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Vescera C, Van Vyve C, Smits Q, Michaux JR. All-you-can-eat buffet: A spider-specialized bat species (Myotis emarginatus) turns into a pest fly eater around cattle. PLoS One 2024; 19:e0302028. [PMID: 38718094 PMCID: PMC11078406 DOI: 10.1371/journal.pone.0302028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 03/26/2024] [Indexed: 05/12/2024] Open
Abstract
Determining the dietary spectrum of European insectivorous bats over time is the cornerstone of their conservation, as it will aid our understanding of foraging behavior plasticity in response to plummeting insect populations. Despite the global decline in insects, a restricted number of arthropod pest species thrive. Yet past research has overlooked the potential of European bats to suppress pests harmful to woodlands or livestock, in spite of their economic relevance. Here we investigated the diet composition, its breeding season variations and pest consumption of an insectivorous bat species (Myotis emarginatus), at the northern edge of its range (Wallonia, Belgium). We also explored the prey ecology to gain insight into the hunting strategies and foraging habitats of this bat species. We used DNA metabarcoding to amplify two COI markers within 195 bat droppings collected in June, July and August, thereby identifying 512 prey taxa predominated by Diptera, Araneae and Lepidoptera. Overall, in 97% of the samples we detected at least one of the 58 potential pest taxa, 41 of which targeting trees. The June samples were marked by a diet rich in orb-weaver spiders, in accordance with the archetypal diet of M. emarginatus bats. However, during the highly energy demanding July-August parturition and lactation period, roughly 55% of the dropping samples contained two cattle fly pests (Stomoxys calcitrans and Musca domestica). Moreover, among the 88 Diptera species preyed upon by M. emarginatus in July and August, these flies accounted for around 50% of the taxa occurrences. This plasticity-the switch from a spider-rich to a fly-rich diet-seems providential considering the dramatic ongoing drop in insect populations but this involves ensuring bat-friendly cattle farming. Our results revealed that bats widely consume pest entomofauna, thereby highlighting their potential role as allies of forest managers and farmers.
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Affiliation(s)
- Chloé Vescera
- Conservation Genetics Laboratory, University of Liège, Liège, Belgium
| | | | - Quentin Smits
- Département de l’Etude du Milieu Naturel et Agricole (DEMNA), Service Public de Wallonie (SPW), Gembloux, Belgium
| | - Johan R. Michaux
- Conservation Genetics Laboratory, University of Liège, Liège, Belgium
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2
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Espinosa Prieto A, Hardion L, Debortoli N, Beisel JN. Finding the perfect pairs: A matchmaking of plant markers and primers for multi-marker eDNA metabarcoding. Mol Ecol Resour 2024; 24:e13937. [PMID: 38363053 DOI: 10.1111/1755-0998.13937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 12/14/2023] [Accepted: 01/09/2024] [Indexed: 02/17/2024]
Abstract
As the scope of plant eDNA metabarcoding diversifies, so do the primers, markers and methods. A wealth of primers exists today, but their comparative evaluation is lacking behind. Similarly, multi-marker approaches are recommended but debates persist regarding barcode complementarity and optimal combinations. After a literature compilation of used primers, we compared in silico 102 primer pairs based on amplicon size, coverage and specificity, followed by an experimental evaluation of 15 primer pairs on a mock community sample covering 268 plant species and genera, and about 100 families. The analysis was done for the four most common plant metabarcoding markers, rbcL, trnL, ITS1 and ITS2 and their complementarity was assessed based on retrieved species. By focusing on existing primers, we identify common designs, promote alternatives and enhance prior-supported primers for immediate applications. The ITS2 was the best-performing marker for flowering vascular plants and was congruent to ITS1. However, the combined taxonomic breadth of ITS2 and rbcL surpassed any other combination, highlighting their high complementarity across Streptophyta. Overall, our study underscores the significance of comprehensive primer and barcode evaluations tailored to metabarcoding applications.
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Affiliation(s)
- Armando Espinosa Prieto
- University of Strasbourg, CNRS, Laboratoire Image Ville Environnement, UMR 7362, Strasbourg, France
| | - Laurent Hardion
- University of Strasbourg, CNRS, Laboratoire Image Ville Environnement, UMR 7362, Strasbourg, France
| | - Nicolas Debortoli
- Namur Molecular Tech, CHU UCL Namur, Yvoir, Belgium
- E-BIOM SA, Namur, Belgium
| | - Jean-Nicolas Beisel
- University of Strasbourg, CNRS, Laboratoire Image Ville Environnement, UMR 7362, Strasbourg, France
- École Nationale du Génie de l'Eau et de l'Environnement de Strasbourg (ENGEES), Strasbourg, France
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3
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Browett SS, Synnott R, O'Meara DB, Antwis RE, Browett SS, Bown KJ, Wangensteen OS, Dawson DA, Searle JB, Yearsley JM, McDevitt AD. Resource competition drives an invasion-replacement event among shrew species on an island. J Anim Ecol 2023; 92:698-709. [PMID: 36617677 DOI: 10.1111/1365-2656.13855] [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: 08/01/2022] [Accepted: 11/17/2022] [Indexed: 01/10/2023]
Abstract
Invasive mammals are responsible for the majority of native species extinctions on islands. While most of these extinction events will be due to novel interactions between species (e.g. exotic predators and naive prey), it is more unusual to find incidences where a newly invasive species causes the decline/extinction of a native species on an island when they normally coexist elsewhere in their overlapping mainland ranges. We investigated if resource competition between two insectivorous small mammals was playing a significant role in the rapid replacement of the native pygmy shrew Sorex minutus in the presence of the recently invading greater white-toothed shrew Crocidura russula on the island of Ireland. We used DNA metabarcoding of gut contents from >300 individuals of both species to determine each species' diet and measured the body size (weight and length) during different stages of the invasion in Ireland (before, during and after the species come into contact with one another) and on a French island where both species have long coexisted (acting as a natural 'control' site). Dietary composition, niche width and overlap and body size were compared in these different stages. The body size of the invasive C. russula and composition of its diet changes between when it first invades an area and after it becomes established. During the initial stages of the invasion, individual shrews are larger and consume larger sized invertebrate prey species. During later stages of the invasion, C. russula switches to consuming smaller prey taxa that are more essential for the native species. As a result, the level of interspecific dietary overlap increases from between 11% and 14% when they first come into contact with each other to between 39% and 46% after the invasion. Here we show that an invasive species can quickly alter its dietary niche in a new environment, ultimately causing the replacement of a native species. In addition, the invasive shrew could also be potentially exhausting local resources of larger invertebrate species. These subsequent changes in terrestrial invertebrate communities could have severe impacts further downstream on ecosystem functioning and services.
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Affiliation(s)
- Samuel S Browett
- School of Science, Engineering and Environment, University of Salford, Salford, UK.,Molecular Ecology Research Group, Eco-Innovation Research Centre, School of Science and Computing, South East Technological University, Waterford, Ireland.,NERC Environmental Omics Facility, School of Biosciences, University of Sheffield, Sheffield, UK
| | - Rebecca Synnott
- Molecular Ecology Research Group, Eco-Innovation Research Centre, School of Science and Computing, South East Technological University, Waterford, Ireland
| | - Denise B O'Meara
- Molecular Ecology Research Group, Eco-Innovation Research Centre, School of Science and Computing, South East Technological University, Waterford, Ireland
| | - Rachael E Antwis
- School of Science, Engineering and Environment, University of Salford, Salford, UK
| | - Stephen S Browett
- School of Science, Engineering and Environment, University of Salford, Salford, UK
| | - Kevin J Bown
- School of Science, Engineering and Environment, University of Salford, Salford, UK
| | - Owen S Wangensteen
- Norwegian College of Fishery Science, University of Tromsø, Tromsø, Norway
| | - Deborah A Dawson
- NERC Environmental Omics Facility, School of Biosciences, University of Sheffield, Sheffield, UK
| | - Jeremy B Searle
- Department of Ecology and Evolution, Corson Hall, Cornell University, Ithaca, New York, USA
| | - Jon M Yearsley
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - Allan D McDevitt
- School of Science, Engineering and Environment, University of Salford, Salford, UK.,Department of Natural Sciences and the Environment, School of Science and Computing, Atlantic Technological University, Galway, Ireland
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4
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Dou H, Wang M, Yin X, Feng L, Yang H. Can the Eurasian otter (Lutra lutra) be used as an effective sampler of fish diversity? Using molecular assessment of otter diet to survey fish communities. METABARCODING AND METAGENOMICS 2023. [DOI: 10.3897/mbmg.7.96733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023] Open
Abstract
The Eurasian otter Lutra lutra is a generalist carnivore that is widely distributed in many aquatic ecosystems. Based on its inherent attributes of opportunistic foraging behaviour and broad dietary range, it is naturally considered a potential sampler of the diversity of aquatic vertebrates. To test the ability and efficiency of otters as a diversity sampler, we used DNA metabarcoding to investigate the composition in vertebrates of the diet of otters that inhabit a forest stream area in northeast China. Twenty vertebrate prey taxa were detected in 98 otter spraints. Otter diet mainly comprised aquatic fishes (59.4%) and amphibians (39.0%). We also used traditional approaches to investigate fish communities at 60 sampling sites in the same area to determine the relationship between fish population composition in the environment and otter diet. The comparison revealed that 28 species of fish were distributed in this area, of which five are simultaneously detected in otter spraints. This indicates that molecular analysis of the diet of otters is not an ideal approach for investigating fish diversity, at least when using the 12SV5 primer pair. Based on a review of the available molecular research on otter diet, we conclude that the low species resolution may be due to the presence of many closely-related prey species in native habitats and lack of suitable barcodes. Considering the remarkable power of diet metabarcoding analysis in capturing elusive and rare species, it represents an approach that can compensate for the defects associated with fishing methods and we suggest that it can be used as an auxiliary means of measuring traditional fish diversity.
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5
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Shelton AO, Gold ZJ, Jensen AJ, D Agnese E, Andruszkiewicz Allan E, Van Cise A, Gallego R, Ramón-Laca A, Garber-Yonts M, Parsons K, Kelly RP. Toward quantitative metabarcoding. Ecology 2023; 104:e3906. [PMID: 36320096 DOI: 10.1002/ecy.3906] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 07/07/2022] [Accepted: 08/23/2022] [Indexed: 12/24/2022]
Abstract
Amplicon-sequence data from environmental DNA (eDNA) and microbiome studies provide important information for ecology, conservation, management, and health. At present, amplicon-sequencing studies-known also as metabarcoding studies, in which the primary data consist of targeted, amplified fragments of DNA sequenced from many taxa in a mixture-struggle to link genetic observations to the underlying biology in a quantitative way, but many applications require quantitative information about the taxa or systems under scrutiny. As metabarcoding studies proliferate in ecology, it becomes more important to develop ways to make them quantitative to ensure that their conclusions are adequately supported. Here we link previously disparate sets of techniques for making such data quantitative, showing that the underlying polymerase chain reaction mechanism explains the observed patterns of amplicon data in a general way. By modeling the process through which amplicon-sequence data arise, rather than transforming the data post hoc, we show how to estimate the starting DNA proportions from a mixture of many taxa. We illustrate how to calibrate the model using mock communities and apply the approach to simulated data and a series of empirical examples. Our approach opens the door to improve the use of metabarcoding data in a wide range of applications in ecology, public health, and related fields.
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Affiliation(s)
- Andrew Olaf Shelton
- Conservation Biology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, Washington, USA
| | - Zachary J Gold
- Conservation Biology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, Washington, USA.,CICOES, University of Washington and Northwest Fisheries Science Center, National Marine Fisheries Service, Seattle, Washington, USA
| | - Alexander J Jensen
- CICOES, University of Washington and Northwest Fisheries Science Center, National Marine Fisheries Service, Seattle, Washington, USA.,School of Marine and Environmental Affairs, University of Washington, Seattle, Washington, USA
| | - Erin D Agnese
- School of Marine and Environmental Affairs, University of Washington, Seattle, Washington, USA
| | | | - Amy Van Cise
- North Gulf Oceanic Society, Visiting Scientist at Northwest Fisheries Science Center, National Oceanic and Atmospheric Administration, Seattle, Washington, USA
| | - Ramón Gallego
- School of Marine and Environmental Affairs, University of Washington, Seattle, Washington, USA.,Departamento de Biologia, Universidad Autonoma de Madrid, Unidad de Genetica, Madrid, Spain
| | - Ana Ramón-Laca
- CICOES, University of Washington and Northwest Fisheries Science Center, National Marine Fisheries Service, Seattle, Washington, USA.,School of Marine and Environmental Affairs, University of Washington, Seattle, Washington, USA
| | - Maya Garber-Yonts
- School of Marine and Environmental Affairs, University of Washington, Seattle, Washington, USA
| | - Kim Parsons
- Conservation Biology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, Washington, USA
| | - Ryan P Kelly
- School of Marine and Environmental Affairs, University of Washington, Seattle, Washington, USA
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6
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Villsen K, Corse E, Meglécz E, Archambaud‐Suard G, Vignes H, Ereskovsky AV, Chappaz R, Dubut V. DNA metabarcoding suggests adaptive seasonal variation of individual trophic traits in a critically endangered fish. Mol Ecol 2022; 31:5889-5908. [PMID: 36125278 PMCID: PMC9828795 DOI: 10.1111/mec.16698] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 09/12/2022] [Accepted: 09/15/2022] [Indexed: 01/13/2023]
Abstract
Dietary studies are critical for understanding foraging strategies and have important applications in conservation and habitat management. We applied a robust metabarcoding protocol to characterize the diet of the critically endangered freshwater fish Zingel asper (the Rhone streber). We conducted modelling and simulation analyses to identify and characterize some of the drivers of individual trophic trait variation in this species. We found that population density and ontogeny had minor effects on the trophic niche of Z. asper. Instead, our results suggest that the majority of trophic niche variation was driven by seasonal variation in ecological opportunity. The total trophic niche width of Z. asper seasonally expanded to include a broader range of prey. Furthermore, null model simulations revealed that the increase of between-individual variation in autumn indicates that Z. asper become more opportunistic relative to summer and spring, rather than being associated with a seasonal specialization of individuals. Overall, our results suggest an adaptive variation of individual trophic traits in Z. asper: the species mainly consumes a few ephemeropteran taxa (Baetis fuscatus and Ecdyonurus) but seems to be capable of adapting its foraging strategy to maintain its body condition. This study illustrates how metabarcoding data obtained from faeces can be validated and combined with individual-based modelling and simulation approaches to explore inter- and intrapopulational individual trophic traits variation and to test hypotheses in the conventional analytic framework of trophic ecology.
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Affiliation(s)
- Kurt Villsen
- Aix Marseille Université, CNRS, IRDAvignon Université, IMBEMarseilleFrance
| | - Emmanuel Corse
- Aix Marseille Université, CNRS, IRDAvignon Université, IMBEMarseilleFrance,Centre Universitaire de Formation et de Recherche de Mayotte (CUFR)DembeniFrance,MARBEC, University of Montpellier, CNRS, Ifremer, IRDMontpellierFrance
| | - Emese Meglécz
- Aix Marseille Université, CNRS, IRDAvignon Université, IMBEMarseilleFrance
| | | | - Hélène Vignes
- CIRAD, University of Montpellier, INRAE, Montpellier SupAgro, AGAPMontpellierFrance
| | - Alexander V. Ereskovsky
- Aix Marseille Université, CNRS, IRDAvignon Université, IMBEMarseilleFrance,St. Petersburg State UniversitySt. PetersburgRussia,Koltzov Institute of Developmental Biology of Russian Academy of SciencesMoscowRussia
| | - Rémi Chappaz
- INRAE, Aix Marseille Université, RECOVERAix‐en‐ProvenceFrance
| | - Vincent Dubut
- Aix Marseille Université, CNRS, IRDAvignon Université, IMBEMarseilleFrance
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7
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Cuff JP, Kitson JJN, Hemprich-Bennett D, Tercel MPTG, Browett SS, Evans DM. The predator problem and PCR primers in molecular dietary analysis: swamped or silenced; depth or breadth? Mol Ecol Resour 2022; 23:41-51. [PMID: 36017818 PMCID: PMC10087656 DOI: 10.1111/1755-0998.13705] [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: 04/28/2022] [Revised: 08/11/2022] [Accepted: 08/24/2022] [Indexed: 11/28/2022]
Abstract
Dietary metabarcoding has vastly improved our ability to analyse the diets of animals, but it is hampered by a plethora of technical limitations including potentially reduced data output due to the disproportionate amplification of the DNA of the focal predator, here termed 'the predator problem'. We review the various methods commonly used to overcome this problem, from deeper sequencing to exclusion of predator DNA during PCR, and how they may interfere with increasingly common multi-predator-taxon studies. We suggest that multi-primer approaches with an emphasis on achieving both depth and breadth of prey detections may overcome the issue to some extent, although multi-taxon studies require further consideration, as highlighted by an empirical example. We also review several alternative methods for reducing the prevalence of predator DNA that are conceptually promising but require additional empirical examination. The predator problem is a key constraint on molecular dietary analyses but, through this synthesis, we hope to guide researchers in overcoming this in an effective and pragmatic way.
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Affiliation(s)
- Jordan P Cuff
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - James J N Kitson
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, UK
| | | | - Maximillian P T G Tercel
- School of Biosciences, Cardiff University, Cardiff, UK.,Durrell Wildlife Conservation Trust, Les Augrès Manor, La Profonde Rue, Trinity, Jersey, JE3 5BP, Channel Islands
| | - Samuel S Browett
- Ecosystems and Environment Research Centre, School of Science, Engineering and Environment, University of Salford, Salford, UK
| | - Darren M Evans
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, UK
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8
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Klure DM, Greenhalgh R, Dearing MD. Addressing nontarget amplification in DNA metabarcoding studies of arthropod-feeding rodents. MAMMAL RES 2022; 67:499-509. [PMID: 36968646 PMCID: PMC10035264 DOI: 10.1007/s13364-022-00646-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Abstract
High-throughput sequencing approaches have revolutionized how we study animal diets by enabling the detection of dietary components from the metabarcoding of DNA in excrement. Mitochondrial cytochrome oxidase C subunit I (mtCOI) DNA metabarcoding is commonly used to study the diets of arthropod-feeding animals; however, this approach is susceptible to nontarget amplification of the consumer species mtCOI locus. Nontarget amplification is often an unforeseen complication that can drastically reduce the quality and utility of the results generated by high-throughput amplicon sequencing. By interrogating the diets of new world rodents in the genus Neotoma (woodrats) in both natural and captive settings, we demonstrate that nontarget amplification can drastically reduce the total read abundance of detected arthropod taxa in fecal samples and inhibit downstream analyses of dietary diversity and composition metrics. Using the results from these investigations, we offer a guide on how to identify concerns for nontarget amplification when selecting degenerate primers for DNA metabarcoding studies and recommend several approaches that can reduce or eliminate nontarget amplification. Lastly, for the community interested in investigating the diets of arthropod-feeding rodents, we generated a database containing the degree of mismatch between publicly available Rodentia mtCOI sequences and four common universal mtCOI primer sets to be used as a resource for inferring the relative risk of nontarget amplification when designing arthropod metabarcoding studies in rodent systems. This guide will be especially useful for researchers working with consumer species that have not previously been studied.
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9
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Stapleton TE, Weinstein SB, Greenhalgh R, Dearing MD. Successes and limitations of quantitative diet metabarcoding in a small, herbivorous mammal. Mol Ecol Resour 2022; 22:2573-2586. [PMID: 35579046 DOI: 10.1111/1755-0998.13643] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 05/11/2022] [Indexed: 12/01/2022]
Abstract
DNA metabarcoding is widely used to determine wild animal diets, however whether this technique provides accurate, quantitative measurements is still under debate. To test our ability to accurately estimate abundance of dietary items using metabarcoding, we fed wild caught desert woodrats (Neotoma lepida) diets comprised of constant amounts of juniper (Juniperus osteosperma, 15%) and varying amounts of creosote (Larrea tridentata, 1-60%), or cactus (Opuntia sp., 0-100%), and commercial chow (0-85%). Using metabarcoding, we compared the representation of items in the original diet samples to that in the fecal samples to test the sensitivity and accuracy of diet metabarcoding, the performance of different bioinformatic pipelines, and our ability to correct sequence counts. Metabarcoding, using standard trnL primers, detected creosote, juniper, and chow. Different pipelines for assigning taxonomy performed similarly. While creosote was detectable at dietary proportions as low as 1%, we failed to detect cactus in most samples, likely due to a primer mismatch. Creosote read counts increased as its proportion in the diet increased, and we could differentiate when creosote was a minor and major component of the diet. However, we found that estimates of juniper and creosote varied. Using previously suggested methods to correct these errors did not improve accuracy estimates of creosote, but did reduce error for juniper and chow. Our results indicate that metabarcoding can provide quantitative information on dietary composition, but may be limited. We suggest that researchers use caution in quantitatively interpreting diet metabarcoding results unless they first experimentally determine the extent of possible biases.
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10
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DNA metabarcoding dietary analyses of the wood mouse Apodemus speciosus on Innoshima Island, Japan, and implications for primer choice. MAMMAL RES 2021. [DOI: 10.1007/s13364-021-00601-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Abstract
We used DNA metabarcoding to assess the seasonal diets of the large Japanese wood mouse, Apodemus speciosus (Muridae, Rodentia), in forest edges adjacent to citrus orchards on Innoshima Island, Japan. We used one chloroplast and three mitochondrial DNA barcoding markers to determine mouse diets. Among the various plant and invertebrate diets, A. speciosus typically consumed Chinese cork oak (Quercus variabilis) in early spring (likely acorns preserved during winter) and gypsy moths (Lymantria dispar, a forest pest) in late spring and summer. In addition, we found that A. speciosus also preyed on orchard pests, including the gutta stink bug and other potentially harmful invertebrates. The season during which A. speciosus preyed on stink bugs corresponded with the harvest of orchard products. This study revealed several of the ecological roles of A. speciosus within the boundary zone between forest and human ecosystems. Furthermore, based on the performance of various mitochondrial markers in dietary profiling of invertebrate food items, we recommend the multi-locus DNA metabarcoding method to comprehensively assess the diet of A. speciosus.
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11
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Andriollo T, Michaux JR, Ruedi M. Food for everyone: Differential feeding habits of cryptic bat species inferred from DNA metabarcoding. Mol Ecol 2021; 30:4584-4600. [PMID: 34245618 PMCID: PMC8518853 DOI: 10.1111/mec.16073] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 07/07/2021] [Accepted: 07/08/2021] [Indexed: 11/29/2022]
Abstract
Ecological theory postulates that niches of co‐occurring species must differ along some ecological dimensions in order to allow their stable coexistence. Yet, many biological systems challenge this competitive exclusion principle. Insectivorous bats from the Northern Hemisphere typically form local assemblages of multiple species sharing highly similar functional traits and pertaining to identical feeding guilds. Although their trophic niche can be accessed with unprecedented details using genetic identification of prey, the underlying mechanisms of resource partitioning remain vastly unexplored. Here, we studied the differential diet of three closely‐related bat species of the genus Plecotus in sympatry and throughout their entire breeding season using DNA metabarcoding. Even at such a small geographic scale, we identified strong seasonal and spatial variation of their diet composition at both intra‐ and interspecific levels. Indeed, while the different bats fed on a distinct array of prey during spring, they showed higher trophic niche overlap during summer and fall, when all three species switched their hunting behaviour to feed on few temporarily abundant moths. By recovering 19 ecological traits for over 600 prey species, we further inferred that each bat species used different feeding grounds and hunting techniques, suggesting that niche partitioning was primarily habitat‐driven. The two most‐closely related bat species exhibited very distinct foraging habitat preferences, while the third, more distantly‐related species was more generalist. These results highlight the need of temporally comprehensive samples to fully understand species coexistence, and that valuable information can be derived from the taxonomic identity of prey obtained by metabarcoding approaches.
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Affiliation(s)
- Tommy Andriollo
- Department of Mammalogy and Ornithology, Natural History Museum of Geneva, Geneva, Switzerland.,Section of Biology, Faculty of Sciences, University of Geneva, Geneva, Switzerland
| | - Johan R Michaux
- Laboratoire de Génétique de la Conservation, Université de Liège, Institut de Botanique B22, Liège, Belgium.,CIRAD, Agirs Unit, TA C- 22/E- Campus international de Baillarguet, Montpellier Cedex 5, France
| | - Manuel Ruedi
- Department of Mammalogy and Ornithology, Natural History Museum of Geneva, Geneva, Switzerland
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12
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Browett SS, Curran TG, O’Meara DB, Harrington AP, Sales NG, Antwis RE, O’Neill D, McDevitt AD. Primer biases in the molecular assessment of diet in multiple insectivorous mammals. Mamm Biol 2021. [DOI: 10.1007/s42991-021-00115-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
AbstractOur understanding of trophic interactions of small insectivorous mammals has been drastically improved with the advent of DNA metabarcoding. The technique has continued to be optimised over the years, with primer choice repeatedly being a vital factor for dietary inferences. However, the majority of dietary studies examining the effect of primer choice often rely on in silico analyses or comparing between species that occupy an identical niche type. Here, we apply DNA metabarcoding to empirically compare the prey detection capabilities of two widely used primer sets when assessing the diets of a flying (lesser horseshoe bat; Rhinolophus hipposideros) and two ground-dwelling insectivores (greater white-toothed shrew; Crocidura russula and pygmy shrew; Sorex minutus). Although R. hipposideros primarily rely on two prey orders (Lepidoptera and Diptera), the unique taxa detected by each primer shows that a combination of primers may be the best approach to fully describe bat trophic ecology. However, random forest classifier analysis suggests that one highly degenerate primer set detected the majority of both shrews’ diet despite higher levels of host amplification. The wide range of prey consumed by ground-dwelling insectivores can therefore be accurately documented from using a single broad-range primer set, which can decrease cost and labour. The results presented here show that dietary inferences will differ depending on the primer or primer combination used for insectivores occupying different niches (i.e., hunting in the air or ground) and demonstrate the importance of performing empirical pilot studies for novel study systems.
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