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Chen G, Xu W, Han D, Wang C, Ye S. Application of high-throughput sequencing to analyze the diet of black croaker (Atrobucca nibe) in southern coastal waters of Zhejiang. MARINE ENVIRONMENTAL RESEARCH 2023; 191:106153. [PMID: 37633172 DOI: 10.1016/j.marenvres.2023.106153] [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: 07/15/2023] [Accepted: 08/16/2023] [Indexed: 08/28/2023]
Abstract
This study investigated the feeding habits of black croaker (Atrobucca nibe) to fully understand its role in the food web in southern coastal waters of Zhejiang, China. In total, 225 black croakers were collected in a bottom trawl survey, of which 195 were used for the stomach contents analysis and 30 for high-throughput sequencing (HTS). Both approaches showed that the main prey was shrimp, with Alpheus japonicus being the most predominant. In addition, black croaker also fed on other benthic species, suggesting that it was a demersal predator. Feeding intensity also varied with black croaker body length, as did prey preference, from small-sized species to larger species with increases in fish size; in addition, prey species were more diverse in the large-bodied prey group. Canonical correspondence analysis indicated that the feeding habit of black croaker was most significantly correlated with temperature and dissolved oxygen. HTS was shown to be a feasible high precision semi-quantitative analytical approach, although it must be combined with morphological methods to obtain more complete feeding data; thus, it could provide an effective scientific basis for feeding ecology studies of marine organisms.
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Affiliation(s)
- Gan Chen
- College of Marine Science, Shanghai Ocean University, Shanghai, 201306, China; National Distant-water Fisheries Engineering Research Center, Shanghai, 201306, China; National Data Centre for Distant-Water Fisheries of China, Shanghai, 201306, China
| | - Wen Xu
- College of Marine Science, Shanghai Ocean University, Shanghai, 201306, China; National Distant-water Fisheries Engineering Research Center, Shanghai, 201306, China; National Data Centre for Distant-Water Fisheries of China, Shanghai, 201306, China
| | - Dongyan Han
- College of Marine Science, Shanghai Ocean University, Shanghai, 201306, China; National Distant-water Fisheries Engineering Research Center, Shanghai, 201306, China; National Data Centre for Distant-Water Fisheries of China, Shanghai, 201306, China.
| | - Congcong Wang
- College of Marine Science, Shanghai Ocean University, Shanghai, 201306, China; National Distant-water Fisheries Engineering Research Center, Shanghai, 201306, China; National Data Centre for Distant-Water Fisheries of China, Shanghai, 201306, China.
| | - Shen Ye
- Zhejiang Maricultural Research Institute, Wenzhou, 325005, Zhejiang, China; Zhejiang Key Laboratory of Exploitation and Preservation of Offshore Bio-resource, Wenzhou, 325005, Zhejiang, China
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Liu G, Zhang S, Zhao X, Li C, Gong M. Advances and Limitations of Next Generation Sequencing in Animal Diet Analysis. Genes (Basel) 2021; 12:genes12121854. [PMID: 34946803 PMCID: PMC8701983 DOI: 10.3390/genes12121854] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 11/17/2021] [Accepted: 11/18/2021] [Indexed: 02/07/2023] Open
Abstract
Diet analysis is a critical content of animal ecology and the diet analysis methods have been constantly improving and updating. Contrary to traditional methods of high labor intensity and low resolution, the next generation sequencing (NGS) approach has been suggested as a promising tool for dietary studies, which greatly improves the efficiency and broadens the application range. Here we present a framework of adopting NGS and DNA metabarcoding into diet analysis, and discuss the application in aspects of prey taxa composition and structure, intra-specific and inter-specific trophic links, and the effects of animal feeding on environmental changes. Yet, the generation of NGS-based diet data and subsequent analyses and interpretations are still challenging with several factors, making it possible still not as widely used as might be expected. We suggest that NGS-based diet methods must be furthered, analytical pipelines should be developed. More application perspectives, including nutrient geometry, metagenomics and nutrigenomics, need to be incorporated to encourage more ecologists to infer novel insights on they work.
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Affiliation(s)
- Gang Liu
- Key Laboratory of Wetland Ecological Function and Restoration in Beijing City, Wetland Research Institute of Chinese Academy of Forestry Sciences, Beijing 100091, China; (G.L.); (X.Z.); (C.L.)
| | - Shumiao Zhang
- Beijing Milu Ecological Research Center, Beijing 100076, China;
| | - Xinsheng Zhao
- Key Laboratory of Wetland Ecological Function and Restoration in Beijing City, Wetland Research Institute of Chinese Academy of Forestry Sciences, Beijing 100091, China; (G.L.); (X.Z.); (C.L.)
| | - Chao Li
- Key Laboratory of Wetland Ecological Function and Restoration in Beijing City, Wetland Research Institute of Chinese Academy of Forestry Sciences, Beijing 100091, China; (G.L.); (X.Z.); (C.L.)
| | - Minghao Gong
- Key Laboratory of Wetland Ecological Function and Restoration in Beijing City, Wetland Research Institute of Chinese Academy of Forestry Sciences, Beijing 100091, China; (G.L.); (X.Z.); (C.L.)
- Correspondence: ; Tel.: +86-010-62884159
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Abstract
Since their inception, DNA barcodes have become a powerful tool for understanding the biodiversity and biology of aquatic species, with multiple applications in diverse fields such as food security, fisheries, environmental DNA, conservation, and exotic species detection. Nevertheless, most aquatic ecosystems, from marine to freshwater, are understudied, with many species disappearing due to environmental stress, mostly caused by human activities. Here we highlight the progress that has been made in studying aquatic organisms with DNA barcodes, and encourage its further development in assisting sustainable use of aquatic resources and conservation.
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eDNA metabarcoding for biodiversity assessment, generalist predators as sampling assistants. Sci Rep 2021; 11:6820. [PMID: 33767219 PMCID: PMC7994446 DOI: 10.1038/s41598-021-85488-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 02/24/2021] [Indexed: 01/31/2023] Open
Abstract
With an accelerating negative impact of anthropogenic actions on natural ecosystems, non-invasive biodiversity assessments are becoming increasingly crucial. As a consequence, the interest in the application of environmental DNA (eDNA) survey techniques has increased. The use of eDNA extracted from faeces from generalist predators, have recently been described as "biodiversity capsules" and suggested as a complementary tool for improving current biodiversity assessments. In this study, using faecal samples from two generalist omnivore species, the Eurasian badger and the red fox, we evaluated the applicability of eDNA metabarcoding in determining dietary composition, compared to macroscopic diet identification techniques. Subsequently, we used the dietary information obtained to assess its contribution to biodiversity assessments. Compared to classic macroscopic techniques, we found that eDNA metabarcoding detected more taxa, at higher taxonomic resolution, and proved to be an important technique to verify the species identification of the predator from field collected faeces. Furthermore, we showed how dietary analyses complemented field observations in describing biodiversity by identifying consumed flora and fauna that went unnoticed during field observations. While diet analysis approaches could not substitute field observations entirely, we suggest that their integration with other methods might overcome intrinsic limitations of single techniques in future biodiversity surveys.
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Zhang XM, Shi ZY, Zhang SQ, Zhang P, Wilson JJ, Shih C, Li J, Li XD, Yu GY, Zhang AB. Plant-herbivorous insect networks: who is eating what revealed by long barcodes using high-throughput sequencing and Trinity assembly. INSECT SCIENCE 2021; 28:127-143. [PMID: 31880864 DOI: 10.1111/1744-7917.12749] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2019] [Revised: 12/12/2019] [Accepted: 12/15/2019] [Indexed: 06/10/2023]
Abstract
Interactions between plants and insects are among the most important life functions for all organism at a particular natural community. Usually a large number of samples are required to identify insect diets in food web studies. Previously, Sanger sequencing and next generation sequencing (NGS) with short DNA barcodes were used, resulting in low species-level identification; meanwhile the costs of Sanger sequencing are expensive for metabarcoding together with more samples. Here, we present a fast and effective sequencing strategy to identify larvae of Lepidoptera and their diets at the same time without increasing the cost on Illumina platform in a single HiSeq run, with long-multiplex-metabarcoding (COI for insects, rbcL, matK, ITS and trnL for plants) obtained by Trinity assembly (SHMMT). Meanwhile, Sanger sequencing (for single individuals) and NGS (for polyphagous) were used to verify the reliability of the SHMMT approach. Furthermore, we show that SHMMT approach is fast and reliable, with most high-quality sequences of five DNA barcodes of 63 larvae individuals (54 species) recovered (full length of 100% of the COI gene and 98.3% of plant DNA barcodes) using Trinity assembly (up-sized to 1015 bp). For larvae diets identification, 95% are reliable; the other 5% failed because their guts were empty. The diets identified by SHMMT approach are 100% consistent with the host plants that the larvae were feeding on during our collection. Our study demonstrates that SHMMT approach is reliable and cost-effective for insect-plants network studies. This will facilitate insect-host plant studies that generally contain a huge number of samples.
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Affiliation(s)
- Xiao-Man Zhang
- College of Life Sciences, Capital Normal University, Beijing, China
| | - Zhi-Yong Shi
- College of Life Sciences, Capital Normal University, Beijing, China
| | - Shao-Qian Zhang
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Peng Zhang
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - John-James Wilson
- Vertebrate Zoology at World Museum, National Museums Liverpool, Liverpool, United Kingdom
- Department of Microbiology and Parasitology, Faculty of Medical Science, Naresuan University, Phitsanulok, Thailand
| | - Chungkun Shih
- College of Life Sciences, Capital Normal University, Beijing, China
- Department of Paleobiology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Jing Li
- College of Life Sciences, Capital Normal University, Beijing, China
| | - Xue-Dong Li
- College of Life Sciences, Capital Normal University, Beijing, China
| | - Guo-Yue Yu
- Institute of Plant and Environment Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Ai-Bing Zhang
- College of Life Sciences, Capital Normal University, Beijing, China
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Metabarcoding for parallel identification of species, sex and diet of obligate scavengers: an application to globally-threatened Gyps vultures. CONSERV GENET RESOUR 2020. [DOI: 10.1007/s12686-020-01171-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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First Gut Content Analysis of 4th Instar Midge Larvae (Diptera: Chronomidae) In Large-Scale Weirs Using a DNA Meta-Barcoding Approach. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2020; 17:ijerph17082856. [PMID: 32326237 PMCID: PMC7215506 DOI: 10.3390/ijerph17082856] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 04/07/2020] [Accepted: 04/15/2020] [Indexed: 12/31/2022]
Abstract
Chironomidae larvae play an important role in the food chain of river ecosystems in Korea, where it is dominant. However, detailed information on the diet of Chironomidae larvae are still lacking. The purpose of this study was to identify the gut contents of 4th instar larvae of a Chironomidae inhabiting four large-scale weirs (Sejong Weir, Juksan Weir, Gangjeong-Goryeong Weir, and Dalseong Weir) using a DNA meta-barcoding approach. We found that dominant Operational Taxonomic Unit (OUT) was assigned to Paractinolaimus sp. (Nematoda), and the sub-dominant OTU was assigned to Dicrotendipes fumidus (Chironomidae). The most common OTUs among the individuals included phytoplankton, such as Tetrahymena sp., D. armatus, Pseudopediastrum sp., Tetradesmus dimorphus, Biddulphia tridens, and Desmodesmus spp. We calculated the selectivity index (E’) and provided scientific evidence that Chironomidae larvae have a significant preference (E’ > 0.5) for Desmodesmus armatus, E. minima, and T. dimorphus, while it does not show preference for other species found in its gut. Differences in physico-chemical factors, such as water quality, nutrients, Chl-a, and carbon concentrations, resulting from anthropogenic impacts (i.e., construction of large-scale weirs) as well as the particle size of prey organisms (small-sized single cell) and effects of chemicals (chemokinesis) could affect the feeding behavior of Chironomidae larvae.
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Hong S, Gim JS, Kim HG, Cowan PE, Joo GJ. A molecular approach to identifying the relationship between resource use and availability in Eurasian otters (Lutra lutra). CAN J ZOOL 2019. [DOI: 10.1139/cjz-2018-0289] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In South Korea, the Eurasian otter (Lutra lutra (Linnaeus, 1758)), a semi-aquatic carnivore, is found mainly in lower order streams that tend to have a low abundance of preferred prey fish species. To investigate the relationship between resource use and availability, we used DNA barcoding to identify otter diet items in 24 otter spraints (faeces) from 16 sites along the Nakdong River basin from 4 to 6 June 2014. At these sites fish availability was assessed using scoop nets and casting nets. Fish formed the bulk of otter diet, which included also frogs, mammals, and reptiles. By DNA barcoding (success rate: 72.38%), we identified 79 prey items from 105 bone remains. The diet comprised mostly fish, but frogs, mammals, and reptiles were also identified. The fish fauna and otter diet composition differed significantly. Across the study sites, members of the Cyprinidae dominated in netted samples, but occurred less frequently in otter diet. Because most Cyprinidae are fast swimmers, otters also fed on benthic fishes and frogs, suggesting limited foraging flexibility in otters and specialization on more slowly moving prey.
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Affiliation(s)
- Sungwon Hong
- Department of Biological Sciences, Pusan National University, Jangjeon-dong, Gumjeong-gu, Busan 46241, Republic of Korea
| | - Jeong-Soo Gim
- Department of Biological Sciences, Pusan National University, Jangjeon-dong, Gumjeong-gu, Busan 46241, Republic of Korea
| | - Hyo Gyeom Kim
- Department of Biological Sciences, Pusan National University, Jangjeon-dong, Gumjeong-gu, Busan 46241, Republic of Korea
| | - Phil E. Cowan
- Manaaki Whenua Landcare Research, Lincoln 7640, New Zealand
| | - Gea-Jae Joo
- Department of Biological Sciences, Pusan National University, Jangjeon-dong, Gumjeong-gu, Busan 46241, Republic of Korea
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10
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Discrimination of Spatial Distribution of Aquatic Organisms in a Coastal Ecosystem Using eDNA. APPLIED SCIENCES-BASEL 2019. [DOI: 10.3390/app9173450] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The nonlinearity and complexity of coastal ecosystems often cause difficulties when analyzing spatial and temporal patterns of ecological traits. Environmental DNA (eDNA) monitoring has provided an alternative to overcoming the aforementioned issues associated with classical monitoring. We determined aquatic community taxonomic composition using eDNA based on a meta-barcoding approach that characterizes the general ecological features in the Gwangyang Bay coastal ecosystem. We selected the V9 region of the 18S rDNA gene (18S V9), primarily because of its broad range among eukaryotes. Our results produced more detailed spatial patterns in the study area previously categorized (inner bay, main channel of the bay and outer bay) by Kim et al. (2019). Specifically, the outer bay zone was clearly identified by CCA using genus-level identification of aquatic organisms based on meta-barcoding data. We also found significant relationships between environmental factors. Therefore, eDNA monitoring based on meta-barcoding approach holds great potential as a complemental monitoring tool to identify spatial taxonomic distribution patterns in coastal areas.
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Jo H, Jeppesen E, Ventura M, Buchaca T, Gim JS, Yoon JD, Kim DH, Joo GJ. Responses of fish assemblage structure to large-scale weir construction in riverine ecosystems. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 657:1334-1342. [PMID: 30677900 DOI: 10.1016/j.scitotenv.2018.11.446] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 11/16/2018] [Accepted: 11/29/2018] [Indexed: 05/20/2023]
Abstract
Worldwide, increasing amounts of dams and weirs have been established in rivers in recent decades, often with drastic effects on their ecosystems. Between late 2009 and 2011, 16 large-scale dams were built in the main channels of the four largest rivers in South Korea, eight of these along the main channel of Nakdong River (300 km, 520 km in total). We studied the effect of these constructions on the fish community in the riparian zone based on intensive fish field surveys conducted in the littoral zone during 2007-2017, analysis of fishermen's catch data and molecular analysis of the diet of the keystone species, largemouth bass (Micropterus salmoides). Our results, based on RDA and GLM analyses, showed that environmental characteristics and fish species composition changed significantly with dam construction. Total fish abundance and biomass decreased after the start of the weir construction and fish richness decreased with time. The abundance and biomass of exotic fish decreased during construction but recovered afterwards, leading to higher proportions of exotics. Dominance and Shannon indices did not change significantly from before to after construction, while the Evenness index showed a significant decreasing trend. A comparison of the diet composition of largemouth bass showed decreasing genetic variation after construction. The changes in Functional Feeding Group (FFG) of the benthic communities at the study sites did not coincide with FFG changes in the prey items of largemouth bass, indicating a transition in feeding mode from before to after construction. In conclusion, the endemic and native fish species were most sensitive and showed lower resilience to disturbance by the large-scale dam construction than the translocated and exotic species, and the lake-like ecosystems after construction markedly improved the competitive capacity of these exotic fish over the native and endemic species in the riparian zone of the river.
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Affiliation(s)
- Hyunbin Jo
- Department of Bioscience, Aarhus University, Vejlsøvej 25, 8600 Silkeborg, Denmark; Department of Integrated Biological Science, Pusan National University, 46241 Busan, Republic of Korea
| | - Erik Jeppesen
- Department of Bioscience, Aarhus University, Vejlsøvej 25, 8600 Silkeborg, Denmark
| | - Marc Ventura
- Integrative Freshwater Ecology Group, Centre for Advanced Studies of Blanes, Spanish National Research Council (CEAB-CSIC), 17300 Blanes, Catalonia, Spain
| | - Teresa Buchaca
- Integrative Freshwater Ecology Group, Centre for Advanced Studies of Blanes, Spanish National Research Council (CEAB-CSIC), 17300 Blanes, Catalonia, Spain
| | - Jeong-Soo Gim
- Department of Integrated Biological Science, Pusan National University, 46241 Busan, Republic of Korea
| | - Ju-Duk Yoon
- Fish Restoration Team, Division of Restoration Research, Endangered Species Restoration Center, National Institute of Ecology (NIE), 36531 Yeongyang, Republic of Korea
| | - Dong-Hwan Kim
- Environmental Impact Assessment Team, National Institute of Ecology (NIE), 33657 Seocheon, Republic of Korea
| | - Gea-Jae Joo
- Department of Integrated Biological Science, Pusan National University, 46241 Busan, Republic of Korea.
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Guo Y, Zhang H, Chen W, Zhang Y. Herbivore-Diet Analysis Based on Illumina MiSeq Sequencing: The Potential Use of an ITS2-Barcoding Approach to Establish Qualitative and Quantitative Predictions of Diet Composition of Mongolian Sheep. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2018; 66:9858-9867. [PMID: 30198261 DOI: 10.1021/acs.jafc.8b02814] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
DNA-barcoding approaches to estimate the diet compositions of grazing animals have received significant attention, and particularly when combined with next-generation sequencing, these techniques have substantially improved in recent years. In this study, the identity and species composition of plant material ingested by Mongolian sheep were estimated through the use of 350 bp ITS2 gene sequences of the vegetation found in fecal samples. Four diets were formulated using varying amounts of eight plant species that are common in the grasslands of northern China. Sixteen Mongolian sheep were taken from pastures and randomly assigned to four groups, and each group received one of four diets. Each sheep was randomly assigned to one of 16 confinement pens and fed its respective diet for 12 consecutive days. Fecal samples were removed from each pen from days 7-12, preserved, and composited for each pen. All herbage species included in the daily diets were detected in each fecal sample, with the exception of Phragmites australis. Moreover, 12 additional different plant species were retrieved from feces of the experimental sheep. The obtained data provided preliminary support for the use of the ITS2 barcode to determine which plants were consumed. Moreover, the proportions of the herbage DNA sequences recovered from sheep feces and those of the herbage masses in the daily diets did not completely match. These results indicate that the non-Gramineae DNA sequences amplified with ITS2 primers (including those of Chenopodium album, Artemisia scoparia, Artemisia tanacetifolia, and Medicago sativa) far exceeded those of the Gramineae species (including Leymus chinensis and Puccinellia distans), which constitute the largest share of the experimental diets. A significant positive correlation (Spearman's ρ = 0.376, P = 0.003) between the actual herbage mass proportions in the experimental diets and the herbage-DNA-sequence proportions provided sufficiently favorable support for the further investigation of DNA barcoding for the quantification of plants in feces. A significant regression coefficient was found between the relative DNA-sequence proportions of L. chinensis ( R2 = 0.82, P < 0.0001), P. distans ( R2 = 0.64, P = 0.0017), and C. album ( R2 = 0.98, P < 0.0001) and their respective herbage mass proportions. The quantitative relationship can be expressed by the linear-regression equations y = 0.90 x - 0.22, y = 0.98 x - 0.03, and y = 5.00 x - 0.25, respectively. Thus, these results demonstrate that dietary-DNA-barcoding methods exhibited potential in providing valuable quantitative information regarding food-item components. However, it should be noted that this explorative data needs to be further improved by using additional genes and by creating a sophisticated reference database, thus enhancing both quality and accuracy of the obtained results.
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Affiliation(s)
- Yanping Guo
- Key Laboratory of Grassland Management and Utilization, Ministry of Agriculture; Department of Grassland Science, College of Animal Science and Technology , China Agricultural University , Beijing 100193 , China
| | - Hao Zhang
- College of Grassland Science , Gansu Agricultural University , Lanzhou 730070 , Gansu , China
| | - Wenqing Chen
- Department of Grassland Science, College of Animal Science and Technology , Northwest A&F University , Yangling 712100 , Shaanxi , China
| | - Yingjun Zhang
- Key Laboratory of Grassland Management and Utilization, Ministry of Agriculture; Department of Grassland Science, College of Animal Science and Technology , China Agricultural University , Beijing 100193 , China
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Zhong W, Tan Z, Wang B, Yan H. Next-generation sequencing analysis of Pardosa pseudoannulata's diet composition in different habitats. Saudi J Biol Sci 2018; 26:165-172. [PMID: 30622422 PMCID: PMC6319085 DOI: 10.1016/j.sjbs.2018.08.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Revised: 08/03/2018] [Accepted: 08/05/2018] [Indexed: 11/24/2022] Open
Abstract
Spiders are the most common and predominant predators in terrestrial ecosystems. The predatory behavior of spiders affects the energy flow across the food web within an ecosystem. Traditiaonal methods for analyzing spider diets such as field observation, anatomy and faeces analysis are not suitable for spider experiments due to spiders’ special dietary behavior. The molecular method based on the specific primers of prey DNA seems to be inefficient either in spite of its wide application in diet analysis. As the next-generation sequencing (NGS) technology becomes prevalent in many different areas, several cases of the NGS-based analysis of mammal diets have been published. This study analyzed the diet differences of Pardosa pseudoannulata (Araneae: Lycosidae) in four habitats (a wetland, a tea plantation, an alpine meadow and a paddy field) by using the NGS technology, combined with the DNA barcode method. The results suggested that the Pardosa pseudoannulata feed on a broad range of prey, and 7 orders and 24 families of insects were detected in the four investigated habitats. Moreover, it is found that the diet diversity of Pardosa pseudoannulata is greatly influenced by their living environments and seasons. In a nutshell, this study established an NGS-based methodology for spider diets analysis, and the results provided some basic materials to inform the protection and utilization of the Pardosa pseudoannulata as a potential eco-friendly predator against pests.
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Affiliation(s)
- Wentao Zhong
- College of Life Sciences, Hunan Normal University, Changsha 410081, Hunan, China
- Testing Institute of Product and Commodity Supervision, Changsha 410007, Hunan, China
| | - Zhaojun Tan
- College of Life Sciences, Hunan Normal University, Changsha 410081, Hunan, China
- Dongkou No.1 Middle School, Dongkou 422300, Hunan, China
| | - Bo Wang
- College of Life Sciences, Hunan Normal University, Changsha 410081, Hunan, China
- College of Engineering and Technology, Beijing Normal University, Zhuhai Campus, Zhuhai 519087, Guangdong, China
| | - Hengmei Yan
- College of Life Sciences, Hunan Normal University, Changsha 410081, Hunan, China
- College of Engineering and Technology, Beijing Normal University, Zhuhai Campus, Zhuhai 519087, Guangdong, China
- Corresponding author at: College of Life Sciences, Hunan Normal University, Changsha 410081, Hunan, China.
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Corse E, Meglécz E, Archambaud G, Ardisson M, Martin JF, Tougard C, Chappaz R, Dubut V. A from-benchtop-to-desktop workflow for validating HTS data and for taxonomic identification in diet metabarcoding studies. Mol Ecol Resour 2017; 17:e146-e159. [PMID: 28776936 DOI: 10.1111/1755-0998.12703] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Revised: 07/17/2017] [Accepted: 07/25/2017] [Indexed: 11/30/2022]
Abstract
The main objective of this work was to develop and validate a robust and reliable "from-benchtop-to-desktop" metabarcoding workflow to investigate the diet of invertebrate-eaters. We applied our workflow to faecal DNA samples of an invertebrate-eating fish species. A fragment of the cytochrome c oxidase I (COI) gene was amplified by combining two minibarcoding primer sets to maximize the taxonomic coverage. Amplicons were sequenced by an Illumina MiSeq platform. We developed a filtering approach based on a series of nonarbitrary thresholds established from control samples and from molecular replicates to address the elimination of cross-contamination, PCR/sequencing errors and mistagging artefacts. This resulted in a conservative and informative metabarcoding data set. We developed a taxonomic assignment procedure that combines different approaches and that allowed the identification of ~75% of invertebrate COI variants to the species level. Moreover, based on the diversity of the variants, we introduced a semiquantitative statistic in our diet study, the minimum number of individuals, which is based on the number of distinct variants in each sample. The metabarcoding approach described in this article may guide future diet studies that aim to produce robust data sets associated with a fine and accurate identification of prey items.
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Affiliation(s)
- Emmanuel Corse
- Aix Marseille Univ, Avignon Univ, CNRS, IRD, UMR IMBE, Marseille, France
| | - Emese Meglécz
- Aix Marseille Univ, Avignon Univ, CNRS, IRD, UMR IMBE, Marseille, France
| | - Gaït Archambaud
- Irstea, UR RECOVER, Equipe FRESCHCO, Aix-en-Provence, France
| | | | | | - Christelle Tougard
- CNRS, Université de Montpellier, IRD, CIRAD, EPHE, UMR ISEM, Montpellier, France
| | - Rémi Chappaz
- Aix Marseille Univ, Avignon Univ, CNRS, IRD, UMR IMBE, Marseille, France
| | - Vincent Dubut
- Aix Marseille Univ, Avignon Univ, CNRS, IRD, UMR IMBE, Marseille, France
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Guillerault N, Bouletreau S, Iribar A, Valentini A, Santoul F. Application of DNA metabarcoding on faeces to identify European catfish Silurus glanis diet. JOURNAL OF FISH BIOLOGY 2017; 90:2214-2219. [PMID: 28345142 DOI: 10.1111/jfb.13294] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 02/08/2017] [Indexed: 06/06/2023]
Abstract
In this study, the results of conventional stomach-content analysis are compared with the recent DNA metabarcoding approach on faeces to identify fish species consumed by non-native European catfish Silurus glanis in the Garonne River (south-western France), with a special emphasis on anadromous prey. Fourteen prey species were identified in the stomach contents or faeces, including four anadromous fish species. Despite higher intestine than stomach emptiness, more species were identified through faecal analysis (11 of 14) than through stomach-content analysis (five of 14) suggesting that DNA metabarcoding on faeces is an efficient, non-intrusive technique to study the diet of predatory fishes.
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Affiliation(s)
- N Guillerault
- EcoLab, Université de Toulouse, CNRS, INPT, UPS, 31062, Toulouse, France
- Station d'Ecologie Expérimental du CNRS à Moulis, Lab. USR 2936, 09 100, Moulis, France
| | - S Bouletreau
- EcoLab, Université de Toulouse, CNRS, INPT, UPS, 31062, Toulouse, France
| | - A Iribar
- CNRS, UPS, ENFA, UMR5174 EDB (Laboratoire Évolution et Diversité Biologique), 31062, Toulouse, France
| | - A Valentini
- SPYGEN, Savoie Technolac-Bât. Koala, 17, Rue du Lac Saint-André-BP 274, 73375, Le Bourget-du-Lac Cedex, France
| | - F Santoul
- EcoLab, Université de Toulouse, CNRS, INPT, UPS, 31062, Toulouse, France
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Arrigoni R, Vacherie B, Benzoni F, Stefani F, Karsenti E, Jaillon O, Not F, Nunes F, Payri C, Wincker P, Barbe V. A new sequence data set of SSU rRNA gene for Scleractinia and its phylogenetic and ecological applications. Mol Ecol Resour 2017; 17:1054-1071. [DOI: 10.1111/1755-0998.12640] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Revised: 11/01/2016] [Accepted: 11/15/2016] [Indexed: 11/29/2022]
Affiliation(s)
- Roberto Arrigoni
- Red Sea Research Center; Division of Biological and Environmental Science and Engineering; King Abdullah University of Science and Technology; Thuwal 23955-6900 Saudi Arabia
- Department of Biotechnology and Biosciences; University of Milano-Bicocca; Piazza della Scienza 2 Milan 20126 Italy
| | | | - Francesca Benzoni
- Department of Biotechnology and Biosciences; University of Milano-Bicocca; Piazza della Scienza 2 Milan 20126 Italy
- Institut de Recherche pour le Développement; UMR227 Coreus2; 101 Promenade Roger Laroque BP A5 Noumea Cedex 98848 New Caledonia
| | - Fabrizio Stefani
- Water Research Institute-National Research Council (IRSA-CNR); Via del Mulino 19 Brugherio I-20861 Italy
| | - Eric Karsenti
- Ecole Normale Supérieure; Institut de Biologie de l'ENS (IBENS), and Inserm U1024, and CNRS UMR 8197; Paris F-75005 France
- Directors’ Research; European Molecular Biology Laboratory; Meyerhofstr. 1 Heidelberg 69117 Germany
| | - Olivier Jaillon
- CEA/DSV/IG/Genoscope; Evry Cedex France
- Université d'Evry; UMR 8030; Evry CP5706 France
| | - Fabrice Not
- UPMC-CNRS; UMR 7144; Station Biologique de Roscoff; Place Georges Teissier Roscoff 29680 France
| | - Flavia Nunes
- Ifremer Centre Bretagne; DYNECO; Laboratoire d’Écologie Benthique Côtière (LEBCO); 29280 Plouzané France
| | - Claude Payri
- Institut de Recherche pour le Développement; UMR227 Coreus2; 101 Promenade Roger Laroque BP A5 Noumea Cedex 98848 New Caledonia
| | - Patrick Wincker
- CEA/DSV/IG/Genoscope; Evry Cedex France
- Université d'Evry; UMR 8030; Evry CP5706 France
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Jackson M, Wasserman R, Grey J, Ricciardi A, Dick J, Alexander M. Novel and Disrupted Trophic Links Following Invasion in Freshwater Ecosystems. ADV ECOL RES 2017. [DOI: 10.1016/bs.aecr.2016.10.006] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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18
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Abstract
AbstractFeeding ecology explains predator’s preference to some preys over others in their habitat and their competitions thereof. The subject, as a functional and applied biology, is highly neglected, and in case of fish, a uniform and consistent methodology is absent. The currently practiced methods are largely centred on mathematical indices and highly erroneous because of non-uniform outcomes. Therefore, it requires a relook into the subject to elucidate functional contributions and to make it more comparable and comprehensive science. In this article, approachable methodological strategies have been forwarded in three hierarchical steps, namely, food occurrence, feeding biology and interpretative ecology. All these steps involve wide ranges of techniques, within the scope of ecology but not limited to, and traverse from narrative to functional evolutionary ecology. The first step is an assumption-observation practice to assess food of fish, followed by feeding biology that links morphological, histological, cytological, bacteriological or enzymological correlations to preferred food in the environment. Interpretative ecology is the higher level of analysis in which the outcomes are tested and discussed against evolutionary theories. A description of possible pedagogics on the methods of feeding ecological studies has also been forwarded.
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