercer R Brugler
- Division of Invertebrate Zoology, American Museum of Natural History, New York, NY, USA
- Department of Natural Sciences, University of South Carolina Beaufort, Beaufort, SC, USA
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