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Zhang S, Zhan A, Zhao J, Yao M. Metropolitan pressures: Significant biodiversity declines and strong filtering of functional traits in fish assemblages. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 944:173885. [PMID: 38871310 DOI: 10.1016/j.scitotenv.2024.173885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 06/06/2024] [Accepted: 06/07/2024] [Indexed: 06/15/2024]
Abstract
Accelerating global urbanization is leading to drastic losses and restructuring of biodiversity. Although it is crucial to understand urban impacts on biodiversity to develop mitigation strategies, there is a dearth of knowledge on the functional structure of fish assemblages spanning the entire city-scale spectrum of urbanization intensity. Here, using environmental DNA sampled from 109 water sites in Beijing, we investigated the taxonomic and functional diversity patterns of fish assemblages across the city and uncovered community-, trait-, and species-level responses to various environmental stressors. By ranking sampling sites into three disturbance levels according to water physiochemical and landcover conditions, we found that both native and non-native fish taxonomic and functional α-diversity decreased significantly with elevating disturbance, as strong disturbance led to the disappearance of many species. However, the quantitative taxonomic and functional β-diversity components of native and non-native fish showed distinct patterns; assemblage turnover dominated native fish β-diversity and decreased with increasing disturbance, whereas species/trait richness differences dominated non-native fish β-diversity and increased with disturbance intensity particularly in lotic waters. RLQ and fourth-corner analyses revealed that fish size, fecundity, diet, and reproductive behaviors were significantly correlated with water quality, with pollution-tolerant, larger-sized native and omnivorous non-native fishes being urban winners, which indicates strong trait-dependent environmental filtering. Potential ecological indicator species were identified based on the sensitivity of fish responses to pollution loads; these were mostly small native species, and many have bivalve-dependent reproduction. Our results demonstrate that, along with native fish assemblage simplification and homogenization, urban stressors exert profound impacts on community trait composition, highlighting the need to consider both biodiversity loss and functional reorganization in combating disturbance of aquatic ecosystems under global urbanization. Furthermore, correlations between cropland cover and water nutrient level suggested that the management of agricultural runoff might be critically important for safeguarding urban water quality.
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Affiliation(s)
- Shan Zhang
- School of Life Sciences, Peking University, Beijing 100871, China; Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China; Ministry of Education Key Laboratory for Biodiversity Science and Engineering, NFGA Key Laboratory for Conservation Ecology of Northeast Tiger and Leopard, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Aibin Zhan
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100049, China
| | - Jindong Zhao
- School of Life Sciences, Peking University, Beijing 100871, China; Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China
| | - Meng Yao
- School of Life Sciences, Peking University, Beijing 100871, China; Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China.
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2
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Macé B, Mouillot D, Dalongeville A, Bruno M, Deter J, Varenne A, Gudefin A, Boissery P, Manel S. The Tree of Life eDNA metabarcoding reveals a similar taxonomic richness but dissimilar evolutionary lineages between seaports and marine reserves. Mol Ecol 2024; 33:e17373. [PMID: 38703047 DOI: 10.1111/mec.17373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 04/08/2024] [Accepted: 04/22/2024] [Indexed: 05/06/2024]
Abstract
Coastal areas host a major part of marine biodiversity but are seriously threatened by ever-increasing human pressures. Transforming natural coastlines into urban seascapes through habitat artificialization may result in loss of biodiversity and key ecosystem functions. Yet, the extent to which seaports differ from nearby natural habitats and marine reserves across the whole Tree of Life is still unknown. This study aimed to assess the level of α and β-diversity between seaports and reserves, and whether these biodiversity patterns are conserved across taxa and evolutionary lineages. For that, we used environmental DNA (eDNA) metabarcoding to survey six seaports on the French Mediterranean coast and four strictly no-take marine reserves nearby. By targeting four different groups-prokaryotes, eukaryotes, metazoans and fish-with appropriate markers, we provide a holistic view of biodiversity on contrasted habitats. In the absence of comprehensive reference databases, we used bioinformatic pipelines to gather similar sequences into molecular operational taxonomic units (MOTUs). In contrast to our expectations, we obtained no difference in MOTU richness (α-diversity) between habitats except for prokaryotes and threatened fishes with higher diversity in reserves than in seaports. However, we observed a marked dissimilarity (β-diversity) between seaports and reserves for all taxa. Surprisingly, this biodiversity signature of seaports was preserved across the Tree of Life, up to the order. This result reveals that seaports and nearby marine reserves share few taxa and evolutionary lineages along urbanized coasts and suggests major differences in terms of ecosystem functioning between both habitats.
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Affiliation(s)
- Bastien Macé
- CEFE, Univ Montpellier, CNRS, EPHE-PSL University, IRD, Montpellier, France
| | - David Mouillot
- MARBEC, Univ Montpellier, CNRS, Ifremer, IRD, Montpellier, France
- Institut Universitaire de France, Paris, France
| | | | - Morgane Bruno
- CEFE, Univ Montpellier, CNRS, EPHE-PSL University, IRD, Montpellier, France
| | - Julie Deter
- MARBEC, Univ Montpellier, CNRS, Ifremer, IRD, Montpellier, France
- Andromède Océanologie, Mauguio, France
| | - Alix Varenne
- Université Côte d'Azur, CNRS, ECOSEAS, Nice, France
- Ecocean, Montpellier, France
| | | | - Pierre Boissery
- Agence de l'eau Rhône-Méditerranée-Corse, Délégation de Marseille, Marseille, France
| | - Stéphanie Manel
- CEFE, Univ Montpellier, CNRS, EPHE-PSL University, IRD, Montpellier, France
- Institut Universitaire de France, Paris, France
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3
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Encinas-Viso F, Bovill J, Albrecht DE, Florez-Fernandez J, Lessard B, Lumbers J, Rodriguez J, Schmidt-Lebuhn A, Zwick A, Milla L. Pollen DNA metabarcoding reveals cryptic diversity and high spatial turnover in alpine plant-pollinator networks. Mol Ecol 2023; 32:6377-6393. [PMID: 36065738 DOI: 10.1111/mec.16682] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 08/18/2022] [Accepted: 08/30/2022] [Indexed: 11/29/2022]
Abstract
Alpine plant-pollinator communities play an important role in the functioning of alpine ecosystems, which are highly threatened by climate change. However, we still have a poor understanding of how environmental factors and spatiotemporal variability shape these communities. Here, we investigate what drives structure and beta diversity in a plant-pollinator metacommunity from the Australian alpine region using two approaches: pollen DNA metabarcoding (MB) and observations. Individual pollinators often carry pollen from multiple plant species, and therefore we expected MB to reveal a more diverse and complex network structure. We used two gene regions (ITS2 and trnL) to identify plant species present in the pollen loads of 154 insect pollinator specimens from three alpine habitats and construct MB networks, and compared them to networks based on observations alone. We compared species and interaction turnover across space for both types of networks, and evaluated their differences for plant phylogenetic diversity and beta diversity. We found significant structural differences between the two types of networks; notably, MB networks were much less specialized but more diverse than observation networks, with MB detecting many cryptic plant species. Both approaches revealed that alpine pollination networks are very generalized, but we estimated a high spatial turnover of plant species (0.79) and interaction rewiring (0.6) as well as high plant phylogenetic diversity (0.68) driven by habitat differences based on the larger diversity of plant species and species interactions detected with MB. Overall, our findings show that habitat and microclimatic heterogeneity drives diversity and fine-scale spatial turnover of alpine plant-pollinator networks.
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Affiliation(s)
- Francisco Encinas-Viso
- Centre for Australian National Biodiversity Research, Australian Capital Territory, Canberra, Australia
| | - Jessica Bovill
- Centre for Australian National Biodiversity Research, Australian Capital Territory, Canberra, Australia
| | - David E Albrecht
- Centre for Australian National Biodiversity Research, Australian Capital Territory, Canberra, Australia
| | - Jaime Florez-Fernandez
- Australian National Insect Collection, Australian Capital Territory, Canberra, Australia
| | - Bryan Lessard
- Australian National Insect Collection, Australian Capital Territory, Canberra, Australia
| | - James Lumbers
- Australian National Insect Collection, Australian Capital Territory, Canberra, Australia
| | - Juanita Rodriguez
- Australian National Insect Collection, Australian Capital Territory, Canberra, Australia
| | - Alexander Schmidt-Lebuhn
- Centre for Australian National Biodiversity Research, Australian Capital Territory, Canberra, Australia
| | - Andreas Zwick
- Australian National Insect Collection, Australian Capital Territory, Canberra, Australia
| | - Liz Milla
- Centre for Australian National Biodiversity Research, Australian Capital Territory, Canberra, Australia
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4
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Baletaud F, Lecellier G, Gilbert A, Mathon L, Côme JM, Dejean T, Dumas M, Fiat S, Vigliola L. Comparing Seamounts and Coral Reefs with eDNA and BRUVS Reveals Oases and Refuges on Shallow Seamounts. BIOLOGY 2023; 12:1446. [PMID: 37998045 PMCID: PMC10669620 DOI: 10.3390/biology12111446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 11/13/2023] [Accepted: 11/13/2023] [Indexed: 11/25/2023]
Abstract
Seamounts are the least known ocean biome. Considered biodiversity hotspots, biomass oases, and refuges for megafauna, large gaps exist in their real diversity relative to other ecosystems like coral reefs. Using environmental DNA metabarcoding (eDNA) and baited video (BRUVS), we compared fish assemblages across five environments of different depths: coral reefs (15 m), shallow seamounts (50 m), continental slopes (150 m), intermediate seamounts (250 m), and deep seamounts (500 m). We modeled assemblages using 12 environmental variables and found depth to be the main driver of fish diversity and biomass, although other variables like human accessibility were important. Boosted Regression Trees (BRT) revealed a strong negative effect of depth on species richness, segregating coral reefs from deep-sea environments. Surprisingly, BRT showed a hump-shaped effect of depth on fish biomass, with significantly lower biomass on coral reefs than in shallowest deep-sea environments. Biomass of large predators like sharks was three times higher on shallow seamounts (50 m) than on coral reefs. The five studied environments showed quite distinct assemblages. However, species shared between coral reefs and deeper-sea environments were dominated by highly mobile large predators. Our results suggest that seamounts are no diversity hotspots for fish. However, we show that shallower seamounts form biomass oases and refuges for threatened megafauna, suggesting that priority should be given to their protection.
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Affiliation(s)
- Florian Baletaud
- ENTROPIE, Institut de Recherche pour le Développement (IRD), UR, UNC, IFREMER, CNRS, Centre IRD de Nouméa, 98848 Noumea, New Caledonia, France; (F.B.); (G.L.); (L.M.); (M.D.); (S.F.)
- GINGER SOPRONER, 98000 Noumea, New Caledonia, France;
- GINGER BURGEAP, 69000 Lyon, France;
- MARBEC, University of Montpellier, CNRS, IFREMER, 34000 Montpellier, France
| | - Gaël Lecellier
- ENTROPIE, Institut de Recherche pour le Développement (IRD), UR, UNC, IFREMER, CNRS, Centre IRD de Nouméa, 98848 Noumea, New Caledonia, France; (F.B.); (G.L.); (L.M.); (M.D.); (S.F.)
- ISEA, University of New Caledonia, 98800 Noumea, New Caledonia, France
| | | | - Laëtitia Mathon
- ENTROPIE, Institut de Recherche pour le Développement (IRD), UR, UNC, IFREMER, CNRS, Centre IRD de Nouméa, 98848 Noumea, New Caledonia, France; (F.B.); (G.L.); (L.M.); (M.D.); (S.F.)
- CEFE, University of Montpellier, CNRS, EPHE-PSL, IRD, 34000 Montpellier, France
| | | | | | - Mahé Dumas
- ENTROPIE, Institut de Recherche pour le Développement (IRD), UR, UNC, IFREMER, CNRS, Centre IRD de Nouméa, 98848 Noumea, New Caledonia, France; (F.B.); (G.L.); (L.M.); (M.D.); (S.F.)
| | - Sylvie Fiat
- ENTROPIE, Institut de Recherche pour le Développement (IRD), UR, UNC, IFREMER, CNRS, Centre IRD de Nouméa, 98848 Noumea, New Caledonia, France; (F.B.); (G.L.); (L.M.); (M.D.); (S.F.)
| | - Laurent Vigliola
- ENTROPIE, Institut de Recherche pour le Développement (IRD), UR, UNC, IFREMER, CNRS, Centre IRD de Nouméa, 98848 Noumea, New Caledonia, France; (F.B.); (G.L.); (L.M.); (M.D.); (S.F.)
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5
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Lamperti L, Sanchez T, Si Moussi S, Mouillot D, Albouy C, Flück B, Bruno M, Valentini A, Pellissier L, Manel S. New deep learning-based methods for visualizing ecosystem properties using environmental DNA metabarcoding data. Mol Ecol Resour 2023; 23:1946-1958. [PMID: 37702270 DOI: 10.1111/1755-0998.13861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 07/29/2023] [Accepted: 08/14/2023] [Indexed: 09/14/2023]
Abstract
Environmental DNA (eDNA) metabarcoding provides an efficient approach for documenting biodiversity patterns in marine and terrestrial ecosystems. The complexity of these data prevents current methods from extracting and analyzing all the relevant ecological information they contain, and new methods may provide better dimensionality reduction and clustering. Here we present two new deep learning-based methods that combine different types of neural networks (NNs) to ordinate eDNA samples and visualize ecosystem properties in a two-dimensional space: the first is based on variational autoencoders and the second on deep metric learning. The strength of our new methods lies in the combination of two inputs: the number of sequences found for each molecular operational taxonomic unit (MOTU) detected and their corresponding nucleotide sequence. Using three different datasets, we show that our methods accurately represent several biodiversity indicators in a two-dimensional latent space: MOTU richness per sample, sequence α-diversity per sample, Jaccard's and sequence β-diversity between samples. We show that our nonlinear methods are better at extracting features from eDNA datasets while avoiding the major biases associated with eDNA. Our methods outperform traditional dimension reduction methods such as Principal Component Analysis, t-distributed Stochastic Neighbour Embedding, Nonmetric Multidimensional Scaling and Uniform Manifold Approximation and Projection for dimension reduction. Our results suggest that NNs provide a more efficient way of extracting structure from eDNA metabarcoding data, thereby improving their ecological interpretation and thus biodiversity monitoring.
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Affiliation(s)
- Letizia Lamperti
- CEFE, Univ Montpellier, CNRS, EPHE-PSL University, IRD, Montpellier, France
- Ecosystems and Landscape Evolution, Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland
- Ecosystems and Landscape Evolution, Land Change Science Research Unit, Swiss Federal Institute for Forest, Snow and Landscape Research (WSL), Switzerland
| | - Théophile Sanchez
- Ecosystems and Landscape Evolution, Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland
- Ecosystems and Landscape Evolution, Land Change Science Research Unit, Swiss Federal Institute for Forest, Snow and Landscape Research (WSL), Switzerland
| | - Sara Si Moussi
- Laboratoire d'Ecologie Alpine, Univ. Grenoble Alpes, Univ. Savoie MontBlanc, CNRS, Grenoble, France
| | - David Mouillot
- MARBEC, Univ Montpellier, CNRS, IFREMER, IRD, Montpellier, France
- Institut Universitaire de France, Paris, France
| | - Camille Albouy
- Ecosystems and Landscape Evolution, Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland
- Ecosystems and Landscape Evolution, Land Change Science Research Unit, Swiss Federal Institute for Forest, Snow and Landscape Research (WSL), Switzerland
| | - Benjamin Flück
- Ecosystems and Landscape Evolution, Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland
- Ecosystems and Landscape Evolution, Land Change Science Research Unit, Swiss Federal Institute for Forest, Snow and Landscape Research (WSL), Switzerland
| | - Morgane Bruno
- CEFE, Univ Montpellier, CNRS, EPHE-PSL University, IRD, Montpellier, France
| | | | - Loïc Pellissier
- Ecosystems and Landscape Evolution, Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland
- Ecosystems and Landscape Evolution, Land Change Science Research Unit, Swiss Federal Institute for Forest, Snow and Landscape Research (WSL), Switzerland
| | - Stéphanie Manel
- CEFE, Univ Montpellier, CNRS, EPHE-PSL University, IRD, Montpellier, France
- Institut Universitaire de France, Paris, France
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6
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Xiang T, Dong X, Ju T, Shi L, Grenouillet G. Anthropogenic activities and environmental filtering have reshaped freshwater fish biodiversity patterns in China over the past 120 years. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 344:118374. [PMID: 37331311 DOI: 10.1016/j.jenvman.2023.118374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 06/06/2023] [Accepted: 06/09/2023] [Indexed: 06/20/2023]
Abstract
Over the past centuries, freshwater fish introductions and extinctions have been the major environmental and ecological crises in various water bodies in China. However, consequences of such crises on freshwater fish biodiversity in China remain only partially or locally studied. Furthermore, identifications of relatively sensitive areas along with stressors (i.e., environmental and anthropogenic drivers) influencing freshwater fish biodiversity patterns are still pending. Taxonomic, functional, and phylogenetic facets of biodiversity can well describe and evaluate the underlying processes affecting freshwater fish biodiversity patterns under different dimensionalities. Here we thus evaluated temporal changes in these facets of freshwater fish biodiversity as well as a new developed biodiversity index, multifaceted changes in fish biodiversity, for over a century at the basin level throughout China using both alpha and beta diversity approaches. We also identified the drivers influencing the changes in fish biodiversity patterns using random forest models. The results showed that fish assemblages in Northwest and Southwest China (e.g., Ili River basin, Tarim basin, and Erhai Lake basin) experienced extreme temporal and multifaceted changes in the facets of biodiversity compared with other regions, and environmental factors (e.g., net primary productivity, average annual precipitation, and unit area) largely drove these changes. Since fish faunas in over 80% of China's water bodies covering more than 80% of China's surface were currently undergoing taxonomic, functional, and phylogenetic homogenization, targeted conservation and management strategies should be proposed and implemented, especially for the areas with relatively high changes in biodiversity.
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Affiliation(s)
- Tao Xiang
- Laboratoire Evolution et Diversité Biologique (EDB), UMR5174, Université Toulouse 3 Paul Sabatier, CNRS, IRD, Toulouse, 31062, France.
| | - Xianghong Dong
- College of Animal Science, Guizhou University, Guiyang, 550025, China.
| | - Tao Ju
- Guangxi Beibu Gulf Marine Research Center, Guangxi Academy of Sciences, Nanning, 530007, China
| | - Lei Shi
- School of Ecology and Environmental Science, Yunnan University, Kunming, 650504, China
| | - Gaël Grenouillet
- Laboratoire Evolution et Diversité Biologique (EDB), UMR5174, Université Toulouse 3 Paul Sabatier, CNRS, IRD, Toulouse, 31062, France; Institut Universitaire de France, Paris, France
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7
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Yang J, Zhang L, Mu Y, Wang J, Yu H, Zhang X. Unsupervised biological integrity assessment by eDNA biomonitoring of multi-trophic aquatic taxa. ENVIRONMENT INTERNATIONAL 2023; 175:107950. [PMID: 37182420 DOI: 10.1016/j.envint.2023.107950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 04/12/2023] [Accepted: 04/23/2023] [Indexed: 05/16/2023]
Abstract
The biological integrity of global freshwater ecosystems is threatened by ever-increasing environmental stressors due to increased human activities, such as land-use change, eutrophication, toxic pollutants, overfishing, and exploitation. Traditional ecological assessments of lake or riverine ecosystems often require human supervision of a pre-selected reference area, using the current state of the reference area as the expected state. However, selecting an appropriate reference area has become increasingly difficult with the expansion of human activities. Here, an unsupervised biological integrity assessment framework based on environmental DNA metabarcoding without a prior reference area is proposed. Taxon richness, species dominance, co-occurrence network density, and phylogenetic distance were used to assess the aquatic communities in the Taihu Lake basin. Multi-gene metabarcoding revealed comprehensive biodiversity at multiple trophic levels including algae, protists, zooplankton, and fish. Fish sequences were mainly derived from 12S, zooplankton mainly from mitochondrial cytochrome C oxidase subunit I, and algae and protists mainly from 18S. There were significant differences in community composition among lakes, rivers, and reservoirs but no significant differences in the four fundamental biological indicators. The algal and zooplankton integrities were positively correlated with protist and fish integrities, respectively. Additionally, the algal integrity of lakes was found to be significantly lower than that of rivers. The unsupervised assessment framework proposed in this study allows different ecosystems, including the same ecosystem in different seasons, to adopt the same indicators and assessment methods, which is more convenient for environmental management and decision-making.
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Affiliation(s)
- Jianghua Yang
- State Key Laboratory of Pollution Control & Resource, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Lijuan Zhang
- State Key Laboratory of Pollution Control & Resource, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Yawen Mu
- State Key Laboratory of Pollution Control & Resource, School of the Environment, Nanjing University, Nanjing 210023, China; Jiangsu Provincial Environmental Monitoring Center, Nanjing 210019, China
| | - Jiangye Wang
- State Key Laboratory of Pollution Control & Resource, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Hongxia Yu
- State Key Laboratory of Pollution Control & Resource, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Xiaowei Zhang
- State Key Laboratory of Pollution Control & Resource, School of the Environment, Nanjing University, Nanjing 210023, China.
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8
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Gonzalez Colmenares GM, Gonzalez Montes AJ, Harms-Tuohy CA, Schizas NV. Using eDNA sampling for species-specific fish detection in tropical oceanic samples: limitations and recommendations for future use. PeerJ 2023; 11:e14810. [PMID: 36751629 PMCID: PMC9899429 DOI: 10.7717/peerj.14810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 01/06/2023] [Indexed: 02/05/2023] Open
Abstract
Background Over the past decade, environmental DNA (eDNA) has become a resourceful tool in conservation and biomonitoring. Environmental DNA has been applied in a variety of environments, but the application to studies of marine fish, particularly at tropical latitudes, are limited. Since many commercially important Caribbean fishes are overexploited, these species are optimal candidates to explore the use of this method as a biomonitoring tool. Specifically, for many of these species, the formation of fish spawning aggregations (FSAs) marks a critical life history event where fishes will gather in large numbers for reproduction. These FSAs are ephemeral in nature, lasting only a few days, but are predictable in time and space which makes them susceptible to overfishing. Methods In this study, we test the feasibility of using an eDNA sampling approach (water and sediment collection) to detect the presence of known FSAs off the west coast of Puerto Rico, with cytochrome c oxidase subunit 1 (CO1) and 12S rRNA (12S) primers designed to target specific species. A total of 290 eDNA samples were collected and, of those, 206 eDNA samples were processed. All eDNA samples varied in DNA concentration, both between replicates and collection methods. A total of 12 primer sets were developed and tested using traditional PCR and qPCR. Results Despite validation of primer accuracy and sample collection during known peak spawning times, the use of traditional PCR and qPCR with both molecular markers failed to produce species-specific amplification. Thus, a trial test was conducted using the CO1 primers in which target fish DNA was 'spiked' at various concentrations into the respective eDNA samples to determine the target species DNA concentration limit of detection. Upon successful amplification of the trial, results indicated that eDNA samples were below the detection threshold of our methods, suggesting that the number of fish present at the spawning aggregations was inadequate for single-species detection methods. In addition, elements such as the unavoidable presence of non-target DNA, oceanic environmental conditions, shedding rates of target fish, among other biotic and abiotic factors could have affected DNA persistence and degradation rates at the sites. Conclusion We provide recommendations for species-specific fish detection in lower latitudes, and suggestions for studies aiming to monitor or detect fish spawning aggregations using eDNA sampling.
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Affiliation(s)
| | | | | | - Nikolaos V. Schizas
- Department of Marine Sciences, Universidad de Puerto Rico, Recinto de Mayagüez, Mayagüez, Puerto Rico
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9
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Yao M, Zhang S, Lu Q, Chen X, Zhang SY, Kong Y, Zhao J. Fishing for fish environmental DNA: Ecological applications, methodological considerations, surveying designs, and ways forward. Mol Ecol 2022; 31:5132-5164. [PMID: 35972241 DOI: 10.1111/mec.16659] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 07/20/2022] [Accepted: 07/27/2022] [Indexed: 12/15/2022]
Abstract
Vast global declines of freshwater and marine fish diversity and population abundance pose serious threats to both ecosystem sustainability and human livelihoods. Environmental DNA (eDNA)-based biomonitoring provides robust, efficient, and cost-effective assessment of species occurrences and population trends in diverse aquatic environments. Thus, it holds great potential for improving conventional surveillance frameworks to facilitate fish conservation and fisheries management. However, the many technical considerations and rapid developments underway in the eDNA arena can overwhelm researchers and practitioners new to the field. Here, we systematically analysed 416 fish eDNA studies to summarize research trends in terms of investigated targets, research aims, and study systems, and reviewed the applications, rationales, methodological considerations, and limitations of eDNA methods with an emphasis on fish and fisheries research. We highlighted how eDNA technology may advance our knowledge of fish behaviour, species distributions, population genetics, community structures, and ecological interactions. We also synthesized the current knowledge of several important methodological concerns, including the qualitative and quantitative power eDNA has to recover fish biodiversity and abundance, and the spatial and temporal representations of eDNA with respect to its sources. To facilitate ecological applications implementing fish eDNA techniques, recent literature was summarized to generate guidelines for effective sampling in lentic, lotic, and marine habitats. Finally, we identified current gaps and limitations, and pointed out newly emerging research avenues for fish eDNA. As methodological optimization and standardization improve, eDNA technology should revolutionize fish monitoring and promote biodiversity conservation and fisheries management that transcends geographic and temporal boundaries.
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Affiliation(s)
- Meng Yao
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, China.,School of Life Sciences, Peking University, Beijing, China
| | - Shan Zhang
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, China.,School of Life Sciences, Peking University, Beijing, China
| | - Qi Lu
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, China.,School of Life Sciences, Peking University, Beijing, China
| | - Xiaoyu Chen
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, China.,School of Life Sciences, Peking University, Beijing, China
| | - Si-Yu Zhang
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, China.,School of Life Sciences, Peking University, Beijing, China
| | - Yueqiao Kong
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, China.,School of Life Sciences, Peking University, Beijing, China
| | - Jindong Zhao
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, China.,School of Life Sciences, Peking University, Beijing, China
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10
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Dalongeville A, Boulanger E, Marques V, Charbonnel E, Hartmann V, Santoni MC, Deter J, Valentini A, Lenfant P, Boissery P, Dejean T, Velez L, Pichot F, Sanchez L, Arnal V, Bockel T, Delaruelle G, Holon F, Milhau T, Romant L, Manel S, Mouillot D. Benchmarking eleven biodiversity indicators based on environmental
DNA
surveys: more diverse functional traits and evolutionary lineages inside marine reserves. J Appl Ecol 2022. [DOI: 10.1111/1365-2664.14276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - Emilie Boulanger
- Aix‐Marseille Université Université de Toulon, CNRS, IRD, Mediterranean Institute of Oceanography (MIO), UM 110 Marseille France
| | - Virginie Marques
- CEFE, Univ Montpellier, CNRS, EPHE‐PSL University, IRD, Univ Paul Valéry Montpellier 3 Montpellier France
| | - Eric Charbonnel
- Parc Marin de la Côte Bleue, Observatoire, plage du Rouet. 31 Av. J. Bart. BP 42. 13820 Carry‐le‐Rouet France
| | - Virginie Hartmann
- Reserve Naturelle Marine de Cerbère‐Banyuls, Département des Pyrénées‐Orientales, 5 rue Roger David 66650 Banyuls‐sur‐mer France
| | | | - Julie Deter
- MARBEC, Univ Montpellier, CNRS, Ifremer, IRD Montpellier France
- Andromède Océanologie, 7 place Cassan – Carnon plage, 34130 Mauguio France
| | - Alice Valentini
- SPYGEN, 17 rue du Lac Saint‐André, 73370 Le Bourget‐du‐Lac France
| | - Philippe Lenfant
- Université Perpignan Via Domitia Centre de Formation et de Recherche sur les Environnements Méditerranéens, UMR 5110, 58 Avenue Paul Alduy Perpignan France
| | - Pierre Boissery
- Agence de l’Eau Rhône‐Méditerranée‐Corse, Délégation de Marseille, 2 rue Barbusse, CS 90464, 13207 Marseille Cedex France
| | - Tony Dejean
- SPYGEN, 17 rue du Lac Saint‐André, 73370 Le Bourget‐du‐Lac France
| | - Laure Velez
- MARBEC, Univ Montpellier, CNRS, Ifremer, IRD Montpellier France
| | - Franck Pichot
- MARBEC, Univ Montpellier, CNRS, Ifremer, IRD Montpellier France
| | - Loic Sanchez
- MARBEC, Univ Montpellier, CNRS, Ifremer, IRD Montpellier France
- CEFE, Univ Montpellier, CNRS, EPHE‐PSL University, IRD, Univ Paul Valéry Montpellier 3 Montpellier France
| | - Veronique Arnal
- CEFE, Univ Montpellier, CNRS, EPHE‐PSL University, IRD, Univ Paul Valéry Montpellier 3 Montpellier France
| | - Thomas Bockel
- Andromède Océanologie, 7 place Cassan – Carnon plage, 34130 Mauguio France
| | | | - Florian Holon
- Andromède Océanologie, 7 place Cassan – Carnon plage, 34130 Mauguio France
| | - Tristan Milhau
- SPYGEN, 17 rue du Lac Saint‐André, 73370 Le Bourget‐du‐Lac France
| | - Lola Romant
- MARBEC, Univ Montpellier, CNRS, Ifremer, IRD Montpellier France
| | - Stéphanie Manel
- CEFE, Univ Montpellier, CNRS, EPHE‐PSL University, IRD, Univ Paul Valéry Montpellier 3 Montpellier France
| | - David Mouillot
- MARBEC, Univ Montpellier, CNRS, Ifremer, IRD Montpellier France
- Institut Universitaire de France Paris France
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11
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Polanco F. A, Waldock C, Keggin T, Marques V, Rozanski R, Valentini A, Dejean T, Manel S, Vermeij M, Albouy C, Pellissier L. Ecological indices from environmental
DNA
to contrast coastal reefs under different anthropogenic pressures. Ecol Evol 2022. [DOI: 10.1002/ece3.9212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Affiliation(s)
- Andrea Polanco F.
- Beauval Nature Association Saint Aignan sur Cher France
- Fundación Biodiversa Colombia Bogotá, D.C. Colombia
| | - Conor Waldock
- Ecosystems and Landscape Evolution, Department of Environmental Systems Science, Institute of Terrestrial Ecosystems ETH Zürich Zürich Switzerland
- Unit of Land Change Science Swiss Federal Research Institute WSL Birmensdorf Switzerland
| | - Thomas Keggin
- Ecosystems and Landscape Evolution, Department of Environmental Systems Science, Institute of Terrestrial Ecosystems ETH Zürich Zürich Switzerland
- Unit of Land Change Science Swiss Federal Research Institute WSL Birmensdorf Switzerland
| | - Virginie Marques
- CEFE, Univ Montpellier, CNRS, EPHE‐PSL University, IRD, Univ Paul Valéry Montpellier 3 Montpellier France
- MARBEC Univ Montpellier, CNRS, Ifremer, IRD Montpellier France
| | - Romane Rozanski
- Fundación Biodiversa Colombia Bogotá, D.C. Colombia
- Ecosystems and Landscape Evolution, Department of Environmental Systems Science, Institute of Terrestrial Ecosystems ETH Zürich Zürich Switzerland
- IFREMER Unité Ecologie et Modèles pour l'Halieutique, EMH Nantes France
| | | | | | - Stéphanie Manel
- CEFE, Univ Montpellier, CNRS, EPHE‐PSL University, IRD, Univ Paul Valéry Montpellier 3 Montpellier France
| | | | - Camille Albouy
- Fundación Biodiversa Colombia Bogotá, D.C. Colombia
- Ecosystems and Landscape Evolution, Department of Environmental Systems Science, Institute of Terrestrial Ecosystems ETH Zürich Zürich Switzerland
- IFREMER Unité Ecologie et Modèles pour l'Halieutique, EMH Nantes France
| | - Loïc Pellissier
- Fundación Biodiversa Colombia Bogotá, D.C. Colombia
- Ecosystems and Landscape Evolution, Department of Environmental Systems Science, Institute of Terrestrial Ecosystems ETH Zürich Zürich Switzerland
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12
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Zhong W, Zhang J, Wang Z, Lin J, Huang X, Liu W, Li H, Pellissier L, Zhang X. Holistic Impact Evaluation of Human Activities on the Coastal Fish Biodiversity in the Chinese Coastal Environment. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:6574-6583. [PMID: 35510674 DOI: 10.1021/acs.est.2c01339] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Ecological qualities and resources in coasts are threatened by various human activities, such as pollution and fishery. Impact evaluation of environmental stressors over a wide coastal stretch has been limited due to lack of efficient and standardizable biodiversity monitoring and assessment tools. Integrating environmental DNA (eDNA) and ecological traits, a holistic approach was developed to assess the impact of pollution and aquaculture on fish biodiversity in Chinese coastal areas. Taking the Yalujiang Estuary (YLJK) from the Yellow Sea and the Nan'ao Island Area (NAO) from the South China Sea as cases, the performance of the eDNA biomonitoring workflow was validated. First, the eDNA results of 22 sampling sites reached more than 85% of the asymptotes of species or ASVs in each area. A total of 115 fish species in both areas were detected and NAO was 1.8 times richer than YLJK using eDNA and the fish eDNA composition was consistent with the historical data. eDNA recovered distinct variations of fish sequence, taxonomic and functional diversity, and the corresponding trends following the offshore distance between the two areas. Fish sequence diversity was decreased primarily by estuarine pollution factors (chemical oxygen demand and zinc) in the YLJK. Compared with no breeding areas, lower fish sequence diversity was in breeding areas in the NAO. By integrating ecological traits, the eDNA approach offers promising opportunities for future fish biodiversity monitoring and assessment in national and global coastal environments.
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Affiliation(s)
- Wenjun Zhong
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, P. R. China
| | - Jinyong Zhang
- State Environmental Protection Key Laboratory of Coastal Ecosystem, National Marine Environmental Monitoring Center, Dalian 116023, P. R. China
| | - Zhihao Wang
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, P. R. China
| | - Jianqing Lin
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Institute of Marine Science, Shantou University, Shantou 515063, P. R. China
| | - Xiangyun Huang
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, P. R. China
| | - Wenhua Liu
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou 511458, P. R. China
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Institute of Marine Science, Shantou University, Shantou 515063, P. R. China
| | - Hongjun Li
- State Environmental Protection Key Laboratory of Coastal Ecosystem, National Marine Environmental Monitoring Center, Dalian 116023, P. R. China
| | - Loïc Pellissier
- Swiss Federal Research Institute WSL, Birmensdorf 8903, Switzerland
- Landscape Ecology, Institute of Terrestrial Ecosystems, Department of Environmental System Science, ETH Zürich, Zürich 8092, Switzerland
| | - Xiaowei Zhang
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, P. R. China
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13
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Bessudo S, Ladino F, Becerril-García EE, Shepard CM, Salinas-De-León P, Hoyos-Padilla EM. The elasmobranchs of Malpelo Flora and Fauna Sanctuary, Colombia. JOURNAL OF FISH BIOLOGY 2021; 99:1769-1774. [PMID: 34382690 DOI: 10.1111/jfb.14874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 07/28/2021] [Accepted: 08/06/2021] [Indexed: 06/13/2023]
Abstract
Management and conservation actions in marine-protected areas require baselines for monitoring threatened marine fauna such as elasmobranchs. This article provides evidence of the occurrence of 34 species of elasmobranchs (21 sharks and 13 batoids) in the Malpelo Flora and Fauna Sanctuary, Colombia, including five new records of sharks and three of rays. From 1987 to 2021, new records were obtained by underwater visual census using SCUBA, manned submersibles and deep-ocean cameras to depths of up to 2211 m. Of the recorded species, 21 are considered as threatened taxa (64%) by the IUCN, making the Malpelo Flora and Fauna Sanctuary an essential conservation area for this highly threatened group of species.
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Affiliation(s)
- Sandra Bessudo
- Fundación Malpelo y otros Ecosistemas Marinos, Bogotá, Colombia
- MigraMar, Olema, California, USA
| | - Felipe Ladino
- Fundación Malpelo y otros Ecosistemas Marinos, Bogotá, Colombia
| | - Edgar Eduardo Becerril-García
- Pelagios Kakunjá A.C., La Paz, Mexico
- Instituto Politécnico Nacional, Centro Interdisciplinario de Ciencias Marinas, La Paz, Mexico
| | - Charles M Shepard
- Exploration Technology Lab, National Geographic Society, Washington, District of Columbia, USA
| | - Pelayo Salinas-De-León
- Pristine Seas, National Geographic Society, Washington, District of Columbia, USA
- Charles Darwin Foundation, Charles Darwin Research Station, Galapagos Islands, Ecuador
| | - Edgar Mauricio Hoyos-Padilla
- MigraMar, Olema, California, USA
- Pelagios Kakunjá A.C., La Paz, Mexico
- Fins Attached Marine Research and Conservation, Colorado Springs, Colorado, USA
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