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Flo S, Vader A, Præbel K. Brute force prey metabarcoding to explore the diets of small invertebrates. Ecol Evol 2024; 14:e11369. [PMID: 38711484 PMCID: PMC11070772 DOI: 10.1002/ece3.11369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 04/16/2024] [Accepted: 04/17/2024] [Indexed: 05/08/2024] Open
Abstract
Prey metabarcoding has become a popular tool in molecular ecology for resolving trophic interactions at high resolution, from various sample types and animals. To date, most predator-prey studies of small-sized animals (<1 mm) have met the problem of overabundant predator DNA in dietary samples by adding blocking primers/peptide nucleic acids. These primers aim to limit the PCR amplification and detection of the predator DNA but may introduce bias to the prey composition identified by interacting with sequences that are similar to those of the predator. Here we demonstrate the use of an alternative method to explore the prey of small marine copepods using whole-body DNA extracts and deep, brute force metabarcoding of an 18S rDNA fragment. After processing and curating raw data from two sequencing runs of varying depths (0.4 and 5.4 billion raw reads), we isolated 1.3 and 52.2 million prey reads, with average depths of ~15,900 and ~120,000 prey reads per copepod individual, respectively. While data from both sequencing runs were sufficient to distinguish dietary compositions from disparate seasons, locations, and copepod species, greater sequencing depth led to better separation of clusters. As computation and sequencing are becoming ever more powerful and affordable, we expect the brute force approach to become a general standard for prey metabarcoding, as it offers a simple and affordable solution to consumers that is impractical to dissect or unknown to science.
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Affiliation(s)
- Snorre Flo
- Department of Arctic BiologyThe University Centre in SvalbardLongyearbyen, SvalbardNorway
- Faculty of Biosciences, Fisheries and EconomicsUiT The Arctic University of NorwayTromsøNorway
| | - Anna Vader
- Department of Arctic BiologyThe University Centre in SvalbardLongyearbyen, SvalbardNorway
| | - Kim Præbel
- The Norwegian College of Fishery Science (NFH)UiT The Arctic University of NorwayTromsøNorway
- Department of Forestry and Wildlife ManagementInland Norway University of Applied SciencesElverumNorway
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Ye L, Peng S, Ma Y, Zhang W, Wang L, Sun X, Zhang C, Yeasmin M, Zhao J, Dong Z. Biodiversity and distribution patterns of blooming jellyfish in the Bohai Sea revealed by eDNA metabarcoding. BMC Ecol Evol 2024; 24:37. [PMID: 38500049 PMCID: PMC10946145 DOI: 10.1186/s12862-024-02224-3] [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: 11/14/2023] [Accepted: 03/12/2024] [Indexed: 03/20/2024] Open
Abstract
BACKGROUND The mass occurrence of scyphozoan jellyfish severely affects marine ecosystems and coastal economies, and the study of blooming jellyfish population dynamics has emerged in response. However, traditional ecological survey methods required for such research have difficulties in detecting cryptic life stages and surveying population dynamics owing to high spatiotemporal variations in their occurrence. The environmental DNA (eDNA) technique is an effective tool for overcoming these limitations. RESULTS In this study, we investigated the biodiversity and spatial distribution characteristics of blooming jellyfish in the Bohai Sea of China using an eDNA metabarcoding approach, which covered the surface, middle, and bottom seawater layers, and sediments. Six jellyfish taxa were identified, of which Aurelia coerulea, Nemopilema nomurai, and Cyanea nozakii were the most dominant. These three blooming jellyfish presented a marked vertical distribution pattern in the offshore regions. A. coerulea was mainly distributed in the surface layer, whereas C. nozakii and N. nomurai showed a upper-middle and middle-bottom aggregation, respectively. Horizontally, A. coerulea and C. nozakii were more abundant in the inshore regions, whereas N. nomurai was mainly distributed offshore. Spearman's correlation analysis revealed a strong correlation between the eDNA of the three dominant blooming jellyfish species and temperature, salinity, and nutrients. CONCLUSIONS Our study confirms the applicability of the eDNA approach to both biodiverstiy evaluation of blooming jellyfish and investigating their spatial distribution, and it can be used as a supplementary tool to traditional survey methods.
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Affiliation(s)
- Lijing Ye
- Yantai University, 264005, Yantai, Shandong, China
- Muping Coastal Environment Research Station, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, 264003, Yantai, Shandong, China
| | - Saijun Peng
- Muping Coastal Environment Research Station, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, 264003, Yantai, Shandong, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Yuanqing Ma
- Shandong Key Laboratory of Marine Ecological Restoration, Shandong Marine Resource and Environment Research Institute, 264006, Yantai, Shandong, China
| | - Wenjing Zhang
- Muping Coastal Environment Research Station, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, 264003, Yantai, Shandong, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Lei Wang
- Muping Coastal Environment Research Station, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, 264003, Yantai, Shandong, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Xiyan Sun
- Muping Coastal Environment Research Station, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, 264003, Yantai, Shandong, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Chen Zhang
- Muping Coastal Environment Research Station, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, 264003, Yantai, Shandong, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Munjira Yeasmin
- Muping Coastal Environment Research Station, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, 264003, Yantai, Shandong, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Jianmin Zhao
- Muping Coastal Environment Research Station, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, 264003, Yantai, Shandong, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Zhijun Dong
- Muping Coastal Environment Research Station, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, 264003, Yantai, Shandong, China.
- University of Chinese Academy of Sciences, 100049, Beijing, China.
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Haddock SHD, Choy CA. Life in the Midwater: The Ecology of Deep Pelagic Animals. ANNUAL REVIEW OF MARINE SCIENCE 2024; 16:383-416. [PMID: 38231738 DOI: 10.1146/annurev-marine-031623-095435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
The water column of the deep ocean is dark, cold, low in food, and under crushing pressures, yet it is full of diverse life. Due to its enormous volume, this mesopelagic zone is home to some of the most abundant animals on the planet. Rather than struggling to survive, they thrive-owing to a broad set of adaptations for feeding, behavior, and physiology. Our understanding of these adaptations is constrained by the tools available for exploring the deep sea, but this tool kit is expanding along with technological advances. Each time we apply a new method to the depths, we gain surprising insights about genetics, ecology, behavior, physiology, diversity, and the dynamics of change. These discoveries show structure within the seemingly uniform habitat, limits to the seemingly inexhaustible resources, and vulnerability in the seemingly impervious environment. To understand midwater ecology, we need to reimagine the rules that govern terrestrial ecosystems. By spending more time at depth-with whatever tools are available-we can fill the knowledge gaps and better link ecology to the environment throughout the water column.
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Affiliation(s)
- Steven H D Haddock
- Monterey Bay Aquarium Research Institute, Moss Landing, California, USA;
| | - C Anela Choy
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA;
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Balazy K, Trudnowska E, Wojczulanis-Jakubas K, Jakubas D, Præbel K, Choquet M, Brandner MM, Schultz M, Bitz-Thorsen J, Boehnke R, Szeligowska M, Descamps S, Strøm H, Błachowiak-Samołyk K. Molecular tools prove little auks from Svalbard are extremely selective for Calanus glacialis even when exposed to Atlantification. Sci Rep 2023; 13:13647. [PMID: 37607972 PMCID: PMC10444800 DOI: 10.1038/s41598-023-40131-7] [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: 01/05/2023] [Accepted: 08/04/2023] [Indexed: 08/24/2023] Open
Abstract
Two Calanus species, C. glacialis and C. finmarchicus, due to different life strategies and environmental preferences act as an ecological indicators of Arctic Atlantification. Their high lipid content makes them important food source for higher trophic levels of Arctic ecosystems including the most abundant Northern Hemisphere's seabird, the little auk (Alle alle). Recent studies indicate a critical need for the use of molecular methods to reliably identify these two sympatric Calanus species. We performed genetic and morphology-based identification of 2600 Calanus individuals collected in little auks foraging grounds and diet in summer seasons 2019-2021 in regions of Svalbard with varying levels of Atlantification. Genetic identification proved that 40% of Calanus individuals were wrongly classified as C. finmarchicus according to morphology-based identification in both types of samples. The diet of little auks consisted almost entirely of C. glacialis even in more Atlantified regions. Due to the substantial bias in morphology-based identification, we expect that the scale of the northern expansion of boreal C. finmarchicus may have been largely overestimated and that higher costs for birds exposed to Atlantification could be mostly driven by a decrease in the size of C. glacialis rather than by shift from C. glacialis to C. finmarchicus.
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Affiliation(s)
- Kaja Balazy
- Department of Marine Ecology, Institute of Oceanology, Polish Academy of Sciences, Powstancow Warszawy 55, 81-222, Sopot, Poland.
| | - Emilia Trudnowska
- Department of Marine Ecology, Institute of Oceanology, Polish Academy of Sciences, Powstancow Warszawy 55, 81-222, Sopot, Poland
| | | | - Dariusz Jakubas
- Department of Vertebrate Ecology and Zoology, Faculty of Biology, University of Gdansk, 80-309, Gdansk, Poland
| | - Kim Præbel
- Norwegian College of Fishery Science, UiT The Arctic University of Norway, Tromsø, Norway
| | - Marvin Choquet
- Faculty of Biosciences and Aquaculture, Nord University, 8049, Bodø, Norway
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Melissa M Brandner
- Norwegian College of Fishery Science, UiT The Arctic University of Norway, Tromsø, Norway
| | - Mads Schultz
- Faculty of Biosciences and Aquaculture, Nord University, 8049, Bodø, Norway
| | - Julie Bitz-Thorsen
- Norwegian College of Fishery Science, UiT The Arctic University of Norway, Tromsø, Norway
| | - Rafał Boehnke
- Department of Marine Ecology, Institute of Oceanology, Polish Academy of Sciences, Powstancow Warszawy 55, 81-222, Sopot, Poland
| | - Marlena Szeligowska
- Department of Marine Ecology, Institute of Oceanology, Polish Academy of Sciences, Powstancow Warszawy 55, 81-222, Sopot, Poland
| | | | - Hallvard Strøm
- Norwegian Polar Institute (NPI), Fram Centre, 9296, Tromsø, Norway
| | - Katarzyna Błachowiak-Samołyk
- Department of Marine Ecology, Institute of Oceanology, Polish Academy of Sciences, Powstancow Warszawy 55, 81-222, Sopot, Poland
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Kalter V, Passow U. Quantitative review summarizing the effects of oil pollution on subarctic and arctic marine invertebrates. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 319:120960. [PMID: 36587783 DOI: 10.1016/j.envpol.2022.120960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Revised: 11/13/2022] [Accepted: 12/26/2022] [Indexed: 06/17/2023]
Abstract
While meta-analyses are common in the health and some biological sciences, there is a lack of such analyses for petroleum-related marine research. Oil is a highly complex substance consisting of thousands of different compounds. Measurement limitations, different protocols and a lack of standards in recording and reporting various elements of laboratory experiments impede attempts to homogenize and compare data and identify trends. Nevertheless, oil toxicology research would benefit from meta-analyses, through which we could develop meaningful research questions and design robust experiments. Here we report findings from an effort to quantitatively summarize results from oil toxicology studies on arctic and subarctic marine invertebrates. We discovered that the vast majority of studies was conducted on crustaceans, followed by molluscs. Analyzing the sensitivity of response measures across taxa we found that the most sensitive responses tend to rank low in ecological relevance, while less sensitive response measures tend to be more ecologically relevant. We further uncovered that crustaceans appear to be more sensitive to mechanically dispersed than chemically dispersed oil while the opposite seems true for molluscs, albeit not statistically significant. Both crustaceans and molluscs show a higher sensitivity to fresh than to weathered oil. No differences in the sensitivities of crustacean life stages were found. However, due to a lack of data, many questions remain unanswered. Our study revealed that while trends in responses can be elucidated, heterogeneous experimental protocols and reporting regimes prevent a proper meta-analysis.
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Affiliation(s)
- Verena Kalter
- Department of Ocean Sciences, Memorial University, St. John's, NL, A1C 5S7; Canada.
| | - Uta Passow
- Department of Ocean Sciences, Memorial University, St. John's, NL, A1C 5S7; Canada
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Dischereit A, Wangensteen OS, Præbel K, Auel H, Havermans C. Using DNA Metabarcoding to Characterize the Prey Spectrum of Two Co-Occurring Themisto Amphipods in the Rapidly Changing Atlantic-Arctic Gateway Fram Strait. Genes (Basel) 2022; 13:2035. [PMID: 36360272 PMCID: PMC9690572 DOI: 10.3390/genes13112035] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 10/28/2022] [Accepted: 10/31/2022] [Indexed: 07/30/2023] Open
Abstract
The two congeneric hyperiids Themisto libellula and T. abyssorum provide an important trophic link between lower and higher trophic levels in the rapidly changing Arctic marine ecosystem. These amphipods are characterized by distinct hydrographic affinities and are hence anticipated to be impacted differently by environmental changes, with major consequences for the Arctic food web. In this study, we applied DNA metabarcoding to the stomach contents of these Themisto species, to comprehensively reveal their prey spectra at an unprecedented-high-taxonomic-resolution and assess the regional variation in their diet across the Fram Strait. Both species feed on a wide variety of prey but their diet strongly differed in the investigated summer season, showing overlap for only a few prey taxa, such as calanoid copepods. The spatially structured prey field of T. libellula clearly differentiated it from T. abyssorum, of which the diet was mainly dominated by chaetognaths. Our approach also allowed the detection of previously overlooked prey in the diet of T. libellula, such as fish species and gelatinous zooplankton. We discuss the reasons for the differences in prey spectra and which consequences these may have in the light of ongoing environmental changes.
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Affiliation(s)
- Annkathrin Dischereit
- Helmholtz Young Investigator Group ARJEL, Functional Ecology, Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, 27570 Bremerhaven, Germany
- BreMarE—Bremen Marine Ecology, FB2, Universität Bremen, 28334 Bremen, Germany
| | - Owen S. Wangensteen
- Faculty for Biosciences, Fisheries and Economics, Norwegian College of Fishery Science, UiT the Arctic University of Norway, 9019 Tromsø, Norway
- Department of Evolutionary Biology, Ecology and Environmental Sciences and Biodiversity Research Institute (IRBIO), University of Barcelona, 08007 Barcelona, Spain
| | - Kim Præbel
- Faculty for Biosciences, Fisheries and Economics, Norwegian College of Fishery Science, UiT the Arctic University of Norway, 9019 Tromsø, Norway
| | - Holger Auel
- BreMarE—Bremen Marine Ecology, FB2, Universität Bremen, 28334 Bremen, Germany
| | - Charlotte Havermans
- Helmholtz Young Investigator Group ARJEL, Functional Ecology, Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, 27570 Bremerhaven, Germany
- BreMarE—Bremen Marine Ecology, FB2, Universität Bremen, 28334 Bremen, Germany
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