1
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Rijal DP, Hanebrekke T, Arneberg P, Johansen T, Sint D, Traugott M, Skern‐Mauritzen M, Westgaard J. Contaminants reach everywhere: Fish dietary samples should be surface decontaminated prior to molecular diet analysis. Ecol Evol 2023; 13:e10187. [PMID: 37342457 PMCID: PMC10277604 DOI: 10.1002/ece3.10187] [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: 09/22/2022] [Revised: 05/12/2023] [Accepted: 05/16/2023] [Indexed: 06/23/2023] Open
Abstract
Knowledge of trophic interaction is necessary to understand the dynamics of ecosystems and develop ecosystem-based management. The key data to measure these interactions should come from large-scale diet analyses with good taxonomic resolution. To that end, molecular methods that analyze prey DNA from guts and feces provide high-resolution dietary taxonomic data. However, molecular diet analysis may also produce unreliable results if the samples are contaminated by external sources of DNA. Employing the freshwater European whitefish (Coregonus lavaretus) as a tracer for sample contamination, we studied the possible route of whitefish in beaked redfish (Sebastes mentella) guts sampled in the Barents Sea. We used whitefish-specific COI primers for diagnostic analysis, and fish-specific 12S and metazoa-specific COI primers for metabarcoding analyses of intestine and stomach contents of fish samples that were either not cleaned, water cleaned, or bleach cleaned after being in contact with whitefish. Both the diagnostic and COI metabarcoding revealed clear positive effects of cleaning samples as whitefish were detected in significantly higher numbers of uncleaned samples compared to water or bleach-cleaned samples. Stomachs were more susceptible to contamination than intestines and bleach cleaning reduced the frequency of whitefish contamination. Also, the metabarcoding approach detected significantly more reads of whitefish in the stomach than in intestine samples. The diagnostic analysis and COI metabarcoding detected contaminants in a higher and comparable number of gut samples than the 12S-based approach. Our study underlines thus the importance of surface decontamination of aquatic samples to obtain reliable diet information from molecular data.
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Affiliation(s)
| | | | | | | | - Daniela Sint
- Applied Animal Ecology, Department of ZoologyUniversity of InnsbruckInnsbruckAustria
| | - Michael Traugott
- Applied Animal Ecology, Department of ZoologyUniversity of InnsbruckInnsbruckAustria
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2
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Tomanović Ž, Kavallieratos NG, Ye Z, Nika EP, Petrović A, Vollhardt IMG, Vorburger C. Cereal Aphid Parasitoids in Europe (Hymenoptera: Braconidae: Aphidiinae): Taxonomy, Biodiversity, and Ecology. INSECTS 2022; 13:1142. [PMID: 36555052 PMCID: PMC9785021 DOI: 10.3390/insects13121142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 12/02/2022] [Accepted: 12/07/2022] [Indexed: 06/17/2023]
Abstract
Cereals are very common and widespread crops in Europe. Aphids are a diverse group of herbivorous pests on cereals and one of the most important limiting factors of cereal production. Here, we present an overview of knowledge about the taxonomy, biodiversity, and ecology of cereal aphid parasitoids in Europe, an important group of natural enemies contributing to cereal aphid control. We review the knowledge obtained from the integrative taxonomy of 26 cereal aphid primary parasitoid species, including two allochthonous species (Lysiphlebus testaceipes and Trioxys sunnysidensis) and two recently described species (Lipolexis labialis and Paralipsis brachycaudi). We further review 28 hyperparasitoid species belonging to three hymenopteran superfamilies and four families (Ceraphronoidea: Megaspillidae; Chalcidoidea: Pteromalidae, Encyrtidae; Cynipoidea: Figitidae). We also compile knowledge on the presence of secondary endosymbionts in cereal aphids, as these are expected to influence the community composition and biocontrol efficiency of cereal aphid parasitoids. To study aphid-parasitoid-hyperparasitoid food webs more effectively, we present two kinds of DNA-based approach: (i) diagnostic PCR (mainly multiplex PCR), and (ii) DNA sequence-based methods. Finally, we also review the effects of landscape complexity on the different trophic levels in the food webs of cereal aphids and their associated parasitoids, as well as the impacts of agricultural practices and environmental variation.
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Affiliation(s)
- Željko Tomanović
- Faculty of Biology, Institute of Zoology, University of Belgrade, 16 Studentski trg, 11000 Belgrade, Serbia
- Serbian Academy of Sciences and Arts, Knez Mihailova 35, 11000 Belgrade, Serbia
| | - Nickolas G. Kavallieratos
- Laboratory of Agricultural Zoology and Entomology, Department of Crop Science, Agricultural University of Athens, 75 Iera Odos Str., 11855 Athens, Greece
| | - Zhengpei Ye
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou 571101, China
| | - Erifili P. Nika
- Laboratory of Agricultural Zoology and Entomology, Department of Crop Science, Agricultural University of Athens, 75 Iera Odos Str., 11855 Athens, Greece
| | - Andjeljko Petrović
- Faculty of Biology, Institute of Zoology, University of Belgrade, 16 Studentski trg, 11000 Belgrade, Serbia
| | - Ines M. G. Vollhardt
- Agroecology, Department of Crop Science, Georg-August University Göttingen, Grisebachstrasse 6, 37077 Göttingen, Germany
| | - Christoph Vorburger
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, 8600 Dübendorf, Switzerland
- Institute of Integrative Biology, Department of Environmental Systems Science, ETH Zürich, 8092 Zürich, Switzerland
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3
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Potapov AM, Beaulieu F, Birkhofer K, Bluhm SL, Degtyarev MI, Devetter M, Goncharov AA, Gongalsky KB, Klarner B, Korobushkin DI, Liebke DF, Maraun M, Mc Donnell RJ, Pollierer MM, Schaefer I, Shrubovych J, Semenyuk II, Sendra A, Tuma J, Tůmová M, Vassilieva AB, Chen T, Geisen S, Schmidt O, Tiunov AV, Scheu S. Feeding habits and multifunctional classification of soil‐associated consumers from protists to vertebrates. Biol Rev Camb Philos Soc 2022; 97:1057-1117. [DOI: 10.1111/brv.12832] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 12/31/2021] [Accepted: 01/05/2022] [Indexed: 12/17/2022]
Affiliation(s)
- Anton M. Potapov
- J.F. Blumenbach Institute of Zoology and Anthropology University of Göttingen Untere Karspüle 2 37073 Göttingen Germany
- A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences Leninsky Prospect 33 119071 Moscow Russia
| | - Frédéric Beaulieu
- Canadian National Collection of Insects, Arachnids and Nematodes, Agriculture and Agri‐Food Canada Ottawa ON K1A 0C6 Canada
| | - Klaus Birkhofer
- Department of Ecology Brandenburg University of Technology Karl‐Wachsmann‐Allee 6 03046 Cottbus Germany
| | - Sarah L. Bluhm
- J.F. Blumenbach Institute of Zoology and Anthropology University of Göttingen Untere Karspüle 2 37073 Göttingen Germany
| | - Maxim I. Degtyarev
- A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences Leninsky Prospect 33 119071 Moscow Russia
| | - Miloslav Devetter
- Biology Centre of the Czech Academy of Sciences, Institute of Soil Biology Na Sádkách 702/7 37005 České Budějovice Czech Republic
| | - Anton A. Goncharov
- A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences Leninsky Prospect 33 119071 Moscow Russia
| | - Konstantin B. Gongalsky
- A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences Leninsky Prospect 33 119071 Moscow Russia
| | - Bernhard Klarner
- J.F. Blumenbach Institute of Zoology and Anthropology University of Göttingen Untere Karspüle 2 37073 Göttingen Germany
| | - Daniil I. Korobushkin
- A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences Leninsky Prospect 33 119071 Moscow Russia
| | - Dana F. Liebke
- J.F. Blumenbach Institute of Zoology and Anthropology University of Göttingen Untere Karspüle 2 37073 Göttingen Germany
| | - Mark Maraun
- J.F. Blumenbach Institute of Zoology and Anthropology University of Göttingen Untere Karspüle 2 37073 Göttingen Germany
| | - Rory J. Mc Donnell
- Department of Crop and Soil Science Oregon State University Corvallis OR 97331 U.S.A
| | - Melanie M. Pollierer
- J.F. Blumenbach Institute of Zoology and Anthropology University of Göttingen Untere Karspüle 2 37073 Göttingen Germany
| | - Ina Schaefer
- J.F. Blumenbach Institute of Zoology and Anthropology University of Göttingen Untere Karspüle 2 37073 Göttingen Germany
| | - Julia Shrubovych
- Biology Centre of the Czech Academy of Sciences, Institute of Soil Biology Na Sádkách 702/7 37005 České Budějovice Czech Republic
- Institute of Systematics and Evolution of Animals PAS Slawkowska 17 Pl 31‐016 Krakow Poland
- State Museum Natural History of NAS of Ukraine Teatralna 18 79008 Lviv Ukraine
| | - Irina I. Semenyuk
- A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences Leninsky Prospect 33 119071 Moscow Russia
- Joint Russian‐Vietnamese Tropical Center №3 Street 3 Thang 2, Q10 Ho Chi Minh City Vietnam
| | - Alberto Sendra
- Colecciones Entomológicas Torres‐Sala, Servei de Patrimoni Històric, Ajuntament de València València Spain
- Departament de Didàctica de les Cièncias Experimentals i Socials, Facultat de Magisteri Universitat de València València Spain
| | - Jiri Tuma
- Biology Centre of the Czech Academy of Sciences, Institute of Soil Biology Na Sádkách 702/7 37005 České Budějovice Czech Republic
- Biology Centre CAS, Institute of Entomology Branisovska 1160/31 370 05 Ceske Budejovice Czech Republic
| | - Michala Tůmová
- Biology Centre of the Czech Academy of Sciences, Institute of Soil Biology Na Sádkách 702/7 37005 České Budějovice Czech Republic
| | - Anna B. Vassilieva
- A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences Leninsky Prospect 33 119071 Moscow Russia
| | - Ting‐Wen Chen
- Biology Centre of the Czech Academy of Sciences, Institute of Soil Biology Na Sádkách 702/7 37005 České Budějovice Czech Republic
| | - Stefan Geisen
- Department of Nematology Wageningen University & Research 6700ES Wageningen The Netherlands
| | - Olaf Schmidt
- UCD School of Agriculture and Food Science University College Dublin Belfield Dublin 4 Ireland
| | - Alexei V. Tiunov
- A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences Leninsky Prospect 33 119071 Moscow Russia
| | - Stefan Scheu
- J.F. Blumenbach Institute of Zoology and Anthropology University of Göttingen Untere Karspüle 2 37073 Göttingen Germany
- Centre of Biodiversity and Sustainable Land Use Büsgenweg 1 37077 Göttingen Germany
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Kim YK, Yum KS. Effects of red ginseng extract on gut microbial distribution. J Ginseng Res 2022; 46:91-103. [PMID: 35035242 PMCID: PMC8753433 DOI: 10.1016/j.jgr.2021.04.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Revised: 03/10/2021] [Accepted: 04/16/2021] [Indexed: 12/20/2022] Open
Abstract
Background Red ginseng extract boosts immunity against inflammation and cancer in the human body. However, studies on the effects of red ginseng extract on the gut microbiome remain unexplored. Methods In 2019, the positive effects and changes in the gut microbiome after administering 1 pack (3 g) of red ginseng extract per day to 53 adults aged 40 to 75 for 24 weeks were investigated. The gut microbial environment changes were qualitatively and quantitatively analyzed using next-generation sequencing and real-time polymerase chain reaction technology. Results On comparing and analyzing alpha diversity and beta diversity, the microbial pattern showed significant differences (OTUs p = 0.003, chao1 p < 0.001, Bray-Curtis p = 0.001) before and after ingestion of red ginseng extract, indicating that gut microbial richness increased after ingestion. Moreover, after comparing and analyzing the gut microbiome's differences after red ginseng extract intake, significant differences were noted between three strains at the phylum level and among 57 strains at the genus level. Conclusion This study proposes the potential use of red ginseng extract as a prebiotic after confirming its positive effects, including increasing gut microbiome richness, reducing harm to the gut microbiome, and increasing the number of some strains in the gut microbiome.
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Affiliation(s)
| | - Keun-Sang Yum
- Corresponding author. Department of Family Medicine, The Catholic University of Korea, Uijeongbu St. Mary's Hospital, Seoul, 11765, Republic of Korea.
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5
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Di Bernardi C, Wikenros C, Hedmark E, Boitani L, Ciucci P, Sand H, Åkesson M. Multiple species-specific molecular markers using nanofluidic array as a tool to detect prey DNA from carnivore scats. Ecol Evol 2021; 11:11739-11748. [PMID: 34522337 PMCID: PMC8427573 DOI: 10.1002/ece3.7918] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 06/29/2021] [Accepted: 07/02/2021] [Indexed: 01/07/2023] Open
Abstract
Large carnivore feeding ecology plays a crucial role for management and conservation for predators and their prey. One of the keys to this kind of research is to identify the species composition in the predator diet, for example, prey determination from scat content. DNA-based methods applied to detect prey in predators' scats are viable alternatives to traditional macroscopic approaches, showing an increased reliability and higher prey detection rate. Here, we developed a molecular method for prey species identification in wolf (Canis lupus) scats using multiple species-specific marker loci on the cytochrome b gene for 18 target species. The final panel consisted of 80 assays, with a minimum of four markers per target species, and that amplified specifically when using a high-throughput Nanofluidic array technology (Fluidigm Inc.). As a practical example, we applied the method to identify target prey species DNA in 80 wolf scats collected in Sweden. Depending on the number of amplifying markers required to obtain a positive species call in a scat, the success in determining at least one prey species from the scats ranged from 44% to 92%. Although we highlight the need to evaluate the optimal number of markers for sensitive target species detection, the developed method is a fast and cost-efficient tool for prey identification in wolf scats and it also has the potential to be further developed and applied to other areas and large carnivores as well.
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Affiliation(s)
- Cecilia Di Bernardi
- Department of Biology and Biotechnologies "Charles Darwin" University of Rome La Sapienza Rome Italy
- Grimsö Wildlife Research Station Department of Ecology Swedish University of Agricultural Sciences Riddarhyttan Sweden
| | - Camilla Wikenros
- Grimsö Wildlife Research Station Department of Ecology Swedish University of Agricultural Sciences Riddarhyttan Sweden
| | - Eva Hedmark
- Grimsö Wildlife Research Station Department of Ecology Swedish University of Agricultural Sciences Riddarhyttan Sweden
| | - Luigi Boitani
- Department of Biology and Biotechnologies "Charles Darwin" University of Rome La Sapienza Rome Italy
| | - Paolo Ciucci
- Department of Biology and Biotechnologies "Charles Darwin" University of Rome La Sapienza Rome Italy
| | - Håkan Sand
- Grimsö Wildlife Research Station Department of Ecology Swedish University of Agricultural Sciences Riddarhyttan Sweden
| | - Mikael Åkesson
- Grimsö Wildlife Research Station Department of Ecology Swedish University of Agricultural Sciences Riddarhyttan Sweden
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6
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Thalinger B, Pütz Y, Traugott M. Endpoint PCR coupled with capillary electrophoresis (celPCR) provides sensitive and quantitative measures of environmental DNA in singleplex and multiplex reactions. PLoS One 2021; 16:e0254356. [PMID: 34297715 PMCID: PMC8301609 DOI: 10.1371/journal.pone.0254356] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Accepted: 06/24/2021] [Indexed: 11/18/2022] Open
Abstract
The use of sensitive methods is key for the detection of target taxa from trace amounts of environmental DNA (eDNA) in a sample. In this context, digital PCR (dPCR) enables direct quantification and is commonly perceived as more sensitive than endpoint PCR. However, endpoint PCR coupled with capillary electrophoresis (celPCR) potentially embodies a viable alternative as it quantitatively measures signal strength after PCR in Relative Fluorescence Units (RFU). Provided comparable levels of sensitivity are reached, celPCR permits the development of cost-efficient multiplex reactions, enabling the simultaneous detection of several target taxa. Here, we compared the sensitivity of singleplex and multiplex celPCR to dPCR for species-specific primer pairs amplifying mitochondrial DNA (COI) of fish species occurring in European freshwaters by analyzing dilution series of tissue extracts as well as field-collected water samples. Both singleplex and multiplex celPCR and dPCR displayed comparable sensitivity with reliable positive amplifications starting at two to 10 target DNA copies per μl extract. celPCR was suitable for quantifying target DNA and direct inference of copy numbers from RFU was possible after accounting for primer effects in linear mixed-effects models and calibration via dPCR. Furthermore, multiplex celPCR and dPCR were successfully used for the detection and quantification of fish-eDNA in field-collected water samples, confirming the results of the dilution series experiment and exemplifying the high sensitivity of the two approaches. The possibility of detection and quantification via multiplex celPCR is appealing for the cost-efficient screening of high sample numbers. The present results confirm the sensitivity of this approach thus enabling its application for future eDNA-based monitoring efforts.
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Affiliation(s)
- Bettina Thalinger
- Department of Zoology, University of Innsbruck, Innsbruck, Austria
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
- Department of Integrative Biology, College of Biological Science, University of Guelph, Guelph, Ontario, Canada
| | - Yannick Pütz
- Department of Zoology, University of Innsbruck, Innsbruck, Austria
| | - Michael Traugott
- Department of Zoology, University of Innsbruck, Innsbruck, Austria
- Sinsoma GmbH, Lannes 6, Völs, Austria
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7
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Gajski D, Pekár S. Assessment of the biocontrol potential of natural enemies against psyllid populations in a pear tree orchard during spring. PEST MANAGEMENT SCIENCE 2021; 77:2358-2366. [PMID: 33415804 DOI: 10.1002/ps.6262] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 12/23/2020] [Accepted: 01/07/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND Modern pest control management systems are based on the support of naturally occurring arthropod predators, as it has been shown that such predators offer an important ecosystem service. However, most naturally occurring arthropod predators are generalists (euryphagous). Their role in the biological control of specific pests has been recognized but remains poorly studied. Here, we focused on the naturally occurring arthropod predators of psyllids - the main insect pest of pear trees. We investigated the abundance of psyllids and all of their potential enemies in an abandoned pear orchard on a weekly basis from early spring to early summer. In addition, employing polymerase chain reaction diagnostics and specific primers, we investigated the predation rate on psyllids in all predators collected. RESULTS We found four predatory groups: spiders were the most abundant (60%, N = 756), followed by coccinellid beetles, anthocorid bugs and cantharid beetles. Anthocorids and spiders had the highest predation rates among the predatory groups. Among spiders, >50% of foliage-dwelling spiders (belonging to the genera Philodromus and Clubiona; N = 206) were positive for psyllids and showed a numerical response to the abundance of psyllids. CONCLUSION We conclude that foliage-dwelling spiders are, of the four groups, the most important natural enemies of psyllids on pear trees during spring in Central Europe, as they outnumber specialized Anthocoris bugs. © 2021 Society of Chemical Industry.
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Affiliation(s)
- Domagoj Gajski
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Stano Pekár
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic
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8
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Traugott M, Thalinger B, Wallinger C, Sint D. Fish as predators and prey: DNA-based assessment of their role in food webs. JOURNAL OF FISH BIOLOGY 2021; 98:367-382. [PMID: 32441321 PMCID: PMC7891366 DOI: 10.1111/jfb.14400] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 03/26/2020] [Accepted: 05/20/2020] [Indexed: 05/04/2023]
Abstract
Fish are both consumers and prey, and as such part of a dynamic trophic network. Measuring how they are trophically linked, both directly and indirectly, to other species is vital to comprehend the mechanisms driving alterations in fish communities in space and time. Moreover, this knowledge also helps to understand how fish communities respond to environmental change and delivers important information for implementing management of fish stocks. DNA-based methods have significantly widened our ability to assess trophic interactions in both marine and freshwater systems and they possess a range of advantages over other approaches in diet analysis. In this review we provide an overview of different DNA-based methods that have been used to assess trophic interactions of fish as consumers and prey. We consider the practicalities and limitations, and emphasize critical aspects when analysing molecular derived trophic data. We exemplify how molecular techniques have been employed to unravel food web interactions involving fish as consumers and prey. In addition to the exciting opportunities DNA-based approaches offer, we identify current challenges and future prospects for assessing fish food webs where DNA-based approaches will play an important role.
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Affiliation(s)
- Michael Traugott
- Applied Animal Ecology, Department of ZoologyUniversity of InnsbruckInnsbruckAustria
| | - Bettina Thalinger
- Applied Animal Ecology, Department of ZoologyUniversity of InnsbruckInnsbruckAustria
- Centre for Biodiversity Genomics, University of GuelphGuelphCanada
| | - Corinna Wallinger
- Institute of Interdisciplinary Mountain Research, Austrian Academy of ScienceInnsbruckAustria
| | - Daniela Sint
- Applied Animal Ecology, Department of ZoologyUniversity of InnsbruckInnsbruckAustria
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9
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Krey KL, Cooper WR, Renkema JM. Revealing the Diet of Generalist Insect Predators in Strawberry Fields: Not Only Pests, But Other Predators Beware. ENVIRONMENTAL ENTOMOLOGY 2020; 49:1300-1306. [PMID: 33135057 DOI: 10.1093/ee/nvaa125] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Indexed: 06/11/2023]
Abstract
Generalist invertebrate predators contribute to pest management in agriculture, providing an important ecosystem service, particularly in organically managed fields. DNA-based methods to study food webs and feeding interactions in unrestricted field conditions have transformed dietary analysis of generalist predators. In this study, we used MiSeq next-generation sequencing (NGS) technology and universal arthropod primers to investigate the diet of several generalist insect predators collected in commercial organic Florida strawberry fields from November 2017 to March 2018. Of 12 predator insect taxa, Geocoris spp. (Say) (Hemiptera: Geocoridae) was the most abundant early in the growing season (November) and was collected consistently until the end of the season (early March). DNA sequences from 105 predator samples were matched to 44 arthropod families, and of these, 17 were categorized as pest families, 10 as nonpest or nonpredator families, and 17 as predator families. Drosophilidae was the most detected pest family, and Dolichopodidae was the most detected predator family. Prey diversity differed among the predators. Chrysoperla spp. (Neuroptera: Chrysopidae) consumed more prey earlier in the season than did other predators, whereas the other predators consumed a greater diversity of other predators regardless of month. Our results showed a high amount of intraguild predation, but also that predators are contributing to pest suppression in organic strawberries and providing an important biological control service in Florida organic strawberries.
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Affiliation(s)
- K L Krey
- Gulf Coast Research and Education Center, University of Florida, Wimauma, FL
- USDA-ARS - Temperate Tree Fruit and Vegetable Research, Wapato, WA
- New address: USDA-ARS - Temperate Tree Fruit and Vegetable Research, Wapato, WA
| | - W R Cooper
- USDA-ARS - Temperate Tree Fruit and Vegetable Research, Wapato, WA
| | - J M Renkema
- Gulf Coast Research and Education Center, University of Florida, Wimauma, FL
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10
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Wang Z, Li M, Ju W, Ye W, Xue L, Boufford DE, Gao X, Yue B, Liu Y, Pierce NE. The entomophagous caterpillar fungus Ophiocordyceps sinensis is consumed by its lepidopteran host as a plant endophyte. FUNGAL ECOL 2020. [DOI: 10.1016/j.funeco.2020.100989] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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11
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Balsamo M, Artois T, Smith JPS, Todaro MA, Guidi L, Leander BS, Van Steenkiste NWL. The curious and neglected soft-bodied meiofauna: Rouphozoa (Gastrotricha and Platyhelminthes). HYDROBIOLOGIA 2020; 847:2613-2644. [PMID: 33551466 PMCID: PMC7864459 DOI: 10.1007/s10750-020-04287-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 04/25/2020] [Accepted: 05/04/2020] [Indexed: 06/11/2023]
Abstract
Gastrotricha and Platyhelminthes form a clade called Rouphozoa. Representatives of both taxa are main components of meiofaunal communities, but their role in the trophic ecology of marine and freshwater communities is not sufficiently studied. Traditional collection methods for meiofauna are optimized for Ecdysozoa, and include the use of fixatives or flotation techniques that are unsuitable for the preservation and identification of soft-bodied meiofauna. As a result, rouphozoans are usually underestimated in conventional biodiversity surveys and ecological studies. Here, we give an updated outline of their diversity and taxonomy, with some phylogenetic considerations. We describe successfully tested techniques for their recovery and study, and emphasize current knowledge on the ecology, distribution and dispersal of freshwater gastrotrichs and microturbellarians. We also discuss the opportunities and pitfalls of (meta)barcoding studies as a means of overcoming the taxonomic impediment. Finally, we discuss the importance of rouphozoans in aquatic ecosystems and provide future research directions to fill in crucial gaps in the biology of these organisms needed for understanding their basic role in the ecology of benthos and their place in the trophic networks linking micro-, meio- and macrofauna of freshwater ecosystems.
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Affiliation(s)
- Maria Balsamo
- Department of Biomolecular Sciences, University of Urbino, Urbino, Italy
| | - Tom Artois
- Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
| | | | - M Antonio Todaro
- Department of Life Sciences, University of Modena-Reggio Emilia, Modena, Italy
| | - Loretta Guidi
- Department of Biomolecular Sciences, University of Urbino, Urbino, Italy
| | - Brian S Leander
- Departments of Botany and Zoology, University of British Columbia, Vancouver, BC, Canada
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12
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Fegley SR, Smith JPS, Johnson D, Schirmer A, Jones-Boggs J, Edmonds A, Bursey J. Nourished, Exposed Beaches Exhibit Altered Sediment Structure and Meiofaunal Communities. DIVERSITY-BASEL 2020; 12. [PMID: 34168518 PMCID: PMC8221582 DOI: 10.3390/d12060245] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
To retain recreational uses and shoreline protection, a large proportion of ocean beaches have been, and continue to be, nourished. Adding sand from subtidal and terrestrial sources to nourish beaches rarely re-creates the original sediment structure of the beach. Numerous studies have demonstrated that meiofaunal communities are altered by changes in sediment composition in low-energy substrates, therefore, we have explored whether beach nourishment has affected exposed, ocean beach meiofaunal communities. Since the early 2000s, we have conducted a series of sampling and experimental studies on meiofauna and sediments on nourished beaches in coastal North Carolina USA that had been sampled previously in the early 1970s, prior to any beach nourishment. Most of our studies consider meiofauna at the level of major taxa only. However, a few studies examine free-living flatworm (turbellarian) species in detail because of the existence of historical studies examining this group. Comparison of contemporary results to historical data and of heavily nourished versus lightly nourished beaches reveals extensive changes to beach sediment structure and meiofaunal community composition, indicating that the beaches are a more heterogeneous habitat than in the past. The effects of these substantial physical and biological changes to the production of beach ecosystem services are unlikely to be inconsequential.
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Affiliation(s)
- Stephen R. Fegley
- Institute of Marine Sciences, University of North Carolina at Chapel Hill, Morehead City, NC 28557, USA
| | - Julian P. S. Smith
- Department of Biology, Winthrop University, Rock Hill, SC 29733, USA
- Correspondence:
| | - Douglas Johnson
- Department of Biology, Winthrop University, Rock Hill, SC 29733, USA
| | - Amelia Schirmer
- Institute of Marine Sciences, University of North Carolina at Chapel Hill, Morehead City, NC 28557, USA
| | | | - Austin Edmonds
- Department of Biology, Barton College, Wilson, NC 27893, USA
| | - Joseph Bursey
- Department of Biology, Winthrop University, Rock Hill, SC 29733, USA
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Assessment of seasonal variation of diet composition in rodents using DNA barcoding and Real-Time PCR. Sci Rep 2019; 9:14124. [PMID: 31575934 PMCID: PMC6773709 DOI: 10.1038/s41598-019-50676-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 09/10/2019] [Indexed: 02/08/2023] Open
Abstract
The study of animal diet and feeding behaviour is a fundamental tool for the illustration of the ecological role of species in the ecosystem. However, size and quality of food intake samples make it hard for researchers to describe the diet composition of many small species. In our study, we exploited genomic tools for the analysis of the diet composition of the Savi’s pine vole (Microtus savii) using DNA barcoding and qPCR techniques for the identification of ingested plant species retrieved from stomach contents. In contrast with previous studies, we found that, despite being a fossorial species, the Savi’s pine vole is a selective feeder that undergoes intense superficial activity in search for food. In addition, our study shows that with a a priori knowledge of the candidate plant species included in animal diet, qPCR is a powerful tool to assess presence/absence, frequency of occurrence and electivity of ingested species. We conclude that this approach offers new opportunities to implement the analysis of food selection in small animals, thereby revealing a detailed picture of plant-animal interactions.
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14
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Combining stable isotope analysis with DNA metabarcoding improves inferences of trophic ecology. PLoS One 2019; 14:e0219070. [PMID: 31329604 PMCID: PMC6645532 DOI: 10.1371/journal.pone.0219070] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Accepted: 06/14/2019] [Indexed: 12/31/2022] Open
Abstract
Knowing what animals eat is fundamental to our ability to understand and manage biodiversity and ecosystems, but researchers often must rely on indirect methods to infer trophic position and food intake. Using an approach that combines evidence from stable isotope analysis and DNA metabarcoding, we assessed the diet and trophic position of Anthene usamba butterflies, for which there are no known direct observations of larval feeding. An earlier study that analyzed adults rather than caterpillars of A. usamba inferred that this butterfly was aphytophagous, but we found that the larval guts of A. usamba and two known herbivorous lycaenid species contain chloroplast 16S sequences. Moreover, chloroplast barcoding revealed high sequence similarity between chloroplasts found in A. usamba guts and the chloroplasts of the Vachellia drepanolobium trees on which the caterpillars live. Stable isotope analysis provided further evidence that A. usamba caterpillars feed on V. drepanolobium, and the possibilities of strict herbivory versus limited omnivory in this species are discussed. These results highlight the importance of combining multiple approaches and considering ontogeny when using stable isotopes to infer trophic ecology where direct observations are difficult or impossible.
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15
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Rennstam Rubbmark O, Sint D, Cupic S, Traugott M. When to use next generation sequencing or diagnostic PCR in diet analyses. Mol Ecol Resour 2019; 19:388-399. [PMID: 30506979 PMCID: PMC6446722 DOI: 10.1111/1755-0998.12974] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Revised: 10/06/2018] [Accepted: 10/17/2018] [Indexed: 11/29/2022]
Abstract
Next‐generation sequencing (NGS) is increasingly used for diet analyses; however, it may not always describe diet samples well. A reason for this is that diet samples contain mixtures of food DNA in different amounts as well as consumer DNA which can reduce the food DNA characterized. Because of this, detections will depend on the relative amount and identity of each type of DNA. For such samples, diagnostic PCR will most likely give more reliable results, as detection probability is only marginally dependent on other copresent DNA. We investigated the reliability of each method to test (a) whether predatory beetle regurgitates, supposed to be low in consumer DNA, allow to retrieve prey sequences using general barcoding primers that co‐amplify the consumer DNA, and (b) to assess the sequencing depth or replication needed for NGS and diagnostic PCR to give stable results. When consumer DNA is co‐amplified, NGS is better suited to discover the range of possible prey, than for comparing co‐occurrences of diet species between samples, as retested samples were repeatedly different in prey detections with this approach. This shows that samples were incompletely described, as prey detected by diagnostic PCR frequently were missed by NGS. As the sequencing depth needed to reliably describe the diet in such samples becomes very high, the cost‐efficiency and reliability of diagnostic PCR make diagnostic PCR better suited for testing large sample‐sets. Especially if the targeted prey taxa are thought to be of ecological importance, as diagnostic PCR gave more nested and consistent results in repeated testing of the same sample.
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Affiliation(s)
- Oskar Rennstam Rubbmark
- Mountain Agriculture Research Unit, Institute of Ecology, University of Innsbruck, Innsbruck, Austria
| | - Daniela Sint
- Mountain Agriculture Research Unit, Institute of Ecology, University of Innsbruck, Innsbruck, Austria
| | - Sandra Cupic
- Mountain Agriculture Research Unit, Institute of Ecology, University of Innsbruck, Innsbruck, Austria
| | - Michael Traugott
- Mountain Agriculture Research Unit, Institute of Ecology, University of Innsbruck, Innsbruck, Austria
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