1
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Thongjued K, Garcia K, Scott D, Gonthier DJ, Dupuis JR. DNA metabarcoding diet analysis in a generalist omnivore: feeding trials reveal the efficacy of extraction kits and a multi-locus approach for identifying diverse diets. Integr Zool 2024. [PMID: 38297429 DOI: 10.1111/1749-4877.12806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2024]
Abstract
Metabarcoding-based diet analysis is a valuable tool for understanding the feeding behavior of a wide range of species. However, many studies using these methods for wild animals assume accuracy and precision without experimental evaluation with known positive control food items. Here, we conducted a feeding trial experiment with a positive control community in pasture-raised chickens and assessed the efficacy of several commonly used DNA extraction kits and primer sets. We hand-fed 22 known food items, including insects and plants, to six backyard laying hens and collected their excreta for eight h. We evaluated the efficacy of three DNA extraction kits, three primer sets for plant identification (targeting rbcL, trnL, and internal transcribed spacer 2 [ITS2]), and three primer sets for arthropod identification (targeting cytochrome oxidase subunit I [COI]). The detection success rate of our positive control food items was highly variable, ranging from 2.04% to 93.88% for all kit/primer combinations and averaging 37.35% and 43.57% for the most effective kit/primer combination for plants and insects, respectively. Extraction kits using bead-based homogenization positively affected the recovery proportion of plant and insect DNA in excreta samples. The minimum time to detect known food items was 44 min post-feeding. Two COI primer sets significantly outperformed the third, and both recovery proportion and taxonomic resolution from ITS2 were significantly higher than those from rbcL and trnL. Taken together, these results display the potential variability that can be inherently present in DNA-based diet analyses and highlight the utility of experimental feeding trials in validating such approaches, particularly for omnivores with diverse diets.
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Affiliation(s)
- Kantima Thongjued
- Department of Entomology, University of Kentucky, Agricultural Science Center, Lexington, Kentucky, USA
| | - Karina Garcia
- Department of Entomology, University of Kentucky, Agricultural Science Center, Lexington, Kentucky, USA
| | - Delia Scott
- Department of Entomology, University of Kentucky, Agricultural Science Center, Lexington, Kentucky, USA
| | - David J Gonthier
- Department of Entomology, University of Kentucky, Agricultural Science Center, Lexington, Kentucky, USA
| | - Julian R Dupuis
- Department of Entomology, University of Kentucky, Agricultural Science Center, Lexington, Kentucky, USA
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2
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Edwards J, Hoffbeck C, West AG, Pas A, Taylor MW. 16S rRNA gene-based microbiota profiles from diverse avian faeces are largely independent of DNA preservation and extraction method. Front Microbiol 2023; 14:1239167. [PMID: 37675430 PMCID: PMC10477782 DOI: 10.3389/fmicb.2023.1239167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 07/24/2023] [Indexed: 09/08/2023] Open
Abstract
The avian gut microbiota has been the subject of considerable recent attention, with potential implications for diverse fields such as the poultry industry, microbial ecology, and conservation. Faecal microbiotas are frequently used as a non-invasive proxy for the gut microbiota, however the extraction of high-quality microbial DNA from avian faeces has often proven challenging. Here we aimed to evaluate the performance of two DNA preservation methods (95% ethanol and RNAlater) and five extraction approaches (IndiSpin Pathogen Kit, QIAamp PowerFecal Pro DNA Kit, MicroGEM PrepGEM Bacteria Kit, ZymoBIOMICS DNA Miniprep Kit, and an in-house phase separation-based method) for studying the avian gut microbiota. Systematic testing of the efficacy of these approaches on faecal samples from an initial three avian species (chicken, ostrich, and the flightless parrot kākāpō) revealed substantial differences in the quality, quantity and integrity of extracted DNA, but negligible influence of applied method on 16S rRNA gene-based microbiota profiles. Subsequent testing with a selected combination of preservation and extraction method on 10 further phylogenetically and ecologically diverse avian species reiterated the efficacy of the chosen approach, with bacterial community structure clustering strongly by technical replicates for a given avian species. Our finding that marked differences in extraction efficacy do not appear to influence 16S rRNA gene-based bacterial community profiles provides an important foundation for ongoing research on the avian gut microbiota.
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Affiliation(s)
- Johnson Edwards
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Carmen Hoffbeck
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Annie G. West
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - An Pas
- New Zealand Centre for Conservation Medicine, Auckland Zoo, Auckland, New Zealand
| | - Michael W. Taylor
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
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3
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Verkuil YI, Nicolaus M, Ubels R, Dietz MW, Samplonius JM, Galema A, Kiekebos K, de Knijff P, Both C. DNA metabarcoding quantifies the relative biomass of arthropod taxa in songbird diets: Validation with camera‐recorded diets. Ecol Evol 2022; 12:e8881. [PMID: 35571761 PMCID: PMC9077022 DOI: 10.1002/ece3.8881] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 04/06/2022] [Accepted: 04/15/2022] [Indexed: 11/24/2022] Open
Abstract
Ecological research is often hampered by the inability to quantify animal diets. Diet composition can be tracked through DNA metabarcoding of fecal samples, but whether (complex) diets can be quantitatively determined with metabarcoding is still debated and needs validation using free‐living animals. This study validates that DNA metabarcoding of feces can retrieve actual ingested taxa, and most importantly, that read numbers retrieved from sequencing can also be used to quantify the relative biomass of dietary taxa. Validation was done with the hole‐nesting insectivorous Pied Flycatcher whose diet was quantified using camera footage. Size‐adjusted counts of food items delivered to nestlings were used as a proxy for provided biomass of prey orders and families, and subsequently, nestling feces were assessed through DNA metabarcoding. To explore potential effects of digestion, gizzard and lower intestine samples of freshly collected birds were subjected to DNA metabarcoding. For metabarcoding with Cytochrome Oxidase subunit I (COI), we modified published invertebrate COI primers LCO1490 and HCO1777, which reduced host reads to 0.03%, and amplified Arachnida DNA without significant changing the recovery of other arthropod taxa. DNA metabarcoding retrieved all commonly camera‐recorded taxa. Overall, and in each replicate year (N = 3), the relative scaled biomass of prey taxa and COI read numbers correlated at R = .85 (95CI:0.68–0.94) at order level and at R = .75 (CI:0.67–0.82) at family level. Similarity in arthropod community composition between gizzard and intestines suggested limited digestive bias. This DNA metabarcoding validation demonstrates that quantitative analyses of arthropod diet is possible. We discuss the ecological applications for insectivorous birds.
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Affiliation(s)
- Yvonne I. Verkuil
- Conservation Ecology Group Groningen Institute for Evolutionary Life Sciences (GELIFES) University of Groningen Groningen The Netherlands
| | - Marion Nicolaus
- Conservation Ecology Group Groningen Institute for Evolutionary Life Sciences (GELIFES) University of Groningen Groningen The Netherlands
| | - Richard Ubels
- Conservation Ecology Group Groningen Institute for Evolutionary Life Sciences (GELIFES) University of Groningen Groningen The Netherlands
| | - Maurine W. Dietz
- Groningen Institute for Evolutionary Life Sciences (GELIFES) University of Groningen Groningen The Netherlands
| | - Jelmer M. Samplonius
- Groningen Institute for Evolutionary Life Sciences (GELIFES) University of Groningen Groningen The Netherlands
| | - Annabet Galema
- Conservation Ecology Group Groningen Institute for Evolutionary Life Sciences (GELIFES) University of Groningen Groningen The Netherlands
| | - Kim Kiekebos
- Conservation Ecology Group Groningen Institute for Evolutionary Life Sciences (GELIFES) University of Groningen Groningen The Netherlands
| | - Peter de Knijff
- Department of Human Genetics Leiden University Medical Centre Leiden The Netherlands
| | - Christiaan Both
- Conservation Ecology Group Groningen Institute for Evolutionary Life Sciences (GELIFES) University of Groningen Groningen The Netherlands
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4
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Olimpi EM, Garcia K, Gonthier DJ, Kremen C, Snyder WE, Wilson‐Rankin EE, Karp DS. Semi‐natural habitat surrounding farms promotes multifunctionality in avian ecosystem services. J Appl Ecol 2022. [DOI: 10.1111/1365-2664.14124] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Elissa M. Olimpi
- Department of Wildlife, Fish, and Conservation Biology University of California Davis CA USA
| | - Karina Garcia
- Department of Entomology University of Kentucky Lexington KY USA
| | | | - Claire Kremen
- Environmental Science, Policy, and Management University of California Berkeley CA USA
- Institute for Resources, Environment and Sustainability, Department of Zoology and Biodiversity Research Center University of British Columbia Vancouver BC Canada
| | | | | | - Daniel S. Karp
- Department of Wildlife, Fish, and Conservation Biology University of California Davis CA USA
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5
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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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6
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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: 2] [Impact Index Per Article: 0.7] [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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7
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Mansor MS, Rozali FZ, Davies S, Nor SM, Ramli R. High-throughput sequencing reveals dietary segregation in Malaysian babblers. Curr Zool 2021; 68:381-389. [PMID: 36090137 PMCID: PMC9450176 DOI: 10.1093/cz/zoab074] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 08/28/2021] [Indexed: 11/24/2022] Open
Abstract
The coexistence of numerous species within a community results from how those species use available resources. Babblers are one of the major groups of Malaysian insectivorous birds, which frequently forage in dense vegetation cover and have a high level of sympatry. Therefore, examining the diet, prey selection, and niche segregation of babblers can be challenging. In this study, we used high-throughput sequencing to investigate potential dietary overlap or segregation among 10 babbler species of the 4 genera of the family Pellorneidae and Timaliidae: Pellorneum, Malacopteron, Stachyris, and Cyanoderma in central peninsular Malaysia. We tested the hypothesis that trophically similar species may differ in resource use to avoid competitive exclusion. We identified 81 distinct arthropod taxa from fecal samples, belonging to 71 families representing 13 orders, which were predominantly from 16 dipteran, 13 lepidopteran, and 10 coleopteran families. Of all the prey taxa consumed, 45% were found to be distinct across the 10 babbler species, and ˂35% were shared simultaneously by ≥3 babbler species, indicating minimal dietary overlap. The black-throated babbler Stachyris nigricollis and moustached babbler Malacopteron magnirostre had the most generalist tendencies because they consumed a greater variety of prey taxa. Small dietary overlap values (Ojk) and a relatively wide range of food resources suggest that dietary segregation occurred among the studied babblers. The great diversity of prey consumed revealed the presence of dietary flexibility among the sympatric insectivorous birds, thus reducing any active dietary competition and facilitating the coexistence through niche partitioning.
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Affiliation(s)
- Mohammad Saiful Mansor
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor, Malaysia
| | | | - Sian Davies
- Micropathology Ltd, University of Warwick Science Park, Coventry, CV4 7EZ, UK
| | - Shukor Md Nor
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor, Malaysia
| | - Rosli Ramli
- Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
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8
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Tosa MI, Dziedzic EH, Appel CL, Urbina J, Massey A, Ruprecht J, Eriksson CE, Dolliver JE, Lesmeister DB, Betts MG, Peres CA, Levi T. The Rapid Rise of Next-Generation Natural History. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.698131] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Many ecologists have lamented the demise of natural history and have attributed this decline to a misguided view that natural history is outdated and unscientific. Although there is a perception that the focus in ecology and conservation have shifted away from descriptive natural history research and training toward hypothetico-deductive research, we argue that natural history has entered a new phase that we call “next-generation natural history.” This renaissance of natural history is characterized by technological and statistical advances that aid in collecting detailed observations systematically over broad spatial and temporal extents. The technological advances that have increased exponentially in the last decade include electronic sensors such as camera-traps and acoustic recorders, aircraft- and satellite-based remote sensing, animal-borne biologgers, genetics and genomics methods, and community science programs. Advances in statistics and computation have aided in analyzing a growing quantity of observations to reveal patterns in nature. These robust next-generation natural history datasets have transformed the anecdotal perception of natural history observations into systematically collected observations that collectively constitute the foundation for hypothetico-deductive research and can be leveraged and applied to conservation and management. These advances are encouraging scientists to conduct and embrace detailed descriptions of nature that remain a critically important component of the scientific endeavor. Finally, these next-generation natural history observations are engaging scientists and non-scientists alike with new documentations of the wonders of nature. Thus, we celebrate next-generation natural history for encouraging people to experience nature directly.
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9
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Génier CSV, Guglielmo CG, Mitchell GW, Falconer M, Hobson KA. Nutritional consequences of breeding away from riparian habitats in Bank Swallows: new evidence from multiple endogenous markers. CONSERVATION PHYSIOLOGY 2021; 9:coaa140. [PMID: 33532072 PMCID: PMC7836397 DOI: 10.1093/conphys/coaa140] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 12/07/2020] [Accepted: 12/28/2020] [Indexed: 06/01/2023]
Abstract
The Bank Swallow (Riparia riparia), a threatened species in Canada, breeds primarily in banks at lakeshores and rivers and in artificial (typically inland) aggregate mining pits. Inland pits may be ecological traps for this species, but relative dietary trade-offs between these two nesting habitats have not been investigated. The availability of aquatic emergent insects at lakeshores may have associated nutritional benefits for growing nestlings due to increased omega-3 fatty acids (FAs) in prey. We compared the diets of juvenile swallows from lakeshore and inland pit sites using assays of stable isotope values (δ13C, δ15N, δ2H) of feathers, faecal DNA metabarcoding and blood plasma FAs. Colony proximity to Lake Erie influenced the use of aquatic versus terrestrial insects by Bank Swallow adults and juveniles. Feather δ2H was particularly useful as a tracer of aquatic emergent versus terrestrial prey, and inland juveniles had feathers enriched in 2H, reflective of diets composed of fewer aquatic emergent insects. DNA metabarcoding of juvenile and adult faecal material indicated that lakeshore birds consumed more aquatic-emergent chironomids than inland birds. Lakeshore juveniles had elevated plasma omega-3 eicosapentaenoic acid levels compared with inland pit-breeding birds. We discuss the need to consider 'nutritional landscapes' and the importance of this concept in conservation of declining species and populations.
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Affiliation(s)
- Corrine S V Génier
- Department of Biology, University of Western Ontario, 1151 Richmond Street, London, Ontario N6A 3K7, Canada
| | - Christopher G Guglielmo
- Department of Biology, University of Western Ontario, 1151 Richmond Street, London, Ontario N6A 3K7, Canada
| | - Greg W Mitchell
- Environment and Climate Change Canada, Wildlife Research Division, 1125 Colonel By Drive, Ottawa, Ontario K1A 0H3, Canada
| | - Myles Falconer
- Birds Canada, 115 Front Rd., P.O. Box 160, Port Rowan, Ontario N0E 1M0, Canada
| | - Keith A Hobson
- Department of Biology, University of Western Ontario, 1151 Richmond Street, London, Ontario N6A 3K7, Canada
- Environment and Climate Change Canada, Wildlife Research Division, 11 Innovation Blvd., Saskatoon, Saskatchewan S7N 3H5, Canada
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10
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Gomes DGE, Hesselberg T, Barber JR. Phantom river noise alters orb‐weaving spider abundance, web size and prey capture. Funct Ecol 2020. [DOI: 10.1111/1365-2435.13739] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Dylan G. E. Gomes
- Department of Biological Sciences Boise State University Boise ID USA
| | | | - Jesse R. Barber
- Department of Biological Sciences Boise State University Boise ID USA
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11
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Bitter fruits of hard labour: diet metabarcoding and telemetry reveal that urban songbirds travel further for lower-quality food. Oecologia 2020; 193:377-388. [PMID: 32533359 PMCID: PMC7320956 DOI: 10.1007/s00442-020-04678-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 05/30/2020] [Indexed: 11/13/2022]
Abstract
Rapidly increasing urbanisation requires mitigation against associated losses of biodiversity and species abundance. In urban-breeding birds, altered food availability for nestlings is thought to reduce reproductive success compared to forest populations. To compensate for shortages of preferred foods, urban parents could increase their search effort for optimal diets or provision other foods. Here, we used telemetry and faecal metabarcoding on blue tits from one urban and one forest populations to compare parental effort and comprehensively describe nestling diet. Urban parents travelled on average 30% further than those in the forest, likely to offset limited availability of high-quality nestling food (i.e. caterpillars) in cities. Metabarcoding, based on a mean number of 30 identified taxa per faeces, revealed that the diets of urban chicks were nonetheless substantially shifted to include alternative foods. While in the forest caterpillars comprised 82 ± 11% of taxa provisioned to nestlings, in the city they constituted just 44 ± 10%. Pre-fledging chick mass as well as offspring numbers were lower in urban than in forest-reared broods. Thus, at least in our comparison of two sites, the hard labour of urban parents did not fully pay off, suggesting that improved habitat management is required to support urban-breeding birds.
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12
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Shutt JD, Nicholls JA, Trivedi UH, Burgess MD, Stone GN, Hadfield JD, Phillimore AB. Gradients in richness and turnover of a forest passerine's diet prior to breeding: A mixed model approach applied to faecal metabarcoding data. Mol Ecol 2020; 29:1199-1213. [PMID: 32100904 DOI: 10.1111/mec.15394] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 02/18/2020] [Accepted: 02/20/2020] [Indexed: 02/06/2023]
Abstract
Rather little is known about the dietary richness and variation of generalist insectivorous species, including birds, due primarily to difficulties in prey identification. Using faecal metabarcoding, we provide the most comprehensive analysis of a passerine's diet to date, identifying the relative magnitudes of biogeographic, habitat and temporal trends in the richness and turnover in diet of Cyanistes caeruleus (blue tit) along a 39 site and 2° latitudinal transect in Scotland. Faecal samples were collected in 2014-2015 from adult birds roosting in nestboxes prior to nest building. DNA was extracted from 793 samples and we amplified COI and 16S minibarcodes. We identified 432 molecular operational taxonomic units that correspond to putative dietary items. Most dietary items were rare, with Lepidoptera being the most abundant and taxon-rich prey order. Here, we present a statistical approach for estimation of gradients and intersample variation in taxonomic richness and turnover using a generalised linear mixed model. We discuss the merits of this approach over existing tools and present methods for model-based estimation of repeatability, taxon richness and Jaccard indices. We found that dietary richness increases significantly as spring advances, but changes little with elevation, latitude or local tree composition. In comparison, dietary composition exhibits significant turnover along temporal and spatial gradients and among sites. Our study shows the promise of faecal metabarcoding for inferring the macroecology of food webs, but we also highlight the challenge posed by contamination and make recommendations of laboratory and statistical practices to minimise its impact on inference.
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Affiliation(s)
- Jack D Shutt
- Institute of Evolutionary Biology, The University of Edinburgh, Edinburgh, UK
| | - James A Nicholls
- Institute of Evolutionary Biology, The University of Edinburgh, Edinburgh, UK
| | - Urmi H Trivedi
- Edinburgh Genomics, The University of Edinburgh, Edinburgh, UK
| | - Malcolm D Burgess
- Centre for Research in Animal Behaviour, University of Exeter, Exeter, UK.,RSPB Centre for Conservation Science, The Lodge, Sandy, UK
| | - Graham N Stone
- Institute of Evolutionary Biology, The University of Edinburgh, Edinburgh, UK
| | - Jarrod D Hadfield
- Institute of Evolutionary Biology, The University of Edinburgh, Edinburgh, UK
| | - Albert B Phillimore
- Institute of Evolutionary Biology, The University of Edinburgh, Edinburgh, UK
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13
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Carroll EL, Gallego R, Sewell MA, Zeldis J, Ranjard L, Ross HA, Tooman LK, O'Rorke R, Newcomb RD, Constantine R. Multi-locus DNA metabarcoding of zooplankton communities and scat reveal trophic interactions of a generalist predator. Sci Rep 2019; 9:281. [PMID: 30670720 PMCID: PMC6342929 DOI: 10.1038/s41598-018-36478-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 11/22/2018] [Indexed: 01/26/2023] Open
Abstract
To understand the ecosystem dynamics that underpin the year-round presence of a large generalist consumer, the Bryde's whale (Balaenoptera edeni brydei), we use a DNA metabarcoding approach and systematic zooplankton surveys to investigate seasonal and regional changes in zooplankton communities and if whale diet reflects such changes. Twenty-four zooplankton community samples were collected from three regions throughout the Hauraki Gulf, New Zealand, over two temperature regimes (warm and cool seasons), as well as 20 samples of opportunistically collected Bryde's whale scat. Multi-locus DNA barcode libraries were constructed from 18S and COI gene fragments, representing a trade-off between identification and resolution of metazoan taxa. Zooplankton community OTU occurrence and relative read abundance showed regional and seasonal differences based on permutational analyses of variance in both DNA barcodes, with significant changes in biodiversity indices linked to season in COI only. In contrast, we did not find evidence that Bryde's whale diet shows seasonal or regional trends, but instead indicated clear prey preferences for krill-like crustaceans, copepods, salps and ray-finned fishes independent of prey availability. The year-round presence of Bryde's whales in the Hauraki Gulf is likely associated with the patterns of distribution and abundance of these key prey items.
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Affiliation(s)
- E L Carroll
- School of Biological Sciences, University of Auckland, Auckland, New Zealand.
| | - R Gallego
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - M A Sewell
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - J Zeldis
- National Institute of Water and Atmospheric Research, Christchurch, New Zealand
| | - L Ranjard
- Research School of Biology, the Australian National University, Canberra, ACT, Australia
| | - H A Ross
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - L K Tooman
- The Institute for Plant & Food Research, Auckland, New Zealand
| | - R O'Rorke
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - R D Newcomb
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
- The Institute for Plant & Food Research, Auckland, New Zealand
| | - R Constantine
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
- Institute of Marine Science, University of Auckland, Auckland, New Zealand
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14
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Rytkönen S, Vesterinen EJ, Westerduin C, Leviäkangas T, Vatka E, Mutanen M, Välimäki P, Hukkanen M, Suokas M, Orell M. From feces to data: A metabarcoding method for analyzing consumed and available prey in a bird-insect food web. Ecol Evol 2019; 9:631-639. [PMID: 30680143 PMCID: PMC6342092 DOI: 10.1002/ece3.4787] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 10/24/2018] [Indexed: 12/24/2022] Open
Abstract
Diets play a key role in understanding trophic interactions. Knowing the actual structure of food webs contributes greatly to our understanding of biodiversity and ecosystem functioning. The research of prey preferences of different predators requires knowledge not only of the prey consumed, but also of what is available. In this study, we applied DNA metabarcoding to analyze the diet of 4 bird species (willow tits Poecile montanus, Siberian tits Poecile cinctus, great tits Parus major and blue tits Cyanistes caeruleus) by using the feces of nestlings. The availability of their assumed prey (Lepidoptera) was determined from feces of larvae (frass) collected from the main foraging habitat, birch (Betula spp.) canopy. We identified 53 prey species from the nestling feces, of which 11 (21%) were also detected from the frass samples (eight lepidopterans). Approximately 80% of identified prey species in the nestling feces represented lepidopterans, which is in line with the earlier studies on the parids' diet. A subsequent laboratory experiment showed a threshold for fecal sample size and the barcoding success, suggesting that the smallest frass samples do not contain enough larval DNA to be detected by high-throughput sequencing. To summarize, we apply metabarcoding for the first time in a combined approach to identify available prey (through frass) and consumed prey (via nestling feces), expanding the scope and precision for future dietary studies on insectivorous birds.
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Affiliation(s)
- Seppo Rytkönen
- Department of Ecology and GeneticsUniversity of OuluOuluFinland
| | - Eero J. Vesterinen
- Biodiversity UnitUniversity of TurkuTurkuFinland
- Spatial Foodweb Ecology GroupUniversity of HelsinkiHelsinkiFinland
| | - Coen Westerduin
- Department of Ecology and GeneticsUniversity of OuluOuluFinland
| | | | - Emma Vatka
- Department of Ecology and GeneticsUniversity of OuluOuluFinland
- Ecological Genetics Research UnitUniversity of HelsinkiHelsinkiFinland
| | - Marko Mutanen
- Department of Ecology and GeneticsUniversity of OuluOuluFinland
| | - Panu Välimäki
- Department of Ecology and GeneticsUniversity of OuluOuluFinland
| | - Markku Hukkanen
- Department of Ecology and GeneticsUniversity of OuluOuluFinland
| | - Marko Suokas
- Department of Ecology and GeneticsUniversity of OuluOuluFinland
| | - Markku Orell
- Department of Ecology and GeneticsUniversity of OuluOuluFinland
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15
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Alberdi A, Aizpurua O, Bohmann K, Gopalakrishnan S, Lynggaard C, Nielsen M, Gilbert MTP. Promises and pitfalls of using high‐throughput sequencing for diet analysis. Mol Ecol Resour 2018; 19:327-348. [DOI: 10.1111/1755-0998.12960] [Citation(s) in RCA: 91] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 09/19/2018] [Accepted: 10/05/2018] [Indexed: 11/28/2022]
Affiliation(s)
- Antton Alberdi
- Section for Evolutionary Genomics, Natural History Museum of Denmark University of Copenhagen Copenhagen Denmark
| | - Ostaizka Aizpurua
- Section for Evolutionary Genomics, Natural History Museum of Denmark University of Copenhagen Copenhagen Denmark
| | - Kristine Bohmann
- Section for Evolutionary Genomics, Natural History Museum of Denmark University of Copenhagen Copenhagen Denmark
- School of Biological Sciences University of East Anglia Norwich Norfolk UK
| | - Shyam Gopalakrishnan
- Section for Evolutionary Genomics, Natural History Museum of Denmark University of Copenhagen Copenhagen Denmark
| | - Christina Lynggaard
- Section for Evolutionary Genomics, Natural History Museum of Denmark University of Copenhagen Copenhagen Denmark
| | - Martin Nielsen
- Section for Evolutionary Genomics, Natural History Museum of Denmark University of Copenhagen Copenhagen Denmark
| | - Marcus Thomas Pius Gilbert
- Section for Evolutionary Genomics, Natural History Museum of Denmark University of Copenhagen Copenhagen Denmark
- NTNU University Museum Trondheim Norway
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16
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Pejchar L, Clough Y, Ekroos J, Nicholas KA, Olsson O, Ram D, Tschumi M, Smith HG. Net Effects of Birds in Agroecosystems. Bioscience 2018. [DOI: 10.1093/biosci/biy104] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Liba Pejchar
- Associate professor of conservation biology at Colorado State University, in Fort Collins
| | - Yann Clough
- Professor of environmental sciences at Lund University, in Lund, Sweden
| | - Johan Ekroos
- Research scientist at the Centre for Environmental and Climate Research, at Lund University, in Lund, Sweden
| | - Kimberly A Nicholas
- Associate professor of sustainability science at the Lund University Centre for Sustainability Studies, in Lund, Sweden
| | - Ola Olsson
- Associate professor and the head of the Biodiversity Unit, Department of Biology at Lund University
| | - Dafne Ram
- Department of Biology at Lund University
| | | | - Henrik G Smith
- Professor of animal ecology and director of the Centre for Environmental and Climate Research at Lund University
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17
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Mahajan R, Attri S, Sharma K, Singh N, Sharma D, Goel G. Statistical assessment of DNA extraction methodology for culture-independent analysis of microbial community associated with diverse environmental samples. Mol Biol Rep 2018; 45:297-308. [PMID: 29453765 DOI: 10.1007/s11033-018-4162-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 02/12/2018] [Indexed: 12/20/2022]
Abstract
Cost-effectiveness, quality, time-effectiveness and ease of the methodology are the most crucial factors in isolating quality DNA from wide variety of samples. Thus, research efforts focusing on the development of an efficient DNA extraction protocol is the need of the hour. The present study therefore, focuses on development of an efficient, rapid and free of inhibitory substances based methodology for extracting metagenomic DNA from diverse environmental samples viz. anaerobic biogas digesta, ruminant stomach, human feces, soil, and microbial starter cultures used for preparation of fermented food. PCR-DGGE based analysis and quality metagenomic library preparation, using DNA extraction methodology, validates the developed protocol. The developed protocol is cost effective, capable of isolating DNA from small sample size (100-1000 µl), time efficient (1.5-2.0 h protocol) and results in significantly higher DNA yield (4-8 times increased yield) when compared to previously available DNA extraction method and a commercial DNA extraction kit. The DNA extracted from the samples using different protocols was evaluated based on its ability to identify diverse microbial species using PCR-DGGE profiles targeting variable region within the 16S rRNA gene. The results of microbial community analysis revealed comparability of the developed protocol to commercial kits, in effectively identifying dominant representatives of the microbial community in different samples. Using the DNA extracted from the presented methodology, metagenomic libraries were prepared, which were found suitable for sequencing on Illumina platform.
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Affiliation(s)
- Rishi Mahajan
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, Solan, 173234, India
| | - Sampan Attri
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, Solan, 173234, India
| | - Kavita Sharma
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, Solan, 173234, India
| | - Niharika Singh
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, Solan, 173234, India
| | - Deepika Sharma
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, Solan, 173234, India
| | - Gunjan Goel
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, Solan, 173234, India.
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18
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Thalinger B, Oehm J, Obwexer A, Traugott M. The influence of meal size on prey DNA detectability in piscivorous birds. Mol Ecol Resour 2017; 17:e174-e186. [PMID: 28776942 PMCID: PMC5725817 DOI: 10.1111/1755-0998.12706] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 07/14/2017] [Accepted: 07/25/2017] [Indexed: 12/01/2022]
Abstract
Molecular methods allow noninvasive assessment of vertebrate predator-prey systems at high taxonomic resolution by examining dietary samples such as faeces and pellets. To facilitate the interpretation of field-derived data, feeding trials, investigating the impacts of biological, methodological and environmental factors on prey DNA detection, have been conducted. The effect of meal size, however, has not yet been explicitly considered for vertebrate consumers. Moreover, different noninvasively obtained sample types remain to be compared in such experiments. Here, we present a feeding trial on abundant piscivorous birds, Great Cormorants (Phalacrocorax carbo), to assess meal size effects on postfeeding prey DNA detection success. Faeces and pellets were sampled twice a day after the feed of large (350-540 g), medium (190-345 g) and small (15-170 g) fish meals contributing either a large (>79%) or small (<38%) share to the daily consumption. Samples were examined for prey DNA and fish hard parts. Molecular analysis of faeces revealed that both large meal size and share had a significantly positive effect on prey DNA detection rate postfeeding. Furthermore, large meals were detectable for a significantly longer time span with a detection limit at ~76 hr and a 50% detection probability at ~32 hr postfeeding. In pellets, molecular methods reliably identified the meal consumed the previous day, which was not possible via morphological analysis or when examining individual faeces. The less reliable prey DNA detection of small meals or meal shares in faeces signifies the importance of large numbers of dietary samples to obtain reliable trophic data.
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Affiliation(s)
| | - Johannes Oehm
- Institute of Ecology, University of Innsbruck, Innsbruck, Austria
| | - Armin Obwexer
- Institute of Ecology, University of Innsbruck, Innsbruck, Austria
| | - Michael Traugott
- Institute of Ecology, University of Innsbruck, Innsbruck, Austria
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19
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King RA, Symondson WOC, Thomas RJ. Molecular analysis of faecal samples from birds to identify potential crop pests and useful biocontrol agents in natural areas. BULLETIN OF ENTOMOLOGICAL RESEARCH 2015; 105:261-272. [PMID: 25572526 DOI: 10.1017/s0007485314000935] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Wild habitats adjoining farmland are potentially valuable sources of natural enemies, but also of pests. Here we tested the utility of birds as 'sampling devices', to identify the diversity of prey available to predators and particularly to screen for pests and natural enemies using natural ecosystems as refugia. Here we used PCR to amplify prey DNA from three sympatric songbirds foraging on small invertebrates in Phragmites reedbed ecosystems, namely the Reed Warbler (Acrocephalus scirpaceus), Sedge Warbler (Acrocephalus schoenobaenus) and Cetti's Warbler (Cettia cetti). A recently described general invertebrate primer pair was used for the first time to analyse diets. Amplicons were cloned and sequenced, then identified by reference to the Barcoding of Life Database and to our own sequences obtained from fresh invertebrates. Forty-five distinct prey DNA sequences were obtained from 11 faecal samples, of which 39 could be identified to species or genus. Targeting three warbler species ensured that species-specific differences in prey choice broadened the range of prey taken. Amongst the prey found in reedbeds were major pests (including the tomato moth Lacanobia oleracea) as well as many potentially valuable natural enemies including aphidophagous hoverflies and braconid wasps. Given the mobility of birds, this approach provides a practical way of sampling a whole habitat at once, providing growers with information on possible invasion by locally resident pests and the colonization potential of natural enemies from local natural habitats.
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Affiliation(s)
- R A King
- Cardiff School of Biosciences,The Sir Martin Evans Building,Cardiff University,Museum Avenue,Cardiff CF10 3AX,UK
| | - W O C Symondson
- Cardiff School of Biosciences,The Sir Martin Evans Building,Cardiff University,Museum Avenue,Cardiff CF10 3AX,UK
| | - R J Thomas
- Cardiff School of Biosciences,The Sir Martin Evans Building,Cardiff University,Museum Avenue,Cardiff CF10 3AX,UK
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20
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Karp DS, Judson S, Daily GC, Hadly EA. Molecular diagnosis of bird-mediated pest consumption in tropical farmland. SPRINGERPLUS 2014; 3:630. [PMID: 25392800 PMCID: PMC4216319 DOI: 10.1186/2193-1801-3-630] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Accepted: 10/14/2014] [Indexed: 01/07/2023]
Abstract
Biodiversity loss will likely have surprising and dramatic consequences for human wellbeing. Identifying species that benefit society represents a critical first step towards predicting the consequences of biodiversity loss. Though natural predators prevent billions of dollars in agricultural pest damage annually, characterizing which predators consume pests has proven challenging. Emerging molecular techniques may illuminate these interactions. In the countryside of Costa Rica, we identified avian predators of coffee's most damaging insect pest, the coffee berry borer beetle (Coleoptera:Scolytidae Hypothenemus hampeii), by assaying 1430 fecal samples of 108 bird species for borer DNA. While feeding trials confirmed the efficacy of our approach, detection rates were low. Nevertheless, we identified six species that consume the borer. These species had narrow diet breadths, thin bills, and short wings; traits shared with borer predators in other systems. Borer predators were not threatened; therefore, safeguarding pest control necessitates managing species beyond those at risk of regional extinction by maintaining populations in farmland habitats. Generally, our results demonstrate potential for pairing molecular methods with ecological analyses to yield novel insights into species interactions.
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Affiliation(s)
- Daniel S Karp
- Department of Biology, Stanford University, Stanford, CA 94305 USA ; Center for Conservation Biology, Stanford University, Stanford, CA 94305 USA ; Now at Department of Environmental Science, Policy, and Management, University of California Berkeley, Berkeley, CA 94720 USA
| | - Seth Judson
- Department of Biology, Stanford University, Stanford, CA 94305 USA
| | - Gretchen C Daily
- Department of Biology, Stanford University, Stanford, CA 94305 USA ; Center for Conservation Biology, Stanford University, Stanford, CA 94305 USA ; Woods Institute for the Environment, Stanford University, Stanford, CA 94305 USA
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21
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Vo ATE, Jedlicka JA. Protocols for metagenomic DNA extraction and Illumina amplicon library preparation for faecal and swab samples. Mol Ecol Resour 2014; 14:1183-97. [PMID: 24774752 DOI: 10.1111/1755-0998.12269] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Revised: 04/20/2014] [Accepted: 04/24/2014] [Indexed: 12/21/2022]
Abstract
Next-generation sequencing (NGS) technology has extraordinarily enhanced the scope of research in the life sciences. To broaden the application of NGS to systems that were previously difficult to study, we present protocols for processing faecal and swab samples into amplicon libraries amenable to Illumina sequencing. We developed and tested a novel metagenomic DNA extraction approach using solid phase reversible immobilization (SPRI) beads on Western Bluebird (Sialia mexicana) samples stored in RNAlater. Compared with the MO BIO PowerSoil Kit, the current standard for the Human and Earth Microbiome Projects, the SPRI-based method produced comparable 16S rRNA gene PCR amplification from faecal extractions but significantly greater DNA quality, quantity and PCR success for both cloacal and oral swab samples. We furthermore modified published protocols for preparing highly multiplexed Illumina libraries with minimal sample loss and without post-adapter ligation amplification. Our library preparation protocol was successfully validated on three sets of heterogeneous amplicons (16S rRNA gene amplicons from SPRI and PowerSoil extractions as well as control arthropod COI gene amplicons) that were sequenced across three independent, 250-bp, paired-end runs on Illumina's MiSeq platform. Sequence analyses revealed largely equivalent results from the SPRI and PowerSoil extractions. Our comprehensive strategies focus on maximizing efficiency and minimizing costs. In addition to increasing the feasibility of using minimally invasive sampling and NGS capabilities in avian research, our methods are notably not avian-specific and thus applicable to many research programmes that involve DNA extraction and amplicon sequencing.
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Affiliation(s)
- A-T E Vo
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA, 94720-3140, USA
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22
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Alonso H, Granadeiro JP, Waap S, Xavier J, Symondson WOC, Ramos JA, Catry P. An holistic ecological analysis of the diet of Cory's shearwaters using prey morphological characters and DNA barcoding. Mol Ecol 2014; 23:3719-33. [PMID: 24806079 DOI: 10.1111/mec.12785] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Revised: 04/29/2014] [Accepted: 04/30/2014] [Indexed: 11/29/2022]
Abstract
Knowledge of the dietary choices and trophic niches of organisms is the key to understanding their roles in ecosystems. In seabird diet studies, prey identification is a difficult challenge, often yielding results with technique-specific biases. Additionally, sampling efforts are often not extensive enough to reveal intrapopulational variation. Immature animals, which may constitute up to 50% of a population, may occupy a significantly different trophic niche to more experienced birds, but this remains largely unexplored. We investigated the diet of Cory's shearwater (Calonectris diomedea) from Selvagem Grande, an island located off the northwest African coast, collecting a total of 698 regurgitate samples over three consecutive breeding seasons. The diet was assessed using two complementary approaches for prey identification: conventional morphological analysis (using fish vertebrae, otoliths and cephalopod beaks) and DNA barcoding of the 16S rRNA mitochondrial gene, in cases where a positive identification could not be retrieved. Species assignments employed BLAST and distance-based methods, as well as direct optimization of the tree length based on unaligned sequences in POY. This method resulted in robust tree estimates and species assignments, showing its potential for DNA barcoding of stomach contents using hypervariable markers such as the 16S. The molecular approach increased taxonomic resolution and revealed an additional 17 taxa. Diet differed significantly according to breeding status, sex, breeding phase (prelaying and chick rearing) and year. Such direct evidence of trophic segregation within the same population has rarely been shown in seabirds and highlights the importance of including such variables in ecosystem-based management approaches.
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Affiliation(s)
- Hany Alonso
- Eco-Ethology Research Unit, ISPA, Rua Jardim do Tabaco 34, 1149-041, Lisboa, Portugal; Institute of Marine Research (IMAR/CMA), Department of Life Sciences, University of Coimbra, 3004-517, Coimbra, Portugal; Museu Nacional de História Natural e da Ciência, Universidade de Lisboa, Rua da Escola Politécnica 58, 1250-102, Lisboa, Portugal
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