1
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Andriienko V, Buczek M, Meier R, Srivathsan A, Łukasik P, Kolasa MR. Implementing high-throughput insect barcoding in microbiome studies: impact of non-destructive DNA extraction on microbiome reconstruction. PeerJ 2024; 12:e18025. [PMID: 39329134 PMCID: PMC11426317 DOI: 10.7717/peerj.18025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2024] [Accepted: 08/10/2024] [Indexed: 09/28/2024] Open
Abstract
Background Symbiotic relationships with diverse microorganisms are crucial for many aspects of insect biology. However, while our understanding of insect taxonomic diversity and the distribution of insect species in natural communities is limited, we know much less about their microbiota. In the era of rapid biodiversity declines, as researchers increasingly turn towards DNA-based monitoring, developing and broadly implementing approaches for high-throughput and cost-effective characterization of both insect and insect-associated microbial diversity is essential. We need to verify whether approaches such as high-throughput barcoding, a powerful tool for identifying wild insects, would permit subsequent microbiota reconstruction in these specimens. Methods High-throughput barcoding ("megabarcoding") methods often rely on non-destructive approaches for obtaining template DNA for PCR amplification by leaching DNA out of insect specimens using alkaline buffers such as HotSHOT. This study investigated the impact of HotSHOT on microbial abundance estimates and the reconstructed bacterial community profiles. We addressed this question by comparing quantitative 16S rRNA amplicon sequencing data for HotSHOT-treated or untreated specimens of 16 insect species representing six orders and selected based on the expectation of limited variation among individuals. Results We find that in 13 species, the treatment significantly reduced microbial abundance estimates, corresponding to an estimated 15-fold decrease in amplifiable 16S rRNA template on average. On the other hand, HotSHOT pre-treatment had a limited effect on microbial community composition. The reconstructed presence of abundant bacteria with known significant effects was not affected. On the other hand, we observed changes in the presence of low-abundance microbes, those close to the reliable detection threshold. Alpha and beta diversity analyses showed compositional differences in only a few species. Conclusion Our results indicate that HotSHOT pre-treated specimens remain suitable for microbial community composition reconstruction, even if abundance may be hard to estimate. These results indicate that we can cost-effectively combine barcoding with the study of microbiota across wild insect communities. Thus, the voucher specimens obtained using megabarcoding studies targeted at characterizing insect communities can be used for microbiome characterizations. This can substantially aid in speeding up the accumulation of knowledge on the microbiomes of abundant and hyperdiverse insect species.
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Affiliation(s)
- Veronika Andriienko
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Krakow, Poland
- Doctoral School of Exact and Natural Sciences, Jagiellonian University, Krakow, Poland
- Institute of Zoology and Biomedical Sciences, Faculty of Biology, Jagiellonian University, Krakow, Poland
| | - Mateusz Buczek
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Krakow, Poland
| | - Rudolf Meier
- Museum für Naturkunde, Leibniz-Institut für Evolutions- und Biodiversitätsforschung, Berlin, Germany
| | - Amrita Srivathsan
- Museum für Naturkunde, Leibniz-Institut für Evolutions- und Biodiversitätsforschung, Berlin, Germany
| | - Piotr Łukasik
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Krakow, Poland
| | - Michał R. Kolasa
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Krakow, Poland
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2
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Leino LI, Vesterinen EJ, Sánchez-Virosta P, Puigbò P, Eeva T, Rainio MJ. Pollution-related changes in nest microbiota: Implications for growth and fledging in three passerine birds. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 357:124434. [PMID: 38936789 DOI: 10.1016/j.envpol.2024.124434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Revised: 06/12/2024] [Accepted: 06/23/2024] [Indexed: 06/29/2024]
Abstract
Non-ferrous smelters emit toxic metals into the environment, posing a threat to wildlife health. Despite the acknowledged role of microbes in host health, the impact of such emissions on host-associated microbiota, especially in wild birds, remains largely unexplored. This study investigates the associations of metal pollution, fitness, and nest microbiota (serving as a proxy for early-life microbial environment) which may influence the nestling health and development. Our study focuses on three passerine birds, the great tit (Parus major), blue tit (Cyanistes caeruleus), and pied flycatcher (Ficedula hypoleuca), within control and metal-polluted sites around a Finnish copper-nickel smelter. The polluted sites had been contaminated with arsenic (As), cadmium (Cd), copper (Cu), nickel (Ni), and zinc (Zn). We performed bacterial 16S rRNA sequencing and metal analyses on 90 nests and monitored nestling body mass, fledging success, and various biotic and abiotic factors. Our findings revealed species-specific responses to metal exposure in terms of both fitness and nest microbiota. P. major and C. caeruleus showed sensitivity to pollution, with decreased nestling growth and fledging in the polluted zone. This was accompanied by a shift in the bacterial community composition, which was characterized by an increase in some pathogenic bacteria (in P. major and C. caeruleus nests) and by a decrease in plant-associated bacteria (within C. caeruleus nests). Conversely, F. hypoleuca and their nest microbiota showed limited responses to pollution, indicating greater tolerance to pollution-induced environmental changes. Although pollution did not correlate with nest alpha diversity or the most abundant bacterial taxa across all species, certain potential pathogens within the nests were enriched in polluted environments and negatively correlated with nestling fitness parameters. Our results suggest that metal pollution may alter the nest bacterial composition in some bird species, either directly or indirectly through environmental changes, promoting pathogenic bacteria and potentially impacting bird survival.
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Affiliation(s)
- Lyydia I Leino
- Department of Biology, University of Turku, Henrikinkatu 2, 20014, Turku, Finland.
| | - Eero J Vesterinen
- Department of Biology, University of Turku, Henrikinkatu 2, 20014, Turku, Finland.
| | - Pablo Sánchez-Virosta
- Department of Biology, Norwegian University of Science and Technology, NO-7491, Trondheim, Norway.
| | - Pere Puigbò
- Department of Biology, University of Turku, Henrikinkatu 2, 20014, Turku, Finland; Eurecat, Technology Centre of Catalonia, Reus, Catalonia, Spain; Department of Biochemistry and Biotechnology, Rovira I Virgili University, Tarragona, Catalonia, Spain.
| | - Tapio Eeva
- Department of Biology, University of Turku, Henrikinkatu 2, 20014, Turku, Finland.
| | - Miia J Rainio
- Department of Biology, University of Turku, Henrikinkatu 2, 20014, Turku, Finland.
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3
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Takada K, Nakagawa S, Kryukov K, Ozawa M, Watanabe T. Metagenomic analysis of the gut microbiota of hooded cranes (Grus monacha) on the Izumi plain in Japan. FEBS Open Bio 2024. [PMID: 39275913 DOI: 10.1002/2211-5463.13881] [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] [Received: 04/25/2024] [Revised: 07/29/2024] [Accepted: 08/05/2024] [Indexed: 09/16/2024] Open
Abstract
Recent advances in DNA sequencing technology have dramatically improved our understanding of the gut microbiota of various animal species. However, research on the gut microbiota of birds lags behind that of many other vertebrates, and information about the gut microbiota of wild birds such as migratory waterfowl is particularly lacking. Because the ecology of migratory waterfowl (e.g., lifestyle, diet, physiological characteristics) differs from that of other birds, the gut microbiota of migratory waterfowl likely also differs, but much is still unknown. The hooded crane (Grus monacha) is an important representative migratory waterbird species and is listed as endangered on the International Union for Conservation of Nature and Natural Resources Red List of Threatened Species. In this study, we analyzed the bacterial and viral microbiota in the gut of hooded cranes by using deep sequencing data from fecal samples of hooded cranes that winter on the Izumi plain in Japan, and found that Cetobacterium, Clupeiformes, and Pbunavirus were clearly present in the fecal samples of hooded cranes. These findings advance our understanding of the ecology of hooded cranes.
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Affiliation(s)
- Kosuke Takada
- Department of Molecular Virology, Research Institute for Microbial Diseases, Osaka University, Japan
- Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Japan
| | - So Nakagawa
- Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Japan
- Division of Omics Sciences, Institute of Medical Sciences, Tokai University, Isehara, Japan
- Division of Interdisciplinary Merging of Health Research, Micro/Nano Technology Center, Tokai University, Isehara, Japan
| | - Kirill Kryukov
- Bioinformation and DDBJ Center, National Institute of Genetics, Shizuoka, Japan
- Center for Genome Informatics, Joint Support-Center for Data Science Research, Research Organization of Information and Systems, Shizuoka, Japan
| | - Makoto Ozawa
- Joint Faculty of Veterinary Medicine, Kagoshima University, Japan
- Joint Graduate School of Veterinary Medicine, Kagoshima University, Japan
- Kagoshima Crane Conservation Committee, Izumi, Japan
| | - Tokiko Watanabe
- Department of Molecular Virology, Research Institute for Microbial Diseases, Osaka University, Japan
- Center for Infectious Disease Education and Research, Osaka University, Japan
- Center for Advanced Modalities and DDS, Osaka University, Japan
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4
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Andriienko V, Buczek M, Meier R, Srivathsan A, Łukasik P, Kolasa MR. Implementing high-throughput insect barcoding in microbiome studies: impact of non-destructive DNA extraction on microbiome reconstruction. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.30.591865. [PMID: 38746196 PMCID: PMC11092579 DOI: 10.1101/2024.04.30.591865] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Background Symbiotic relationships with diverse microorganisms are crucial for many aspects of insect biology. However, while our understanding of insect taxonomic diversity and the distribution of insect species in natural communities is limited, we know much less about their microbiota. In the era of rapid biodiversity declines, as researchers increasingly turn towards DNA-based monitoring, developing and broadly implementing approaches for high-throughput and cost-effective characterization of both insect and insect-associated microbial diversity is essential. We need to verify whether approaches such as high-throughput barcoding, a powerful tool for identifying wild insects, would permit subsequent microbiota reconstruction in these specimens. Methods High-throughput barcoding ("megabarcoding") methods often rely on non-destructive approaches for obtaining template DNA for PCR amplification by leaching DNA out of insect specimens using alkaline buffers such as HotSHOT. This study investigated the impact of HotSHOT on microbial abundance estimates and the reconstructed bacterial community profiles. We addressed this question by comparing quantitative 16S rRNA amplicon sequencing data for HotSHOT-treated or untreated specimens of 16 insect species representing six orders and selected based on the expectation of limited variation among individuals. Results We find that in 13 species, the treatment significantly reduced microbial abundance estimates, corresponding to an estimated 15-fold decrease in amplifiable 16S rRNA template on average. On the other hand, HotSHOT pre-treatment had a limited effect on microbial community composition. The reconstructed presence of abundant bacteria with known significant effects was not affected. On the other hand, we observed changes in the presence of low-abundance microbes, those close to the reliable detection threshold. Alpha and beta diversity analyses showed compositional differences in only a few species. Conclusion Our results indicate that HotSHOT pre-treated specimens remain suitable for microbial community composition reconstruction, even if abundance may be hard to estimate. These results indicate that we can cost-effectively combine barcoding with the study of microbiota across wild insect communities. Thus, the voucher specimens obtained using megabarcoding studies targeted at characterizing insect communities can be used for microbiome characterizations. This can substantially aid in speeding up the accumulation of knowledge on the microbiomes of abundant and hyperdiverse insect species.
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Affiliation(s)
- Veronika Andriienko
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Kraków, Poland
- Institute of Zoology and Biomedical Sciences, Faculty of Biology, Jagiellonian University, Kraków, Poland
- Doctoral School of Exact and Natural Sciences, Jagiellonian University, Kraków, Poland
| | - Mateusz Buczek
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Kraków, Poland
| | | | | | - Piotr Łukasik
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Kraków, Poland
| | - Michał R Kolasa
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Kraków, Poland
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5
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Morrill A, Forbes MR, Vesterinen EJ, Tamminen M, Sääksjärvi IE, Kaunisto KM. Molecular Characterisation of Faecal Bacterial Assemblages Among Four Species of Syntopic Odonates. MICROBIAL ECOLOGY 2023; 87:16. [PMID: 38108886 PMCID: PMC10728244 DOI: 10.1007/s00248-023-02328-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 12/04/2023] [Indexed: 12/19/2023]
Abstract
Factors such as host species, phylogeny, diet, and both timing and location of sampling are thought to influence the composition of gut-associated bacteria in insects. In this study, we compared the faecal-associated bacterial taxa for three Coenagrion and one Enallagma damselfly species. We expected high overlap in representation of bacterial taxa due to the shared ecology and diet of these species. Using metabarcoding based on the 16S rRNA gene, we identified 1513 sequence variants, representing distinct bacterial 'taxa'. Intriguingly, the damselfly species showed somewhat different magnitudes of richness of ZOTUs, ranging from 480 to 914 ZOTUs. In total, 921 (or 60.8% of the 1513) distinct ZOTUs were non-shared, each found only in one species, and then most often in only a single individual. There was a surfeit of these non-shared incidental ZOTUs in the Enallagma species accounting for it showing the highest bacterial richness and accounting for a sample-wide pattern of more single-species ZOTUs than expected, based on comparisons to the null model. Future studies should address the extent to which faecal bacteria represent non-incidental gut bacteria and whether abundant and shared taxa are true gut symbionts. Pictures of odonates adopted from Norske Art databank under Creative Commons License (CC BY 4.0).
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Affiliation(s)
- A Morrill
- Department of Biology, Carleton University, Ottawa, Ontario, Canada
| | - M R Forbes
- Department of Biology, Carleton University, Ottawa, Ontario, Canada
| | - E J Vesterinen
- Department of Biology, University of Turku, Turku, Finland
| | - M Tamminen
- Department of Biology, University of Turku, Turku, Finland
| | | | - K M Kaunisto
- Biodiversity Unit, University of Turku, Turku, Finland.
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6
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Dürrbaum E, Fornoff F, Scherber C, Vesterinen EJ, Eitzinger B. Metabarcoding of trap nests reveals differential impact of urbanization on cavity-nesting bee and wasp communities. Mol Ecol 2023; 32:6449-6460. [PMID: 36479967 DOI: 10.1111/mec.16818] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 11/08/2022] [Accepted: 11/28/2022] [Indexed: 12/13/2022]
Abstract
Urbanization is affecting arthropod communities worldwide, for example by changing the availability of food resources. However, the strength and direction of a community's response is species-specific and depends on species' trophic level. Here, we investigated interacting species at different trophic levels in nests of cavity-nesting bees and wasps along two urbanization gradients in four German cities using trap nests. We analysed bee and wasp diversity and their trophic interaction partners by metabarcoding the DNA of bee pollen and preyed arthropods found in wasp nests. We found that the pollen richness increased with increasing distance from city centres and at sites characterized by a high percentage of impervious and developed surface, while the richness of pollinators was unaffected by urbanization. In contrast, species richness of wasps, but not their arthropod prey, was highest at sites with low levels of urbanization. However, the community structure of wasp prey changed with urbanization at both local and regional scales. Throughout the study area, the community of wasps consisted of specialists, while bee species were generalists. Our results suggest that Hymenoptera and their food resources are negatively affected by increasing urbanization. However, to understand distribution patterns of both, wasps and bees in urban settings other factors besides food availability should be considered.
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Affiliation(s)
- Ellen Dürrbaum
- Institute of Landscape Ecology, University of Münster, Münster, Germany
| | - Felix Fornoff
- Chair of Nature Conservation and Landscape Ecology, University of Freiburg, Freiburg im Breisgau, Germany
| | - Christoph Scherber
- Institute of Landscape Ecology, University of Münster, Münster, Germany
- Centre for Biodiversity Monitoring and Conservation Science, Leibniz Institute for the Analysis of Biodiversity Change, Bonn, Germany
| | - Eero J Vesterinen
- Biodiversity Unit, University of Turku, Turku, Finland
- Department of Biology, University of Turku, Turku, Finland
| | - Bernhard Eitzinger
- Chair of Nature Conservation and Landscape Ecology, University of Freiburg, Freiburg im Breisgau, Germany
- iES Landau, Institute for Environmental Sciences, University of Koblenz-Landau, Landau, Germany
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7
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Tuneu-Corral C, Puig-Montserrat X, Riba-Bertolín D, Russo D, Rebelo H, Cabeza M, López-Baucells A. Pest suppression by bats and management strategies to favour it: a global review. Biol Rev Camb Philos Soc 2023; 98:1564-1582. [PMID: 37157976 DOI: 10.1111/brv.12967] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 04/13/2023] [Accepted: 04/17/2023] [Indexed: 05/10/2023]
Abstract
Fighting insect pests is a major challenge for agriculture worldwide, and biological control and integrated pest management constitute well-recognised, cost-effective ways to prevent and overcome this problem. Bats are important arthropod predators globally and, in recent decades, an increasing number of studies have focused on the role of bats as natural enemies of agricultural pests. This review assesses the state of knowledge of the ecosystem services provided by bats as pest consumers at a global level and provides recommendations that may favour the efficiency of pest predation by bats. Through a systematic review, we assess evidence for predation, the top-down effect of bats on crops and the economic value of ecosystem services these mammals provide, describing the different methodological approaches used in a total of 66 reviewed articles and 18 agroecosystem types. We also provide a list of detailed conservation measures and management recommendations found in the scientific literature that may favour the delivery of this important ecosystem service, including actions aimed at restoring bat populations in agroecosystems. The most frequent recommendations include increasing habitat heterogeneity, providing additional roosts, and implementing laws to protect bats and reduce agrochemical use. However, very little evidence is available on the direct consequences of these practices on bat insectivory in farmland. Additionally, through a second in-depth systematic review of scientific articles focused on bat diet and, as part of the ongoing European Cost Action project CA18107, we provide a complete list of 2308 documented interactions between bat species and their respective insect pest prey. These pertain to 81 bat species belonging to 36 different genera preying upon 760 insect pests from 14 orders in agroecosystems and other habitats such as forest or urban areas. The data set is publicly available and updatable.
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Affiliation(s)
- Carme Tuneu-Corral
- BiBio, Biodiversity and Bioindicators Research Group, Natural Sciences Museum of Granollers, Av. Francesc Macià 51, Granollers, Catalonia, 08402, Spain
- CIBIO-InBIO, Centro de Investigaçaõ em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, 4485-661, Portugal
- Global Change and Conservation Lab, Organismal and Evolutionary Biology Research Program, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Xavier Puig-Montserrat
- BiBio, Biodiversity and Bioindicators Research Group, Natural Sciences Museum of Granollers, Av. Francesc Macià 51, Granollers, Catalonia, 08402, Spain
| | - Daniel Riba-Bertolín
- BiBio, Biodiversity and Bioindicators Research Group, Natural Sciences Museum of Granollers, Av. Francesc Macià 51, Granollers, Catalonia, 08402, Spain
| | - Danilo Russo
- Laboratory of Animal Ecology and Evolution (AnEcoEvo), Dipartimento di Agraria, Università degli Studi di Napoli Federico II, via Università, 100, Portici, Naples, 80055, Italy
| | - Hugo Rebelo
- CIBIO-InBIO, Centro de Investigaçaõ em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, 4485-661, Portugal
| | - Mar Cabeza
- Global Change and Conservation Lab, Organismal and Evolutionary Biology Research Program, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Adrià López-Baucells
- BiBio, Biodiversity and Bioindicators Research Group, Natural Sciences Museum of Granollers, Av. Francesc Macià 51, Granollers, Catalonia, 08402, Spain
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8
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Westerduin C, Suokas M, Petäjä T, Saarela U, Vainio S, Mutanen M. Exploring and validating observations of non-local species in eDNA samples. Ecol Evol 2023; 13:e10612. [PMID: 37841221 PMCID: PMC10576249 DOI: 10.1002/ece3.10612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 09/26/2023] [Accepted: 10/04/2023] [Indexed: 10/17/2023] Open
Abstract
The development of DNA-based methods in recent decades has opened the door to numerous new lines of research in the biological sciences. While the speed and accuracy of DNA methodologies are clearly beneficial, the sensitivity of these methods has the adverse effect of increased susceptibility to false positives resulting from contamination in field or lab. Here, we present findings from a metabarcoding study on the diet of and food availability for five insectivorous birds, in which multiple lepidopteran species not known to occur locally were discovered. After describing the pattern of occurrences of these non-local species in the samples, we discuss various potential origins of these sequences. First, we assessed that the taxonomic assignments appeared reliable, and local occurrences of many of the species could be plausibly ruled out. Then, we looked into the possibilities of natural environmental contamination, judging it to be unlikely, albeit impossible to fully falsify. Finally, while dissimilar combinations of non-local species' occurrences across the samples did not initially suggest lab contamination, we found overlap with taxa and sequences handled in the same lab, which was undoubtedly not coincidental. Even so, not all exact sequences were accounted for in these locally conducted studies, nor was it clear if these and other sequences could remain detectable years later. Although the full explanation for the observations of non-local species remains inconclusive, these findings highlight the importance of critical examination of metabarcoding results, and showcase how species-level taxonomic assignments utilizing comprehensive reference libraries may be a tool in detecting potential contamination events, and false positives in general.
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Affiliation(s)
- Coen Westerduin
- Ecology and Genetics Research Unit, Faculty of ScienceUniversity of OuluOuluFinland
| | - Marko Suokas
- Ecology and Genetics Research Unit, Faculty of ScienceUniversity of OuluOuluFinland
| | - Tuukka Petäjä
- Department of Physics, Institute for Atmospheric and Earth System Research (INAR)University of HelsinkiHelsinkiFinland
| | - Ulla Saarela
- CRC, The Faculty of MedicineUniversity of OuluOuluFinland
- Laboratory of Developmental Biology, Faculty of Biochemistry and Molecular MedicineUniversity of OuluOuluFinland
| | - Seppo Vainio
- Laboratory of Developmental Biology, Faculty of Biochemistry and Molecular MedicineUniversity of OuluOuluFinland
| | - Marko Mutanen
- Ecology and Genetics Research Unit, Faculty of ScienceUniversity of OuluOuluFinland
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9
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Iwaszkiewicz-Eggebrecht E, Łukasik P, Buczek M, Deng J, Hartop EA, Havnås H, Prus-Frankowska M, Ugarph CR, Viteri P, Andersson AF, Roslin T, Tack AJM, Ronquist F, Miraldo A. FAVIS: Fast and versatile protocol for non-destructive metabarcoding of bulk insect samples. PLoS One 2023; 18:e0286272. [PMID: 37467453 DOI: 10.1371/journal.pone.0286272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 05/11/2023] [Indexed: 07/21/2023] Open
Abstract
Insects are diverse and sustain essential ecosystem functions, yet remain understudied. Recent reports about declines in insect abundance and diversity have highlighted a pressing need for comprehensive large-scale monitoring. Metabarcoding (high-throughput bulk sequencing of marker gene amplicons) offers a cost-effective and relatively fast method for characterizing insect community samples. However, the methodology applied varies greatly among studies, thus complicating the design of large-scale and repeatable monitoring schemes. Here we describe a non-destructive metabarcoding protocol that is optimized for high-throughput processing of Malaise trap samples and other bulk insect samples. The protocol details the process from obtaining bulk samples up to submitting libraries for sequencing. It is divided into four sections: 1) Laboratory workspace preparation; 2) Sample processing-decanting ethanol, measuring the wet-weight biomass and the concentration of the preservative ethanol, performing non-destructive lysis and preserving the insect material for future work; 3) DNA extraction and purification; and 4) Library preparation and sequencing. The protocol relies on readily available reagents and materials. For steps that require expensive infrastructure, such as the DNA purification robots, we suggest alternative low-cost solutions. The use of this protocol yields a comprehensive assessment of the number of species present in a given sample, their relative read abundances and the overall insect biomass. To date, we have successfully applied the protocol to more than 7000 Malaise trap samples obtained from Sweden and Madagascar. We demonstrate the data yield from the protocol using a small subset of these samples.
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Affiliation(s)
| | - Piotr Łukasik
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Kraków, Poland
| | - Mateusz Buczek
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Kraków, Poland
| | - Junchen Deng
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Kraków, Poland
- Doctoral School of Exact and Natural Sciences, Jagiellonian University, Kraków, Poland
| | - Emily A Hartop
- Station Linné, Färjestaden, Sweden
- Center for Integrative Biodiversity Discovery, Museum für Naturkunde-Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
| | | | - Monika Prus-Frankowska
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Kraków, Poland
| | | | - Paulina Viteri
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Anders F Andersson
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Tomas Roslin
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Ayco J M Tack
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
| | - Fredrik Ronquist
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Andreia Miraldo
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
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10
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Stenhouse EH, Bellamy P, Kirby W, Vaughan IP, Symondson WOC, Orozco-terWengel P. Herbivorous dietary selection shown by hawfinch ( Coccothraustes coccothraustes) within mixed woodland habitats. ROYAL SOCIETY OPEN SCIENCE 2023; 10:230156. [PMID: 37181798 PMCID: PMC10170347 DOI: 10.1098/rsos.230156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 04/23/2023] [Indexed: 05/16/2023]
Abstract
Knowledge of diet and dietary selectivity is vital, especially for the conservation of declining species. Accurately obtaining this information, however, is difficult, especially if the study species feeds on a wide range of food items within heterogeneous and inaccessible environments, such as the tree canopy. Hawfinches (Coccothraustes coccothraustes), like many woodland birds, are declining for reasons that are unclear. We investigated the possible role that dietary selection may have in these declines in the UK. Here, we used a combination of high-throughput sequencing of 261 hawfinch faecal samples assessed against tree occurrence data from quadrats sampled in three hawfinch population strongholds in the UK to test for evidence of selective foraging. This revealed that hawfinches show selective feeding and consume certain tree genera disproportionally to availability. Positive selection was shown for beech (Fagus), cherry (Prunus), hornbeam (Carpinus), maples (Acer) and oak (Quercus), while Hawfinch avoided ash (Fraxinus), birch (Betula), chestnut (Castanea), fir (Abies), hazel (Corylus), rowan (Sorbus) and lime (Tilia). This approach provided detailed information on hawfinch dietary choice and may be used to predict the effects of changing food resources on other declining passerines populations in the future.
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Affiliation(s)
- Ewan H. Stenhouse
- School of Biosciences, Cardiff University, Cardiff CF10 3AT, Wales, UK
- RSPB Centre for Conservation Science, The Lodge, Sandy SG19 2DL, UK
| | - Paul Bellamy
- RSPB Centre for Conservation Science, The Lodge, Sandy SG19 2DL, UK
| | - Will Kirby
- RSPB Centre for Conservation Science, The Lodge, Sandy SG19 2DL, UK
| | - Ian P. Vaughan
- School of Biosciences, Cardiff University, Cardiff CF10 3AT, Wales, UK
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11
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Iwaszkiewicz-Eggebrecht E, Granqvist E, Buczek M, Prus M, Kudlicka J, Roslin T, Tack AJ, Andersson AF, Miraldo A, Ronquist F, Łukasik P. Optimizing insect metabarcoding using replicated mock communities. Methods Ecol Evol 2023; 14:1130-1146. [PMID: 37876735 PMCID: PMC10593422 DOI: 10.1111/2041-210x.14073] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 01/20/2023] [Indexed: 10/26/2023]
Abstract
1: Metabarcoding (high-throughput sequencing of marker gene amplicons) has emerged as a promising and cost-effective method for characterizing insect community samples. Yet, the methodology varies greatly among studies and its performance has not been systematically evaluated to date. In particular, it is unclear how accurately metabarcoding can resolve species communities in terms of presence-absence, abundances, and biomass. 2: Here we use mock community experiments and a simple probabilistic model to evaluate the effect of different DNA extraction protocols on metabarcoding performance. Specifically, we ask four questions: (Q1) How consistent are the recovered community profiles across replicate mock communities?; (Q2) How does the choice of lysis buffer affect the recovery of the original community?; (Q3) How are community estimates affected by differing lysis times and homogenization?; and (Q4) Is it possible to obtain adequate species abundance estimates through the use of biological spike-ins? 3: We show that estimates are quite variable across community replicates. In general, a mild lysis protocol is better at reconstructing species lists and approximate counts, while homogenization is better at retrieving biomass composition. Small insects are more likely to be detected in lysates, while some tough species require homogenization to be detected. Results are less consistent across biological replicates for lysates than for homogenates. Some species are associated with strong PCR amplification bias, which complicates the reconstruction of species counts. Yet, with adequate spike-in data, species abundance can be determined with roughly 40% standard error for homogenates, and with roughly 50% standard error for lysates, under ideal conditions. In the latter case, however, this often requires species-specific reference data, while spike-in data generalizes better across species for homogenates. 4: We conclude that a non-destructive, mild lysis approach shows the highest promise for presence/absence description of the community, while also allowing future morphological or molecular work on the material. However, homogenization protocols perform better for characterizing community composition, in particular in terms of biomass.
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Affiliation(s)
| | - Emma Granqvist
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Box 50007, SE-104 05 Stockholm, Sweden
| | - Mateusz Buczek
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, ul. Gronostajowa 7, 30-387 Kraków, Poland
| | - Monika Prus
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, ul. Gronostajowa 7, 30-387 Kraków, Poland
| | - Jan Kudlicka
- Department of Data Science and Analytics, BI Norwegian Business School, NO-0442 Oslo, Norway
| | - Tomas Roslin
- Department of Ecology; Box 7044, Swedish University of Agricultural Sciences, SE-750 07 Uppsala, Sweden
| | - Ayco J.M. Tack
- Department of Ecology, Environment and Plant Sciences, Stockholm University, SE-114 18 Stockholm, Sweden
| | - Anders F. Andersson
- KTH Royal Institute of Technology, Science for Life Laboratory, Department of Gene Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health, Stockholm, Sweden
| | - Andreia Miraldo
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Box 50007, SE-104 05 Stockholm, Sweden
| | - Fredrik Ronquist
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Box 50007, SE-104 05 Stockholm, Sweden
| | - Piotr Łukasik
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Box 50007, SE-104 05 Stockholm, Sweden
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, ul. Gronostajowa 7, 30-387 Kraków, Poland
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12
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Artificial Waterholes for European Bison as Biodiversity Hotspots in Forest Ecosystems: Ecological Effects of Species Reintroduction Activities. DIVERSITY 2023. [DOI: 10.3390/d15030446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/22/2023]
Abstract
Despite the growing population of European bison (Bison bonasus), it is necessary to plan the reintroduction of these animals to new areas. Reintroduction of European bison often requires the improvement of natural conditions. Such preparatory activities allow European bison to more easily adapt to new places, but also impact the functioning of animals from other taxa. The aim of the presented study was to examine the impact of waterholes for European bison on the development of local populations of amphibians and dragonflies (Odonata), as well as the creation of new feeding grounds for bats. We examined 15 reservoirs in the Augustów Forest District located in northeastern Poland, of which five were waterholes for European bison built in 2013–2014, four were semi-natural reservoirs transformed into waterholes for European bison in 2018, and six were natural reservoirs. Dragonflies were studied in 2021–2022; amphibians in 2018 and 2020; and bats in 2018, 2019, and 2020. In total, 24 species of dragonflies (Odonata), 10 species of amphibians, and 13 species of bats were found. The results of the inventory of three taxonomic groups using different comparative variants indicate a significant impact of the construction of waterholes for European bison on the biodiversity of the forest ecosystem. We concluded that the waterholes for European bison present better resistance to drying out than natural reservoirs. In addition, waterholes warm up more quickly, supporting better conditions for amphibians. The surface of the reservoirs and their exposed surroundings are favorable for insects (including dragonflies), and these are a source of food for bats, becoming attractive feeding grounds for them.
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13
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Ayala-Berdon J, Martínez Gómez M, Ponce AR, Beamonte-Barrientos R, Vázquez J, Rodriguez-Peña ON. Weather, ultrasonic, cranial and body traits predict insect diet hardness in a Central Mexican bat community. MAMMAL RES 2023. [DOI: 10.1007/s13364-023-00678-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/28/2023]
Abstract
AbstractInsectivorous bats exhibit food preferences for specific attributes in their prey. Hardness has been defined as an important prey attribute, and in some cases a limiting factor in foraging decisions for smaller compared to larger bat species. The goal of this study was to identify which factors influence the selection of prey hardness in a vespertilionid bat community. We investigated food consumed by bats by analyzing fecal samples obtained from eight bat species coexisting in a mountain ecosystem of central Mexico and correlate non-phylogenetically and phylogenetically prey hardness to weather, bat´s body, cranial and ultrasonic call structure variables. Results showed that diet of vespertilionid bats was mainly represented by Diptera, Neuroptera, Lepidoptera and Coleoptera consumption. The qualitative prey hardness index (From soft 1 to hard 5) ranked bats as: Myotis melanorhinus, Corynorhinus mexicanus, Myotis volans, Myotis californicus (< 3); Myotis velifer (< 4); Eptesicus fuscus, Idionycteris phyllotis and Myotis thysanodes (> 4.2). Prey hardness was positively correlated to minimum and mean temperatures, bat´s body weight, total and forearm lengths, cranial variables as: zygomatic breadth, mandibular length, height of the coronoid process, lower molar width, C-M3 superior and inferior rows length and upper molar width; and negatively to ultrasonic variables as total slope, call duration, low and high frequencies, band width and frequency maximum power. Considering phylogenies, prey hardness positively correlated to mandibular length, C-M3 inferior and superior rows lengths (p < 0.05). Our results showed that environmental, morphological and echolocation variables can be used as predictors of preferred insect prey in a community of vespertilionid bats.
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14
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Tuomi MW, Murguzur FJA, Hoset KS, Soininen EM, Vesterinen EJ, Utsi TA, Kaino S, Bråthen KA. Novel frontier in wildlife monitoring: Identification of small rodent species from fecal pellets using near-infrared reflectance spectroscopy (NIRS). Ecol Evol 2023; 13:e9857. [PMID: 36950367 PMCID: PMC10024998 DOI: 10.1002/ece3.9857] [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] [Received: 09/26/2022] [Revised: 01/13/2023] [Accepted: 02/03/2023] [Indexed: 03/21/2023] Open
Abstract
Small rodents are prevalent and functionally important across the world's biomes, making their monitoring salient for ecosystem management, conservation, forestry, and agriculture. There is a growing need for cost-effective and noninvasive methods for large-scale, intensive sampling. Fecal pellet counts readily provide relative abundance indices, and given suitable analytical methods, feces could also allow for the determination of multiple ecological and physiological variables, including community composition. In this context, we developed calibration models for rodent taxonomic determination using fecal near-infrared reflectance spectroscopy (fNIRS). Our results demonstrate fNIRS as an accurate and robust method for predicting genus and species identity of five coexisting subarctic microtine rodent species. We show that sample exposure to weathering increases the method's accuracy, indicating its suitability for samples collected from the field. Diet was not a major determinant of species prediction accuracy in our samples, as diet exhibited large variation and overlap between species. fNIRS could also be applied across regions, as calibration models including samples from two regions provided a good prediction accuracy for both regions. We show fNIRS as a fast and cost-efficient high-throughput method for rodent taxonomic determination, with the potential for cross-regional calibrations and the use on field-collected samples. Importantly, appeal lies in the versatility of fNIRS. In addition to rodent population censuses, fNIRS can provide information on demography, fecal nutrients, stress hormones, and even disease. Given the development of such calibration models, fNIRS analytics could complement novel genetic methods and greatly support ecosystem- and interaction-based approaches to monitoring.
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Affiliation(s)
- Maria W. Tuomi
- Department of Arctic and Marine BiologyUiT The Arctic University of NorwayTromsøNorway
- Section of EcologyDepartment of BiologyUniversity of TurkuTurkuFinland
| | | | - Katrine S. Hoset
- Section of EcologyDepartment of BiologyUniversity of TurkuTurkuFinland
| | - Eeva M. Soininen
- Department of Arctic and Marine BiologyUiT The Arctic University of NorwayTromsøNorway
| | - Eero J. Vesterinen
- Department of EcologySwedish University of Agricultural SciencesUppsalaSweden
- Biodiversity UnitUniversity of TurkuTurkuFinland
- Department of Agricultural SciencesUniversity of HelsinkiHelsinkiFinland
| | - Tove Aa. Utsi
- Department of Arctic and Marine BiologyUiT The Arctic University of NorwayAltaNorway
| | - Sissel Kaino
- Department of Arctic and Marine BiologyUiT The Arctic University of NorwayTromsøNorway
| | - Kari Anne Bråthen
- Department of Arctic and Marine BiologyUiT The Arctic University of NorwayTromsøNorway
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15
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Woo C, Kumari P, Eo KY, Lee WS, Kimura J, Yamamoto N. Combining vertebrate mitochondrial 12S rRNA gene sequencing and shotgun metagenomic sequencing to investigate the diet of the leopard cat (Prionailurus bengalensis) in Korea. PLoS One 2023; 18:e0281245. [PMID: 36719887 PMCID: PMC9888693 DOI: 10.1371/journal.pone.0281245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 01/18/2023] [Indexed: 02/01/2023] Open
Abstract
The leopard cat (Prionailurus bengalensis), an endangered species in South Korea, is a small feline widely distributed in Asia. Here, we investigated the diet of leopard cats in the inland areas of Korea by examining their fecal contents using vertebrate mitochondrial 12S rRNA gene sequencing and shotgun metagenomic sequencing. Shotgun metagenomic sequencing revealed that the feces were rich in DNA not only of vertebrates but also of arthropods and plants, but care should be taken when using shotgun metagenomic sequencing to identify vertebrates at low taxonomic levels (e.g., genus level), as it was often erroneous. Meanwhile, vertebrate mitochondrial 12S rRNA gene sequencing was found to be accurate in the genus-level identification, as the genera identified were consistent with the Korean fauna. We found that small mammals such as murids were their main prey. By using these two sequencing methods in combination, this study demonstrated that accurate information about the overall dietary content and vertebrate prey of leopard cats could be obtained. We expect that the continued community efforts to expand the genome database of wildlife, including vertebrates, will alleviate the problem of erroneous identification of prey at low taxonomic levels by shotgun metagenomic sequencing in the near future.
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Affiliation(s)
- Cheolwoon Woo
- Department of Environmental Health Sciences, Graduate School of Public Health, Seoul National University, Seoul, Republic of Korea
| | - Priyanka Kumari
- Department of Environmental Health Sciences, Graduate School of Public Health, Seoul National University, Seoul, Republic of Korea
- Institute of Health and Environment, Graduate School of Public Health, Seoul National University, Seoul, Republic of Korea
| | - Kyung Yeon Eo
- Department of Animal Health and Welfare, College of Healthcare and Biotechnology, Semyung University, Jecheon, Republic of Korea
| | - Woo-Shin Lee
- Department of Forest Sciences, College of Agriculture and Life Science, Seoul National University, Seoul, Republic of Korea
| | - Junpei Kimura
- College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea
| | - Naomichi Yamamoto
- Department of Environmental Health Sciences, Graduate School of Public Health, Seoul National University, Seoul, Republic of Korea
- Institute of Health and Environment, Graduate School of Public Health, Seoul National University, Seoul, Republic of Korea
- * E-mail:
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16
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Xu L, Zhang X, Guo H, Yang X, Xing Z, Yang W, Zhang J, Tian X. Species diversity analysis of commercial Mantidis Ootheca samples contaminated by store pests based on DNA metabarcoding. BMC Genomics 2022; 23:720. [PMID: 36271325 PMCID: PMC9587553 DOI: 10.1186/s12864-022-08955-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 10/19/2022] [Indexed: 11/10/2022] Open
Abstract
Mantidis Ootheca (Sangpiaoxiao, mantis egg case) is a typical multi-origin Chinese medicinal material. The Chinese Pharmacopoeia stipulates that the Mantidis Ootheca originates from three species of Mantis: Tenodera sinensis, Statilia maculate, and Hierodula patellifera. However, Mantidis Ootheca mainly relies on field collection, which leads to confusion of its actual origin in the market. As the clinical use of Mantidis Ootheca with unknown original mantis species will pose potential risks to drug safety, it is necessary to survey the commercially available Mantidis Ootheca origin species. However, as the egg case of Mantis, the morphological characters of Mantidis Ootheca are limited and usually cannot serve as accurate identification tool. DNA barcoding, which is widely used in taxonomic studies of animals, is severely affected by the impact of storage pests and DNA degradation. Thus, this study collected a total of 4580 Mantidis Ootheca and pooled separately Mantidis Ootheca samples according to 18 different sources as DNA samples to analyze the origin diversity of Mantidis Ootheca individuals contaminated by common store pests collected in in the market using DNA metabarcoding, and to provide a basis for quality control of Mantidis Ootheca. 37 Mantis ASVs and 9 Mantis MOTUs were identified through species delimitation, and the high-level intraspecific diversity was depicted as haplotype network plot. Besides Tenodera sinensis and Hierodula patellifera as genuine original mantis species defined in the Chinese Pharmacopoeia, Tenodera angustipennis was also the origin species of these Mantidis Ootheca samples.
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Affiliation(s)
- Liuwei Xu
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China.,Haihe Laboratory of Modern Chinese Medicine, Tianjin, 301617, China
| | - Xiaoying Zhang
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China.,Haihe Laboratory of Modern Chinese Medicine, Tianjin, 301617, China
| | - Hua Guo
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China.,Haihe Laboratory of Modern Chinese Medicine, Tianjin, 301617, China
| | - Xia Yang
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China.,Haihe Laboratory of Modern Chinese Medicine, Tianjin, 301617, China
| | - Zhimei Xing
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China.,Haihe Laboratory of Modern Chinese Medicine, Tianjin, 301617, China
| | - Wenzhi Yang
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China.,Haihe Laboratory of Modern Chinese Medicine, Tianjin, 301617, China
| | - Jian Zhang
- School of Chinese Materia, Tianjin Universtity of Traditional Chinese Medicine, Tianjin, 301617, China.
| | - Xiaoxuan Tian
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China. .,Haihe Laboratory of Modern Chinese Medicine, Tianjin, 301617, China.
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17
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O'Rourke D, Rouillard NP, Parise KL, Foster JT. Spatial and temporal variation in New Hampshire bat diets. Sci Rep 2022; 12:14334. [PMID: 35995911 PMCID: PMC9395357 DOI: 10.1038/s41598-022-17631-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Accepted: 07/28/2022] [Indexed: 11/09/2022] Open
Abstract
Insectivorous bats consume a diverse array of arthropod prey, with diets varying by bat species, sampling location, and season. North American bat diets remain incompletely described, which is concerning at a time when many bat and insect populations appear to be declining. Understanding the variability in foraging is thus an essential component for effective bat conservation. To comprehensively evaluate local foraging, we assessed the spatial and temporal variability in prey consumed by the little brown bat, Myotis lucifugus, in New Hampshire, USA. We collected bat guano samples from 20 sites over 2 years and analyzed sequence data for 899 of these samples using a molecular metabarcoding approach targeting the cytochrome oxidase I subunit (COI) gene. Some prey items were broadly shared across locations and sampling dates, with the most frequently detected arthropod orders broadly similar to previous morphological and molecular analyses; at least one representative sequence variant was assigned to Coleoptera in 92% of samples, with other frequently detected orders including Diptera (73%), Lepidoptera (65%), Trichoptera (38%), and Ephemeroptera (32%). More specifically, two turf and forest pests were routinely detected: white grubs in the genus Phyllophaga (50%), and the Asiatic Garden beetle, Maladera castanea (36%). Despite the prevalence of a few taxa shared among many samples and distinct seasonal peaks in consumption of specific arthropods, diet composition varied both temporally and spatially. However, species richness did not strongly vary indicating consumption of a broad diversity of taxa throughout the summer. These data characterize little brown bats as flexible foragers adept at consuming a broad array of locally available prey resources.
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Affiliation(s)
- Devon O'Rourke
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH, USA. .,Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA.
| | - Nicholas P Rouillard
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH, USA
| | - Katy L Parise
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH, USA.,Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Jeffrey T Foster
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH, USA.,Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
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18
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Didorenko SI, Botvinkin AD, Takhteev VV. Myotis petax (Chiroptera, Vespertilionidae) Preys on Pelagic Amphipoda (Crustacea, Gammaroidea) of Lake Baikal. ACTA CHIROPTEROLOGICA 2022. [DOI: 10.3161/15081109acc2022.24.1.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Sergey I. Didorenko
- Baikal Museum of Irkutsk Scientific Center, Siberian Branch of Russian Academy of Science, Listvyanka, Irkutsk 664520, Russia
| | | | - Vadim V. Takhteev
- Irkutsk State University, 1 Karl Marx Street, Irkutsk 664003, Russia
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19
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Kirse A, Bourlat SJ, Langen K, Zapke B, Zizka VMA. Comparison of destructive and non-destructive DNA extraction methods for the metabarcoding of arthropod bulk samples. Mol Ecol Resour 2022; 23:92-105. [PMID: 35932285 DOI: 10.1111/1755-0998.13694] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 07/07/2022] [Accepted: 07/25/2022] [Indexed: 11/28/2022]
Abstract
DNA metabarcoding is routinely used for biodiversity assessment, especially targeting highly diverse groups for which limited taxonomic expertise is available. Various protocols are currently in use, although standardization is key to its application in large-scale monitoring. DNA metabarcoding of arthropod bulk samples can be either conducted destructively from sample tissue, or non-destructively from sample fixative or lysis buffer. Non-destructive methods are highly desirable for the preservation of sample integrity but have yet to be experimentally evaluated in detail. Here, we compare diversity estimates from 14 size sorted Malaise trap samples processed consecutively with three non-destructive approaches (one using fixative ethanol and two using lysis buffers) and one destructive approach (using homogenized tissue). Extraction from commercial lysis buffer yielded comparable species richness and high overlap in species composition to the ground tissue extracts. A significantly divergent community was detected from preservative ethanol-based DNA extraction. No consistent trend in species richness was found with increasing incubation time in lysis buffer. These results indicate that non-destructive DNA extraction from incubation in lysis buffer could provide a comparable alternative to destructive approaches with the added advantage of preserving the specimens for post-metabarcoding taxonomic work but at a higher cost per sample.
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Affiliation(s)
- Ameli Kirse
- LIB/Zoological Research Museum Alexander Koenig (ZFMK), Centre for Biodiversity Monitoring, Bonn, Germany
| | - Sarah J Bourlat
- LIB/Zoological Research Museum Alexander Koenig (ZFMK), Centre for Biodiversity Monitoring, Bonn, Germany
| | - Kathrin Langen
- LIB/Zoological Research Museum Alexander Koenig (ZFMK), Centre for Biodiversity Monitoring, Bonn, Germany
| | - Björn Zapke
- LIB/Zoological Research Museum Alexander Koenig (ZFMK), Centre for Biodiversity Monitoring, Bonn, Germany
| | - Vera M A Zizka
- LIB/Zoological Research Museum Alexander Koenig (ZFMK), Centre for Biodiversity Monitoring, Bonn, Germany
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20
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Woo C, Kumari P, Eo KY, Lee WS, Kimura J, Yamamoto N. Using DNA metabarcoding and a novel canid-specific blocking oligonucleotide to investigate the composition of animal diets of raccoon dogs (Nyctereutes procyonoides) inhabiting the waterside area in Korea. PLoS One 2022; 17:e0271118. [PMID: 35877678 PMCID: PMC9312373 DOI: 10.1371/journal.pone.0271118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 06/23/2022] [Indexed: 11/29/2022] Open
Abstract
The raccoon dog (Nyctereutes procyonoides) is known to be an opportunistic generalist who feeds on a wide variety of foods. Historically, their diet has been investigated by morphological observation of undigested remains in feces, requiring specialized knowledge such as osteology, zoology, and phytology. Here, we used DNA metabarcoding of vertebrate 12S rRNA gene and invertebrate 16S rRNA gene to investigate their fecal contents. Additionally, we developed a blocking oligonucleotide that specifically inhibits the amplification of the canid 12S rRNA gene. We confirmed that the blocking oligonucleotide selectively inhibit the amplification of raccoon dog’s DNA without significantly changing the composition of the preys’ DNA. We found that the main foods of raccoon dogs in our study area, the waterside of paddy fields in Korea, were fishes such as Cyprinidae and insects such as mole crickets, which makes sense given the Korean fauna and their well-known opportunistic feeding behaviors. As a method to conveniently and objectively investigate feeding habits of raccoon dogs, this study provided baseline information on DNA metabarcoding. By using DNA metabarcoding, it is expected that the diet habits and ecology of raccoon dogs will be better understood by future research.
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Affiliation(s)
- Cheolwoon Woo
- Department of Environmental Health Sciences, Graduate School of Public Health, Seoul National University, Seoul, Republic of Korea
| | - Priyanka Kumari
- Department of Environmental Health Sciences, Graduate School of Public Health, Seoul National University, Seoul, Republic of Korea
- Institute of Health and Environment, Graduate School of Public Health, Seoul National University, Seoul, Republic of Korea
| | - Kyung Yeon Eo
- Department of Animal Health and Welfare, College of Healthcare and Biotechnology, Semyung University, Jecheon, Republic of Korea
- * E-mail: (KYE); (NY)
| | - Woo-Shin Lee
- Department of Forest Sciences, College of Agriculture and Life Science, Seoul National University, Seoul, Republic of Korea
| | - Junpei Kimura
- College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea
| | - Naomichi Yamamoto
- Department of Environmental Health Sciences, Graduate School of Public Health, Seoul National University, Seoul, Republic of Korea
- Institute of Health and Environment, Graduate School of Public Health, Seoul National University, Seoul, Republic of Korea
- * E-mail: (KYE); (NY)
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21
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Marquina D, Roslin T, Łukasik P, Ronquist F. Evaluation of non-destructive DNA extraction protocols for insect metabarcoding: gentler and shorter is better. METABARCODING AND METAGENOMICS 2022. [DOI: 10.3897/mbmg.6.78871] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
DNA metabarcoding can accelerate research on insect diversity, as it is cheap and fast compared to manual sorting and identification. Most metabarcoding protocols require homogenisation of the sample, preventing further work on the specimens. Mild digestion of the tissue by incubation in a lysis buffer has been proposed as an alternative, and, although some mild lysis protocols have already been presented, they have so far not been evaluated against each other. Here, we analyse how two mild lysis buffers (one more aggressive, one gentler in terms of tissue degradation), two different incubation times, and two DNA purification methods (a manual precipitation and an automated protocol) affect the accuracy of retrieving the true composition of mock communities using two mitochondrial markers (COI and 16S). We found that protocol-specific variation in concentration and purity of the DNA extracts produced had little effect on the recovery of species. However, the two lysis treatments differed in quantification of species abundances. Digestion in the gentler buffer and for a shorter time yielded better representation of original sample composition. Digestion in a more aggressive buffer or longer incubation time yielded lower alpha diversity values and increased differences between metabarcoding results and the true species-abundance distribution. We conclude that the details of non-destructive protocols can have a significant effect on metabarcoding performance. A short and mild lysis treatment appears the best choice for recovering the true composition of the sample. This not only improves accuracy, but also comes with a faster processing time than the other treatments.
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22
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Ružinská R, Lőbbová D, Kaňuch P. Demographic characteristics shape patterns of dawn swarming during roost switching in tree-dwelling Daubenton's bat. Sci Rep 2022; 12:10014. [PMID: 35705697 PMCID: PMC9200770 DOI: 10.1038/s41598-022-14246-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 06/03/2022] [Indexed: 11/19/2022] Open
Abstract
Frequent roost switching in fission-fusion societies of tree-dwelling bats is closely associated with swarming behaviour entailing ritualised night-time displays around the roost tree and/or at the roost entrance to signal its actual location, particularly immediately prior to sunrise. However, effects of demographic characteristics of individuals in this social behaviour remain unanswered. Using passive integrated transponders (PIT) and automatic readers, we recorded swarming activity of members of a Daubenton's bat (Myotis daubentonii) maternity colony in the vicinity of their roosts. In total, 59,622 activity events of 281 PIT-tagged individuals were recorded on ten monitored roosts during three summer seasons. We found a gradual increase of swarming activity from midnight to sunrise in old adult females, whereas young females and juveniles primarily swarmed later at dawn. We attribute this difference to the learning status of younger bats, which are not yet able to perform a defined pattern of swarming activity, whereas older bats likely take a more active role in signalling the position of the roost. Old males exhibited the least swarming activity at maternity roosts, which mostly occurred between crepuscular periods, presumably due to their solitary lives. A negative correlation between genetic distance and swarming activity suggests an important role of kinship in the formation of the maternity colony as well as group cohesion during roost switching.
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Affiliation(s)
- Romana Ružinská
- Institute of Forest Ecology, Slovak Academy of Sciences, Zvolen, Slovakia
- Faculty of Ecology and Environmental Sciences, Technical University in Zvolen, Zvolen, Slovakia
| | | | - Peter Kaňuch
- Institute of Forest Ecology, Slovak Academy of Sciences, Zvolen, Slovakia.
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23
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Koskinen JS, Abrego N, Vesterinen EJ, Schulz T, Roslin T, Nyman T. Imprints of latitude, host taxon, and decay stage on fungus‐associated arthropod communities. ECOL MONOGR 2022. [DOI: 10.1002/ecm.1516] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Janne S. Koskinen
- Department of Environmental and Biological Sciences University of Eastern Finland Joensuu Finland
- Department of Agricultural Sciences University of Helsinki Finland
| | - Nerea Abrego
- Department of Agricultural Sciences University of Helsinki Finland
- Department of Biological and Environmental Science University of Jyväskylä Finland
| | | | - Torsti Schulz
- Organismal and Evolutionary Biology Research Programme University of Helsinki Finland
| | - Tomas Roslin
- Department of Agricultural Sciences University of Helsinki Finland
- Department of Ecology Swedish University of Agricultural Sciences Uppsala Sweden
| | - Tommi Nyman
- Department of Ecosystems in the Barents Region Norwegian Institute of Bioeconomy Research Svanvik Norway
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24
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Kyrö K, Kankaanpää T, Vesterinen EJ, Lehvävirta S, Kotze DJ. Arthropod Communities on Young Vegetated Roofs Are More Similar to Each Other Than to Communities at Ground Level. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.785448] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Vegetated roofs are human-manufactured ecosystems and potentially promising conservation tools for various taxa and habitats. Focussing on arthropods, we conducted a 3 year study on newly constructed vegetated roofs with shallow substrates (up to 10 cm) and vegetation established with pre-grown mats, plug plants and seeds to describe pioneer arthropod communities on roofs and to compare them with ground level communities. We vacuum sampled arthropods from the roofs and nearby ground level sites with low, open vegetation, i.e., potential source habitats. We showed that the roofs and ground sites resembled each other for ordinal species richness but differed in community composition: with time the roofs started to resemble each other rather than their closest ground level habitats. Species richness increased with time on roofs and at ground level, but the roofs had consistently less species than the ground sites and only a few species were unique to the roofs. Also, the proportion of predators increased on roofs, while not at ground level. We conclude that vegetated roofs established with similar substrates and vegetation, filter arthropods in a way that produces novel communities that are different from those at ground level but similar to one another. The role of these insular communities in species networks and ecosystem function remains to be investigated.
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25
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Zhang X, Wang W, Yu X, Liu Y, Li W, Yang H, Cui Y, Tian X. Biological composition analysis of a natural medicine, Faeces Vespertilionis, with complex sources using DNA metabarcoding. Sci Rep 2022; 12:375. [PMID: 35013500 PMCID: PMC8748881 DOI: 10.1038/s41598-021-04387-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 12/20/2021] [Indexed: 11/09/2022] Open
Abstract
Faeces Vespertilionis is a commonly used fecal traditional Chinese medicine. Traditionally, it is identified relying only on morphological characters. This poses a serious challenge to the composition analysis accuracy of this complex biological mixture. Thus, for quality control purposes, an accurate and effective method should be provided for taxonomic identification of Faeces Vespertilionis. In this study, 26 samples of Faeces Vespertilionis from ten provinces in China were tested using DNA metabarcoding. Seven operational taxonomic units (OTUs) were detected as belonging to bats. Among them, Hipposideros armiger (Hodgson, 1835) and Rhinolophus ferrumequinum (Schober and Grimmberger, 1997) were the main host sources of Faeces Vespertilionis samples, with average relative abundances of 59.3% and 24.1%, respectively. Biodiversity analysis showed that Diptera and Lepidoptera were the most frequently consumed insects. At the species level, 19 taxa were clearly identified. Overall, our study used DNA metabarcoding to analyze the biological composition of Faeces Vespertilionis, which provides a new idea for the quality control of this special traditional Chinese medicine.
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Affiliation(s)
- Xiaoying Zhang
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China
| | - Wenxiu Wang
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China
| | - Xiaolei Yu
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China
| | - Yuxia Liu
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China
| | - Wenhui Li
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China
| | - Hongxia Yang
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China
| | - Ying Cui
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China.
| | - Xiaoxuan Tian
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China.
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26
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Didorenko SI, Botvinkin AD, Takhteev VV. A New Trophic Relationship in the Baikal Ecosystem: The Pelagic Amphipod Macrohectopus branickii (Crustacea, Amphipoda) and the Bat Myotis petax (Mammalia, Chiroptera). BIOL BULL+ 2021. [DOI: 10.1134/s1062359021070116] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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27
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Morrill A, Kaunisto KM, Mlynarek JJ, Sippola E, Vesterinen EJ, Forbes MR. Metabarcoding prey DNA from fecal samples of adult dragonflies shows no predicted sex differences, and substantial inter-individual variation, in diets. PeerJ 2021; 9:e12634. [PMID: 35003931 PMCID: PMC8686731 DOI: 10.7717/peerj.12634] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 11/22/2021] [Indexed: 11/20/2022] Open
Abstract
Sexes often differ in foraging and diet, which is associated with sex differences in size, trophic morphology, use of habitats, and/or life history tactics. Herein, strikingly similar diets were found for adult sexes of a dragonfly (Leucorrhinia intacta), based on comparing 141 dietary taxa identified from the metabarcoding of mitochondrial DNA archived in feces. Arthropods in > 5% of samples included five species of dipterans, two hemipterans, two spider species and one parasitic mite. The mite was not traditional prey as its presence was likely due to DNA contamination of samples arising through parasitism or possibly via accidental consumption during grooming, and therefore the mite was excluded from diet characterizations. Common prey species were found with statistically indistinguishable frequencies in male and female diets, with one exception of an aphid more often found in male diets, although this pattern was not robust to corrections for multiple statistical tests. While rare prey species were often found in diets of only one sex, instances of this were more frequent in the more oft-sampled females, suggesting sampling artefact. Sexes did not differ in the mean prey species richness in their diets. Overall, sexes showed statistically indistinguishable diets both on a prey species-by-species basis and in terms of multivariate characterizations of diet composition, derived from presence-absence data of prey species analyzed via PERMANOVA and accumulation curves. Males and females may have similar diets by being both opportunistic and generalist predators of arthropods, using the same foraging habitats and having similar sizes and flight agilities. Notably, similarities in diet between sexes occur alongside large interindividual differences in diet, within sexes. Researchers intending on explaining adaptive sex differences in diet should consider characteristics of species whose sexes show similar diets.
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Affiliation(s)
- André Morrill
- Department of Biology, Carleton University, Ottawa, Ontario, Canada
| | | | | | - Ella Sippola
- Biodiversity Unit, University of Turku, Turku, Finland
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland
| | - Eero J. Vesterinen
- Department of Biology, University of Turku, Turku, Finland
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Mark R. Forbes
- Department of Biology, Carleton University, Ottawa, Ontario, Canada
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28
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Heim O, Puisto AIE, Sääksjärvi I, Fukui D, Vesterinen EJ. Dietary analysis reveals differences in the prey use of two sympatric bat species. Ecol Evol 2021; 11:18651-18661. [PMID: 35003699 PMCID: PMC8717349 DOI: 10.1002/ece3.8472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 11/08/2021] [Accepted: 11/12/2021] [Indexed: 11/05/2022] Open
Abstract
One mechanism for morphologically similar and sympatric species to avoid competition and facilitate coexistence is to feed on different prey items within different microhabitats. In the current study, we investigated and compared the diet of the two most common and similar-sized bat species in Japan-Murina ussuriensis (Ognev, 1913) and Myotis ikonnikovi (Ognev, 1912)-to gain more knowledge about the degree of overlap in their diet and their foraging behavior. We found that both bat species consumed prey from the orders of Lepidoptera and Diptera most frequently, while the proportion of Dipterans was higher in the diet of M. ikonnikovi. Furthermore, we found a higher prey diversity in the diet of M. ikonnikovi compared to that of M. ussuriensis that might indicate that the former is a more generalist predator than the latter. In contrast, the diet of M. ussuriensis contained many Lepidopteran families. The higher probability of prey items likely captured via gleaning to occur in the diet of M. ussuriensis in contrast to M. ikonnikovi indicates that M. ussuriensis might switch between aerial-hawking and gleaning modes of foraging behavior. We encourage further studies across various types of habitats and seasons to investigate the flexibility of the diet composition and foraging behavior of these two bat species.
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Affiliation(s)
- Olga Heim
- Faculty of Life and Medical SciencesDoshisha UniversityKyotanabeJapan
| | - Anna I. E. Puisto
- Centre for Population Health ResearchUniversity of TurkuTurkuFinland
| | | | - Dai Fukui
- The University of Tokyo Hokkaido ForestThe University of TokyoFuranoJapan
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29
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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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30
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Li J, Chu Y, Yao W, Wu H, Feng J. Differences in Diet and Gut Microbiota Between Lactating and Non-lactating Asian Particolored Bats ( Vespertilio sinensis): Implication for a Connection Between Diet and Gut Microbiota. Front Microbiol 2021; 12:735122. [PMID: 34712210 PMCID: PMC8546350 DOI: 10.3389/fmicb.2021.735122] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 09/15/2021] [Indexed: 12/31/2022] Open
Abstract
In mammals, lactation is considered the most energetically costly phase for females. To meet nutritional and energy demands, lactating females usually change feeding patterns by eating food that is higher in protein and calories. Their gut microbes respond accordingly to help adapt to the changes in diet. In this study, we examined differences in diet and gut microbial composition between lactating and non-lactating Asian particolored bats (Vespertilio sinensis) using COI and 16S amplicon sequencing. When compared with non-lactating bats, we found that the diversity and composition of lactating bats' diets differed; the proportion of Diptera increased and Coleoptera and Orthoptera decreased significantly. This could be attributed to the easy availability and high protein content of Diptera. Comparative analysis of the gut microbiota of lactating and non-lactating females showed that although the diversity of gut microbiota did not change, the relative abundance of specific gut microbiota associated with a particular diet did change. For example, when the consumption of Coleoptera decreased in lactating bats, the relative abundance of Lactobacillaceae was also reduced. Lactobacillaceae are thought to be involved in the digestion of Coleopteran exoskeletons. This study suggests that during lactation, Asian particolored bats eat a diet that yields higher levels of protein, and at the same time, the abundance of specific gut microbes change to help their hosts adapt to these changes in diet.
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Affiliation(s)
- Jingjing Li
- College of Life Science, Jilin Agricultural University, Changchun, China
| | - Yujia Chu
- College of Life Science, Jilin Agricultural University, Changchun, China
| | - Wenwen Yao
- College of Life Science, Jilin Agricultural University, Changchun, China
| | - Hui Wu
- College of Life Science, Jilin Agricultural University, Changchun, China
| | - Jiang Feng
- College of Life Science, Jilin Agricultural University, Changchun, China.,Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China
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31
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Roslin T, Somervuo P, Pentinsaari M, Hebert PDN, Agda J, Ahlroth P, Anttonen P, Aspi J, Blagoev G, Blanco S, Chan D, Clayhills T, deWaard J, deWaard S, Elliot T, Elo R, Haapala S, Helve E, Ilmonen J, Hirvonen P, Ho C, Itämies J, Ivanov V, Jakovlev J, Juslén A, Jussila R, Kahanpää J, Kaila L, Jari-PekkaKaitila, Kakko A, Kakko I, Karhu A, Karjalainen S, Kjaerandsen J, Koskinen J, Laasonen EM, Laasonen L, Laine E, Lampila P, Levesque-Beaudin V, Lu L, Lähteenaro M, Majuri P, Malmberg S, Manjunath R, Martikainen P, Mattila J, McKeown J, Metsälä P, Miklasevskaja M, Miller M, Miskie R, Muinonen A, Veli-MattiMukkala, Naik S, Nikolova N, Nupponen K, Ovaskainen O, Österblad I, Paasivirta L, Pajunen T, Parkko P, Paukkunen J, Penttinen R, Perez K, Pohjoismäki J, Prosser S, Raekunnas M, Rahulan M, Rannisto M, Ratnasingham S, Raukko P, Rinne A, Rintala T, Miranda Romo S, Salmela J, Salokannel J, Savolainen R, Schulman L, Sihvonen P, Soliman D, Sones J, Steinke C, Ståhls G, Tabell J, Tiusanen M, Várkonyi G, Vesterinen EJ, Viitanen E, Vikberg V, Viitasaari M, Vilen J, Warne C, Wei C, Winqvist K, Zakharov E, Mutanen M. A molecular-based identification resource for the arthropods of Finland. Mol Ecol Resour 2021; 22:803-822. [PMID: 34562055 DOI: 10.1111/1755-0998.13510] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
To associate specimens identified by molecular characters to other biological knowledge, we need reference sequences annotated by Linnaean taxonomy. In this study, we (1) report the creation of a comprehensive reference library of DNA barcodes for the arthropods of an entire country (Finland), (2) publish this library, and (3) deliver a new identification tool for insects and spiders, as based on this resource. The reference library contains mtDNA COI barcodes for 11,275 (43%) of 26,437 arthropod species known from Finland, including 10,811 (45%) of 23,956 insect species. To quantify the improvement in identification accuracy enabled by the current reference library, we ran 1000 Finnish insect and spider species through the Barcode of Life Data system (BOLD) identification engine. Of these, 91% were correctly assigned to a unique species when compared to the new reference library alone, 85% were correctly identified when compared to BOLD with the new material included, and 75% with the new material excluded. To capitalize on this resource, we used the new reference material to train a probabilistic taxonomic assignment tool, FinPROTAX, scoring high success. For the full-length barcode region, the accuracy of taxonomic assignments at the level of classes, orders, families, subfamilies, tribes, genera, and species reached 99.9%, 99.9%, 99.8%, 99.7%, 99.4%, 96.8%, and 88.5%, respectively. The FinBOL arthropod reference library and FinPROTAX are available through the Finnish Biodiversity Information Facility (www.laji.fi) at https://laji.fi/en/theme/protax. Overall, the FinBOL investment represents a massive capacity-transfer from the taxonomic community of Finland to all sectors of society.
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Affiliation(s)
- Tomas Roslin
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden.,Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland
| | - Panu Somervuo
- Organismal and Evolutionary Biology Research Programme, University of Helsinki, Helsinki, Finland
| | - Mikko Pentinsaari
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Paul D N Hebert
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Jireh Agda
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Petri Ahlroth
- Finnish Environment Institute (SYKE), Helsinki, Finland
| | - Perttu Anttonen
- Institute of Biology/Geobotany and Botanical Garden, Martin Luther University Halle-Wittenberg, Halle, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Jouni Aspi
- Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland
| | - Gergin Blagoev
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Santiago Blanco
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Dean Chan
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | | | - Jeremy deWaard
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Stephanie deWaard
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Tyler Elliot
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Riikka Elo
- Zoological Museum, Biodiversity Unit, University of Turku, Turku, Finland.,Zoology Unit, Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
| | | | | | - Jari Ilmonen
- Metsähallitus, Parks & Wildlife Finland, Vantaa, Finland
| | | | - Chris Ho
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | | | - Vladislav Ivanov
- Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland
| | | | - Aino Juslén
- Finnish Museum of Natural History 'Luomus', University of Helsinki, Helsinki, Finland
| | | | - Jere Kahanpää
- Zoology Unit, Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
| | - Lauri Kaila
- Zoology Unit, Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
| | | | | | - Iiro Kakko
- Forssa Museum of Natural History, Forssa, Finland
| | | | | | - Jostein Kjaerandsen
- The Arctic University Museum of Norway, UiT -The Arctic University of Norway, Langnes, Tromsø, Norway
| | - Janne Koskinen
- Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland.,Department of Environmental and Biological Sciences, University of Eastern Finland, Joensuu, Finland
| | | | | | | | | | | | - Liuqiong Lu
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Meri Lähteenaro
- Division of Systematics, Department of Zoology, Stockholm University, Stockholm, Sweden.,Department of Entomology, Swedish Museum of Natural History, Stockholm, Sweden
| | | | | | - Ramya Manjunath
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | | | | | - Jaclyn McKeown
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | | | | | - Meredith Miller
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Renee Miskie
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | | | | | - Suresh Naik
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Nadia Nikolova
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | | | - Otso Ovaskainen
- Organismal and Evolutionary Biology Research Programme, University of Helsinki, Helsinki, Finland.,Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland.,Department of Biology, Centre for Biodiversity Dynamics, Norwegian University of Science and Technology, Trondheim, Norway
| | | | | | - Timo Pajunen
- Finnish Museum of Natural History 'Luomus', University of Helsinki, Helsinki, Finland
| | | | - Juho Paukkunen
- Zoology Unit, Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
| | - Ritva Penttinen
- Zoological Museum, Biodiversity Unit, University of Turku, Turku, Finland.,Zoology Unit, Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
| | - Kate Perez
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Jaakko Pohjoismäki
- Department of Environmental and Biological Sciences, University of Eastern Finland, Joensuu, Finland
| | - Sean Prosser
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | | | - Miduna Rahulan
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Meeri Rannisto
- Finnish Museum of Natural History 'Luomus', University of Helsinki, Helsinki, Finland
| | | | | | | | | | | | - Jukka Salmela
- Regional Museum of Lapland, Arktikum, Rovaniemi, Finland.,Arctic Centre, University of Lapland, Rovaniemi, Finland
| | | | - Riitta Savolainen
- Organismal and Evolutionary Biology Research Programme, University of Helsinki, Helsinki, Finland
| | - Leif Schulman
- Finnish Environment Institute (SYKE), Helsinki, Finland.,Finnish Museum of Natural History 'Luomus', University of Helsinki, Helsinki, Finland
| | - Pasi Sihvonen
- Finnish Museum of Natural History 'Luomus', University of Helsinki, Helsinki, Finland
| | - Dina Soliman
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Jayme Sones
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Claudia Steinke
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Gunilla Ståhls
- Finnish Museum of Natural History 'Luomus', University of Helsinki, Helsinki, Finland
| | | | - Mikko Tiusanen
- Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland
| | - Gergely Várkonyi
- Biodiversity Centre, Finnish Environment Institute SYKE, Kuhmo, Finland
| | - Eero J Vesterinen
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden.,Department of Biology, University of Turku, Turku, Finland
| | | | | | | | | | - Connor Warne
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Catherine Wei
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | | | - Evgeny Zakharov
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Marko Mutanen
- Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland
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Guo Y, Zhao X, Liu M, Zhang C, Zhang Y, Ma Q, Wang B, Luo H. Using Fecal DNA Metabarcoding to Investigate Foraging Reveals the Effects of Specific Herbage on the Improved n-3 Fatty Acid (PUFA) Composition in the Longissimus Dorsi Muscle of Grazing Tan Sheep. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:9725-9734. [PMID: 34378390 DOI: 10.1021/acs.jafc.1c03788] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Understanding the natural diet of grazing sheep can help fulfill their nutritional requirements and positively affect the quality of their meat. Emerging fecal DNA (fDNA) metabarcoding technology can provide more accurate estimates for the dietary composition of free-ranging animals. This study has shown that pasture feeding can promote deposition of n-3 polyunsaturated fatty acids (PUFAs) in Tan lambs' muscle and decrease the ratio of n-6/n-3 fatty acids (FAs), and thus, we investigated the dietary composition of grazing lambs using fDNA metabarcoding to assess the prevalence of medicinal herbage plants in their diet. Herein, based on the full-time natural pasture grazing and 4-h natural pasture grazing with indoor feeding patterns, the herbage taxa (Bassia scoparia, Euphorbia humifusa, Arnebia euchroma, and Salsola sp.) most correlated to n-3 PUFAs were highlighted to elucidate how diversification in dietary components was associated with the muscle FA profile of lambs. Our findings provide experimental evidence for future feeding research.
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Affiliation(s)
- Yanping Guo
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Xingang Zhao
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Ming Liu
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Can Zhang
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Yingjun Zhang
- Key Laboratory of Grasslands Management and Utilization, College of Grassland Science and Technology, China Agricultural University, Beijing 100193, China
| | - Qing Ma
- Research Center of Grass and Livestock, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan 750002, Ningxia, China
| | - Bing Wang
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Hailing Luo
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
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Macher TH, Schütz R, Arle J, Beermann AJ, Koschorreck J, Leese F. Beyond fish eDNA metabarcoding: Field replicates disproportionately improve the detection of stream associated vertebrate species. METABARCODING AND METAGENOMICS 2021. [DOI: 10.3897/mbmg.5.66557] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Fast, reliable, and comprehensive biodiversity monitoring data are needed for environmental decision making and management. Recent work on fish environmental DNA (eDNA) metabarcoding shows that aquatic diversity can be captured fast, reliably, and non-invasively at moderate costs. Because water in a catchment flows to the lowest point in the landscape, often a stream, it can collect traces of terrestrial species via surface or subsurface runoff along its way or when specimens come into direct contact with water (e.g., when drinking). Thus, fish eDNA metabarcoding data can provide information on fish but also on other vertebrate species that live in riparian habitats. This additional data may offer a much more comprehensive approach for assessing vertebrate diversity at no additional costs. Studies on how the sampling strategy affects species detection especially of stream-associated communities, however, are scarce. We therefore performed an analysis on the effects of biological replication on both fish as well as (semi-)terrestrial species detection. Along a 2 km stretch of the river Mulde (Germany), we collected 18 1-L water samples and analyzed the relation of detected species richness and quantity of biological replicates taken. We detected 58 vertebrate species, of which 25 were fish and lamprey, 18 mammals, and 15 birds, which account for 50%, 22.2%, and 7.4% of all native species to the German federal state of Saxony-Anhalt. However, while increasing the number of biological replicates resulted in only 24.8% more detected fish and lamprey species, mammal, and bird species richness increased disproportionately by 68.9% and 77.3%, respectively. Contrary, PCR replicates showed little stochasticity. We thus emphasize to increase the number of biological replicates when the aim is to improve general species detections. This holds especially true when the focus is on rare aquatic taxa or on (semi-)terrestrial species, the so-called ‘bycatch’. As a clear advantage, this information can be obtained without any additional sampling or laboratory effort when the sampling strategy is chosen carefully. With the increased use of eDNA metabarcoding as part of national fish bioassessment and monitoring programs, the complimentary information provided on bycatch can be used for biodiversity monitoring and conservation on a much broader scale.
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van Schrojenstein Lantman IM, Vesterinen EJ, Hertzog LR, Martel A, Verheyen K, Lens L, Bonte D. Body size and tree species composition determine variation in prey consumption in a forest-inhabiting generalist predator. Ecol Evol 2021; 11:8295-8309. [PMID: 34188887 PMCID: PMC8216911 DOI: 10.1002/ece3.7659] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 04/19/2021] [Accepted: 04/19/2021] [Indexed: 11/14/2022] Open
Abstract
Trophic interactions may strongly depend on body size and environmental variation, but this prediction has been seldom tested in nature. Many spiders are generalist predators that use webs to intercept flying prey. The size and mesh of orb webs increases with spider size, allowing a more efficient predation on larger prey. We studied to this extent the orb-weaving spider Araneus diadematus inhabiting forest fragments differing in edge distance, tree diversity, and tree species. These environmental variables are known to correlate with insect composition, richness, and abundance. We anticipated these forest characteristics to be a principle driver of prey consumption. We additionally hypothesized them to impact spider size at maturity and expect shifts toward larger prey size distributions in larger individuals independently from the environmental context. We quantified spider diet by means of metabarcoding of nearly 1,000 A. diadematus from a total of 53 forest plots. This approach allowed a massive screening of consumption dynamics in nature, though at the cost of identifying the exact prey identity, as well as their abundance and putative intraspecific variation. Our study confirmed A. diadematus as a generalist predator, with more than 300 prey ZOTUs detected in total. At the individual level, we found large spiders to consume fewer different species, but adding larger species to their diet. Tree species composition affected both prey species richness and size in the spider's diet, although tree diversity per se had no influence on the consumed prey. Edges had an indirect effect on the spider diet as spiders closer to the forest edge were larger and therefore consumed larger prey. We conclude that both intraspecific size variation and tree species composition shape the consumed prey of this generalist predator.
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Affiliation(s)
| | - Eero J. Vesterinen
- Spatial Foodweb Ecology GroupDepartment of Agricultural SciencesUniversity of HelsinkiHelsinkiFinland
- Department of EcologySwedish University of Agricultural SciencesUppsalaSweden
- Department of BiologyUniversity of TurkuTurkuFinland
| | - Lionel R. Hertzog
- Terrestrial Ecology UnitDepartment of BiologyGhent UniversityGentBelgium
- Thünen Institut for BiodiversityBraunschweigGermany
- Department Pathology, Bacteriology and Avian DiseasesGhent UniversityMerelbekeBelgium
| | - An Martel
- Thünen Institut for BiodiversityBraunschweigGermany
- Department Pathology, Bacteriology and Avian DiseasesGhent UniversityMerelbekeBelgium
| | - Kris Verheyen
- Forest & Nature LabDepartment of EnvironmentGhent UniversityGontrodeBelgium
| | - Luc Lens
- Terrestrial Ecology UnitDepartment of BiologyGhent UniversityGentBelgium
| | - Dries Bonte
- Terrestrial Ecology UnitDepartment of BiologyGhent UniversityGentBelgium
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Lee YF, Kuo YM, Chu WC, Lin YH, Chang HY, Chang HY, Chen WM. Perch time allocation and feeding efficiency of flycatching Rhinolophus formosae: an optimal foraging behavior? BMC ZOOL 2021; 6:13. [PMID: 37170294 PMCID: PMC10127097 DOI: 10.1186/s40850-021-00077-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 04/12/2021] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Flycatching bats are species-rare and comprise predominantly horseshoe bats (Rhinolophidae). Their hang-and-wait foraging mode and long constant-frequency echolocation calls offer advantages in energetics and prey detection, and may enable them apt to foraging optimally, yet not much is known about the foraging behavior of flycatching bats. Thus we assessed the perch use and foraging performance in the field by one of the largest horseshoe bats, Rhinolophus formosae, and offered insights on their perch time allocation.
Results
The perching-foraging behaviors of the bats did not differ significantly between forest settings, but the residence and giving-up time, mean attack, and attack rate were higher in the late spring-early summer, whereas the mean capture, capture rate, and attack efficiency were lower in the late summer when volant juveniles joined the nocturnal activity. The bats maintained flycatching and exhibited largely similar attack rates through the night with peak residence time around the midnight, but the capture rate and attack efficiency both reduced toward midnight and then increased toward the hours right before dawn. The attack rate was negatively correlated to the number of perches used and perch switch; by contrast, the capture rate was positively correlated with both factors. The total residence time at a site increased but mean residence time per perch decreased as the number of perches used and perch-switch increased. The giving-up time was inversely correlated to the attack rate and attack efficiency, and decreased with an increasing capture rate.
Conclusions
The bats increased perch switch at lower attack rates in early spring, but switched less frequently in late spring and prime summer months when insect abundance is higher. By scanning through a broad angular range for prey detection, and switching more frequently among perches, R. formosae foraged with an increased capture rate, and were able to remain at the site longer by slightly reducing their mean residence time per perch. Our results concur with the predictions of optimal foraging theory for patch selection and offer implications for further exploration of the foraging behavior of flycatching horseshoe bats.
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Furneaux B, Bahram M, Rosling A, Yorou NS, Ryberg M. Long- and short-read metabarcoding technologies reveal similar spatiotemporal structures in fungal communities. Mol Ecol Resour 2021; 21:1833-1849. [PMID: 33811446 DOI: 10.1111/1755-0998.13387] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 02/19/2021] [Accepted: 03/01/2021] [Indexed: 01/04/2023]
Abstract
Fungi form diverse communities and play essential roles in many terrestrial ecosystems, yet there are methodological challenges in taxonomic and phylogenetic placement of fungi from environmental sequences. To address such challenges, we investigated spatiotemporal structure of a fungal community using soil metabarcoding with four different sequencing strategies: short-amplicon sequencing of the ITS2 region (300-400 bp) with Illumina MiSeq, Ion Torrent Ion S5 and PacBio RS II, all from the same PCR library, as well as long-amplicon sequencing of the full ITS and partial LSU regions (1200-1600 bp) with PacBio RS II. Resulting community structure and diversity depended more on statistical method than sequencing technology. The use of long-amplicon sequencing enables construction of a phylogenetic tree from metabarcoding reads, which facilitates taxonomic identification of sequences. However, long reads present issues for denoising algorithms in diverse communities. We present a solution that splits the reads into shorter homologous regions prior to denoising, and then reconstructs the full denoised reads. In the choice between short and long amplicons, we suggest a hybrid approach using short amplicons for sampling breadth and depth, and long amplicons to characterize the local species pool for improved identification and phylogenetic analyses.
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Affiliation(s)
- Brendan Furneaux
- Program in Systematic Biology, Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | - Mohammad Bahram
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden.,Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Anna Rosling
- Program in Evolutionary Biology, Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
| | - Nourou S Yorou
- Research Unit in Tropical Mycology and Plant-Fungi Interactions, LEB, University of Parakou, Parakou, Benin
| | - Martin Ryberg
- Program in Systematic Biology, Department of Organismal Biology, Uppsala University, Uppsala, Sweden
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Wirta H, Abrego N, Miller K, Roslin T, Vesterinen E. DNA traces the origin of honey by identifying plants, bacteria and fungi. Sci Rep 2021; 11:4798. [PMID: 33637887 PMCID: PMC7910293 DOI: 10.1038/s41598-021-84174-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 02/03/2021] [Indexed: 01/31/2023] Open
Abstract
The regional origin of a food product commonly affects its value. To this, DNA-based identification of tissue remains could offer fine resolution. For honey, this would allow the usage of not only pollen but all plant tissue, and also that of microbes in the product, for discerning the origin. Here we examined how plant, bacterial and fungal taxa identified by DNA metabarcoding and metagenomics differentiate between honey samples from three neighbouring countries. To establish how the taxonomic contents of honey reflect the country of origin, we used joint species distribution modelling. At the lowest taxonomic level by metabarcoding, with operational taxonomic units, the country of origin explained the majority of variation in the data (70-79%), with plant and fungal gene regions providing the clearest distinction between countries. At the taxonomic level of genera, plants provided the most separation between countries with both metabarcoding and metagenomics. The DNA-based methods distinguish the countries more than the morphological pollen identification and the removal of pollen has only a minor effect on taxonomic recovery by DNA. As we find good resolution among honeys from regions with similar biota, DNA-based methods hold great promise for resolving honey origins among more different regions.
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Affiliation(s)
- Helena Wirta
- Faculty of Agriculture and Forestry, University of Helsinki, P.O. Box 27, 00014, Helsinki, Finland.
| | - Nerea Abrego
- Faculty of Agriculture and Forestry, University of Helsinki, P.O. Box 27, 00014, Helsinki, Finland
- Department of Biological and Environmental Science, University of Jyväskylä, P.O. Box 35, 40014, Jyväskylä, Finland
| | - Kirsten Miller
- Department of Ecology, Swedish University of Agricultural Sciences, P.O. Box 7044, 750 07, Uppsala, Sweden
- School of Natural and Environmental Sciences, Newcastle University, Newcastle-upon-Tyne, NE1 7RU, UK
| | - Tomas Roslin
- Faculty of Agriculture and Forestry, University of Helsinki, P.O. Box 27, 00014, Helsinki, Finland
- Department of Ecology, Swedish University of Agricultural Sciences, P.O. Box 7044, 750 07, Uppsala, Sweden
| | - Eero Vesterinen
- Department of Ecology, Swedish University of Agricultural Sciences, P.O. Box 7044, 750 07, Uppsala, Sweden
- Department of Biology, University of Turku, Turku, Finland
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38
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O'Rourke DR, Mangan MT, Mangan KE, Bokulich NA, MacManes MD, Foster JT. Lord of the Diptera (and Moths and a Spider): Molecular Diet Analyses and Foraging Ecology of Indiana Bats in Illinois. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.623655] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Effective management of endangered or threatened wildlife requires an understanding of how foraging habitats are used by those populations. Molecular diet analysis of fecal samples offers a cost-effective and non-invasive method to investigate how diets of wild populations vary with respect to spatial and temporal factors. For the federally endangered Indiana bat (Myotis sodalis), documenting its preferred food sources can provide critical information to promote effective conservation of this federally endangered species. Using cytochrome oxidase I amplicon sequence data from Indiana bat guano samples collected at two roosting areas in Cypress Creek National Wildlife Refuge, we found that dipteran taxa (i.e., flies) associated with riparian habitats were the most frequently detected taxon and represented the majority of the sequence diversity among the arthropods sampled. A select few arthropods from other taxa—especially spiders—are also likely important to Indiana bat diets in this refuge. A supervised learning analysis of diet components suggest only a small fraction of the frequently detected taxa are important contributors to spatial and temporal variation. Overall, these data depict the Indiana bat as a generalist consumer whose diet includes some prey items associated with particular seasonal or spatial components, along with other taxa repeatedly consumed throughout the entire foraging season. These molecular diet analyses suggest that protecting foraging resources specifically associated with the riparian habitat of Cypress Creek National Wildlife Refuge is essential to promote effective Indiana bat conservation.
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Marquina D, Buczek M, Ronquist F, Łukasik P. The effect of ethanol concentration on the morphological and molecular preservation of insects for biodiversity studies. PeerJ 2021; 9:e10799. [PMID: 33614282 PMCID: PMC7883690 DOI: 10.7717/peerj.10799] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 12/29/2020] [Indexed: 12/20/2022] Open
Abstract
Traditionally, insects collected for scientific purposes have been dried and pinned, or preserved in 70% ethanol. Both methods preserve taxonomically informative exoskeletal structures well but are suboptimal for preserving DNA for molecular biology. Highly concentrated ethanol (95–100%), preferred as a DNA preservative, has generally been assumed to make specimens brittle and prone to breaking. However, systematic studies on the correlation between ethanol concentration and specimen preservation are lacking. Here, we tested how preservative ethanol concentration in combination with different sample handling regimes affect the integrity of seven insect species representing four orders, and differing substantially in the level of sclerotization. After preservation and treatments (various levels of disturbance), we counted the number of appendages (legs, wings, antennae, or heads) that each specimen had lost. Additionally, we assessed the preservation of DNA after long-term storage by comparing the ratio of PCR amplicon copy numbers to an added artificial standard. We found that high ethanol concentrations indeed induce brittleness in insects. However, the magnitude and nature of the effect varied strikingly among species. In general, ethanol concentrations at or above 90% made the insects more brittle, but for species with robust, thicker exoskeletons, this did not translate to an increased loss of appendages. Neither freezing the samples nor drying the insects after immersion in ethanol had a negative effect on the retention of appendages. However, the morphology of the insects was severely damaged if they were allowed to dry. We also found that DNA preserves less well at lower ethanol concentrations when stored at room temperature for an extended period. However, the magnitude of the effect varies among species; the concentrations at which the number of COI amplicon copies relative to the standard was significantly decreased compared to 95% ethanol ranged from 90% to as low as 50%. While higher ethanol concentrations positively affect long-term DNA preservation, there is a clear trade-off between preserving insects for morphological examination and genetic analysis. The optimal ethanol concentration for the latter is detrimental for the former, and vice versa. These trade-offs need to be considered in large insect biodiversity surveys and other projects aiming to combine molecular work with traditional morphology-based characterization of collected specimens.
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Affiliation(s)
- Daniel Marquina
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.,Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Mateusz Buczek
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Krakow, Poland
| | - Fredrik Ronquist
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Piotr Łukasik
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.,Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Krakow, Poland
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40
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Eitzinger B, Roslin T, Vesterinen EJ, Robinson SI, O'Gorman EJ. Temperature affects both the Grinnellian and Eltonian dimensions of ecological niches – A tale of two Arctic wolf spiders. Basic Appl Ecol 2021. [DOI: 10.1016/j.baae.2021.01.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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41
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Wray AK, Peery MZ, Jusino MA, Kochanski JM, Banik MT, Palmer JM, Lindner DL, Gratton C. Predator preferences shape the diets of arthropodivorous bats more than quantitative local prey abundance. Mol Ecol 2020; 30:855-873. [PMID: 33301628 DOI: 10.1111/mec.15769] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 10/27/2020] [Accepted: 11/19/2020] [Indexed: 01/03/2023]
Abstract
Although most predators are generalists, the majority of studies on the association between prey availability and prey consumption have focused on specialist predators. To investigate the role of highly generalist predators in a complex food web, we measured the relationships between prey consumption and prey availability in two common arthropodivorous bats. Specifically, we used high-throughput amplicon sequencing coupled with a known mock community to characterize seasonal changes in little brown and big brown bat diets. We then linked spatiotemporal variation in prey consumption with quantitative prey availability estimated from intensive prey community sampling. We found that although quantitative prey availability fluctuated substantially over space and time, the most commonly consumed prey items were consistently detected in bat diets independently of their respective abundance. Positive relationships between prey abundance and probability of consumption were found only among prey groups that were less frequently detected in bat diets. While the probability of prey consumption was largely unrelated to abundance, the community structure of prey detected in bat diets was influenced by the local or regional abundance of prey. Observed patterns suggest that while little brown and big brown bats maintain preferences for particular prey independently of quantitative prey availability, total dietary composition may reflect some degree of opportunistic foraging. Overall, our findings suggest that generalist predators can display strong prey preferences that persist despite quantitative changes in prey availability.
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Affiliation(s)
- Amy K Wray
- Department of Forest and Wildlife Ecology, University of Wisconsin-Madison, Madison, WI, USA.,Department of Entomology, University of Wisconsin-Madison, Madison, WI, USA
| | - M Zachariah Peery
- Department of Forest and Wildlife Ecology, University of Wisconsin-Madison, Madison, WI, USA
| | - Michelle A Jusino
- Center for Forest Mycology Research, Northern Research Station, USDA Forest Service, Madison, WI, USA.,Department of Plant Pathology, University of Florida, Gainesville, FL, USA
| | - Jade M Kochanski
- Department of Entomology, University of Wisconsin-Madison, Madison, WI, USA
| | - Mark T Banik
- Center for Forest Mycology Research, Northern Research Station, USDA Forest Service, Madison, WI, USA
| | - Jonathan M Palmer
- Center for Forest Mycology Research, Northern Research Station, USDA Forest Service, Madison, WI, USA
| | - Daniel L Lindner
- Center for Forest Mycology Research, Northern Research Station, USDA Forest Service, Madison, WI, USA
| | - Claudio Gratton
- Department of Entomology, University of Wisconsin-Madison, Madison, WI, USA
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Novella‐Fernandez R, Ibañez C, Juste J, Clare EL, Doncaster CP, Razgour O. Trophic resource partitioning drives fine-scale coexistence in cryptic bat species. Ecol Evol 2020; 10:14122-14136. [PMID: 33391705 PMCID: PMC7771180 DOI: 10.1002/ece3.7004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 10/14/2020] [Accepted: 10/20/2020] [Indexed: 01/01/2023] Open
Abstract
Understanding the processes that enable species coexistence has important implications for assessing how ecological systems will respond to global change. Morphology and functional similarity increase the potential for competition, and therefore, co-occurring morphologically similar but genetically unique species are a good model system for testing coexistence mechanisms. We used DNA metabarcoding and high-throughput sequencing to characterize for the first time the trophic ecology of two recently described cryptic bat species with parapatric ranges, Myotis escalerai and Myotis crypticus. We collected fecal samples from allopatric and sympatric regions and from syntopic and allotopic locations within the sympatric region to describe the diets both taxonomically and functionally and compare prey consumption with prey availability. The two bat species had highly similar diets characterized by high arthropod diversity, particularly Lepidoptera, Diptera and Araneae, and a high proportion of prey that is not volant at night, which points to extensive use of gleaning. Diet overlap at the prey item level was lower in syntopic populations, supporting trophic shift under fine-scale co-occurrence. Furthermore, the diet of M. escalerai had a marginally lower proportion of not nocturnally volant prey in syntopic populations, suggesting that the shift in diet may be driven by a change in foraging mode. Our findings suggest that fine-scale coexistence mechanisms can have implications for maintaining broad-scale diversity patterns. This study highlights the importance of including both allopatric and sympatric populations and choosing meaningful spatial scales for detecting ecological patterns. We conclude that a combination of high taxonomic resolution with a functional approach helps identify patterns of niche shift.
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Affiliation(s)
| | | | - Javier Juste
- Estación Biológica de Doñana (CSIC)SevillaSpain
- CIBER Epidemiology and Public Health (CIBERESP)MadridSpain
| | - Elizabeth L. Clare
- School of Biological and Chemical SciencesQueen Mary University of LondonLondonUK
| | | | - Orly Razgour
- School of Biological SciencesUniversity of SouthamptonSouthamptonUK
- BiosciencesUniversity of ExeterExeterUK
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Puig-Montserrat X, Flaquer C, Gómez-Aguilera N, Burgas A, Mas M, Tuneu C, Marquès E, López-Baucells A. Bats actively prey on mosquitoes and other deleterious insects in rice paddies: Potential impact on human health and agriculture. PEST MANAGEMENT SCIENCE 2020; 76:3759-3769. [PMID: 32431084 DOI: 10.1002/ps.5925] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 04/28/2020] [Accepted: 05/20/2020] [Indexed: 05/11/2023]
Abstract
BACKGROUND The fact that bats suppress agricultural pests has been measured for some particular dyads of predator and prey species in both economic and food security terms. The recent emergence of new molecular techniques allows for more precise screenings of bat's diet than the traditional visual identification systems and provides further evidence that bats consume an ample array of agricultural pest species. The main focus of the regulatory services that bats provide in agroecosystems has been on crop pests that cause yield losses. Rice paddies constitute a particular agronomic system with specific challenges, not only related to crop productivity but also to human health. Dipteran density in such ecosystems poses a serious threat to human wellbeing and hinders crop production. Mosquitoes cause direct harm to human populations, transmitting a number of infectious diseases. Non-biting midges (Chironomidae) can consume and weaken rice seedlings and can cause major yield losses. RESULTS Mosquito populations and bat activity were assessed in rice paddies of Montgrí, Medes i Baix Ter Natural Park (NE Iberian Peninsula). Molecular analyses of bats faeces (6-weekly samples of 15 faeces each between mid-August and September) proved the presence of both mosquitoes and nonbiting midges in all diet samples. Furthermore, bat activity at the sampling locations was related to adult mosquito density. CONCLUSION Our results suggest that bats actively exploit the emergence of adult mosquitoes and further prove that they prey on mosquitoes, nonbiting midges and other deleterious insects. Promoting the presence of bats next to human settlements in such agroecosystems may constitute a biological control system with direct impact on both human health and crop yield. © 2020 Society of Chemical Industry.
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Affiliation(s)
- Xavier Puig-Montserrat
- Natural Sciences Museum of Granollers, Granollers, Spain
- Galanthus Association, Celrà, Spain
| | - Carles Flaquer
- Natural Sciences Museum of Granollers, Granollers, Spain
| | | | | | - Maria Mas
- Natural Sciences Museum of Granollers, Granollers, Spain
| | - Carme Tuneu
- Natural Sciences Museum of Granollers, Granollers, Spain
| | - Eduard Marquès
- Servei de Control de Mosquits de la Badia de Roses i del Baix Ter, Castelló d'Empúries, Spain
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44
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Pervushina EM, Gizullina OR. Experience in Researching of Feeding Selectivity of Vespertilio murinus (Chiroptera, Vespertilionidae). RUSS J ECOL+ 2020. [DOI: 10.1134/s1067413620050094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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45
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Vesterinen EJ, Kaunisto KM, Lilley TM. A global class reunion with multiple groups feasting on the declining insect smorgasbord. Sci Rep 2020; 10:16595. [PMID: 33024156 PMCID: PMC7539006 DOI: 10.1038/s41598-020-73609-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 09/15/2020] [Indexed: 12/05/2022] Open
Abstract
We report a detection of a surprising similarity in the diet of predators across distant phyla. Though just a first glimpse into the subject, our discovery contradicts traditional aspects of biology, as the earliest notions in ecology have linked the most severe competition of resources with evolutionary relatedness. We argue that our finding deserves more research, and propose a plan to reveal more information on the current biodiversity loss around the world. While doing so, we expand the recently proposed conservation roadmaps into a parallel study of global interaction networks.
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Affiliation(s)
- Eero J Vesterinen
- Department of Biology, University of Turku, Turku, Finland.
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden.
| | | | - Thomas M Lilley
- Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
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46
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O'Rourke DR, Bokulich NA, Jusino MA, MacManes MD, Foster JT. A total crapshoot? Evaluating bioinformatic decisions in animal diet metabarcoding analyses. Ecol Evol 2020; 10:9721-9739. [PMID: 33005342 PMCID: PMC7520210 DOI: 10.1002/ece3.6594] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 06/29/2020] [Accepted: 07/01/2020] [Indexed: 01/01/2023] Open
Abstract
Metabarcoding studies provide a powerful approach to estimate the diversity and abundance of organisms in mixed communities in nature. While strategies exist for optimizing sample and sequence library preparation, best practices for bioinformatic processing of amplicon sequence data are lacking in animal diet studies. Here we evaluate how decisions made in core bioinformatic processes, including sequence filtering, database design, and classification, can influence animal metabarcoding results. We show that denoising methods have lower error rates compared to traditional clustering methods, although these differences are largely mitigated by removing low-abundance sequence variants. We also found that available reference datasets from GenBank and BOLD for the animal marker gene cytochrome oxidase I (COI) can be complementary, and we discuss methods to improve existing databases to include versioned releases. Taxonomic classification methods can dramatically affect results. For example, the commonly used Barcode of Life Database (BOLD) Classification API assigned fewer names to samples from order through species levels using both a mock community and bat guano samples compared to all other classifiers (vsearch-SINTAX and q2-feature-classifier's BLAST + LCA, VSEARCH + LCA, and Naive Bayes classifiers). The lack of consensus on bioinformatics best practices limits comparisons among studies and may introduce biases. Our work suggests that biological mock communities offer a useful standard to evaluate the myriad computational decisions impacting animal metabarcoding accuracy. Further, these comparisons highlight the need for continual evaluations as new tools are adopted to ensure that the inferences drawn reflect meaningful biology instead of digital artifacts.
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Affiliation(s)
- Devon R. O'Rourke
- Department of Molecular, Cellular, and Biomedical SciencesUniversity of New HampshireDurhamNHUSA
- Pathogen and Microbiome InstituteNorthern Arizona UniversityFlagstaffAZUSA
| | - Nicholas A. Bokulich
- Laboratory of Food Systems BiotechnologyInstitute of Food, Nutrition, and HealthETH ZurichZurichSwitzerland
| | - Michelle A. Jusino
- Biology DepartmentWilliam & MaryWilliamsburgVAUSA
- Center for Forest Mycology ResearchUSDA Forest ServiceNorthern Research StationMadisonUSA
| | - Matthew D. MacManes
- Department of Molecular, Cellular, and Biomedical SciencesUniversity of New HampshireDurhamNHUSA
| | - Jeffrey T. Foster
- Department of Molecular, Cellular, and Biomedical SciencesUniversity of New HampshireDurhamNHUSA
- Pathogen and Microbiome InstituteNorthern Arizona UniversityFlagstaffAZUSA
- Department of Biological SciencesNorthern Arizona UniversityFlagstaffAZUSA
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47
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Gaultier SP, Blomberg AS, Ijäs A, Vasko V, Vesterinen EJ, Brommer JE, Lilley TM. Bats and Wind Farms: The Role and Importance of the Baltic Sea Countries in the European Context of Power Transition and Biodiversity Conservation. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:10385-10398. [PMID: 32830494 PMCID: PMC7497642 DOI: 10.1021/acs.est.0c00070] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2020] [Revised: 07/01/2020] [Accepted: 07/30/2020] [Indexed: 06/11/2023]
Abstract
Although labeled as environmentally friendly, wind power can have negative impacts on the environment, such as habitat destruction or wildlife fatalities. Considering the distribution and migratory characteristics of European bats, the negative effects of wind power should be addressed on an appropriate scale. This review summarizes the current state of knowledge on interactions between wind farms and bats in Europe, and compares it with the situation in the countries of the European boreal biogeographic region. We analyzed data from papers published in international and national scientific journals, focusing on studies conducted in Europe. The issue of the impacts wind power has on bats is clearly overlooked in most of the countries of the European boreal region, with low volumes of research available on the topic. This is probably due to fewer wind farms in the area, making this recent issue a less-prioritized topic. However, the Baltic Sea, and the countries surrounding it, are of extreme importance with regards to bat migration, especially for the Pipistrellus nathusii. Therefore, more research on wind power and bats is needed in this region, as well as more cooperation between all the stakeholders.
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Affiliation(s)
- Simon P. Gaultier
- Biodiversity
Unit, University of Turku, Vesilinnantie 5 20500 Turku, Finland
| | - Anna S. Blomberg
- Department
of Biology, University of Turku, Vesilinnantie 5 20500 Turku, Finland
| | - Asko Ijäs
- Brahea
Centre/Centre for Maritime Studies, University
of Turku, Pohjoisranta 11 D 28100 Pori, Finland
| | - Ville Vasko
- Finnish
Museum of Natural History, University of
Helsinki, Pohjoinen Rautatiekatu 13, 00100 Helsinki, Finland
| | - Eero J. Vesterinen
- Biodiversity
Unit, University of Turku, Vesilinnantie 5 20500 Turku, Finland
- Department
of Biology, University of Turku, Vesilinnantie 5 20500 Turku, Finland
- Department
of Insect Ecology, Swedish University of
Agricultural Sciences, Almas Allé 8, 750 07 Uppsala, Sweden
| | - Jon E. Brommer
- Department
of Biology, University of Turku, Vesilinnantie 5 20500 Turku, Finland
| | - Thomas M. Lilley
- Finnish
Museum of Natural History, University of
Helsinki, Pohjoinen Rautatiekatu 13, 00100 Helsinki, Finland
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48
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Geiser F. Seasonal Expression of Avian and Mammalian Daily Torpor and Hibernation: Not a Simple Summer-Winter Affair †. Front Physiol 2020; 11:436. [PMID: 32508673 PMCID: PMC7251182 DOI: 10.3389/fphys.2020.00436] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Accepted: 04/08/2020] [Indexed: 12/17/2022] Open
Abstract
Daily torpor and hibernation (multiday torpor) are the most efficient means for energy conservation in endothermic birds and mammals and are used by many small species to deal with a number of challenges. These include seasonal adverse environmental conditions and low food/water availability, periods of high energetic demands, but also reduced foraging options because of high predation pressure. Because such challenges differ among regions, habitats and food consumed by animals, the seasonal expression of torpor also varies, but the seasonality of torpor is often not as clear-cut as is commonly assumed and differs between hibernators and daily heterotherms expressing daily torpor exclusively. Hibernation is found in mammals from all three subclasses from the arctic to the tropics, but is known for only one bird. Several hibernators can hibernate for an entire year or express torpor throughout the year (8% of species) and more hibernate from late summer to spring (14%). The most typical hibernation season is the cold season from fall to spring (48%), whereas hibernation is rarely restricted to winter (6%). In hibernators, torpor expression changes significantly with season, with strong seasonality mainly found in the sciurid and cricetid rodents, but seasonality is less pronounced in the marsupials, bats and dormice. Daily torpor is diverse in both mammals and birds, typically is not as seasonal as hibernation and torpor expression does not change significantly with season. Torpor in spring/summer has several selective advantages including: energy and water conservation, facilitation of reproduction or growth during development with limited resources, or minimisation of foraging and thus exposure to predators. When torpor is expressed in spring/summer it is usually not as deep and long as in winter, because of higher ambient temperatures, but also due to seasonal functional plasticity. Unlike many other species, subtropical nectarivorous blossom-bats and desert spiny mice use more frequent and pronounced torpor in summer than in winter, which is related to seasonal availability of nectar or water. Thus, seasonal use of torpor is complex and differs among species and habitats.
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Affiliation(s)
- Fritz Geiser
- Centre for Behavioural and Physiological Ecology, Zoology CO2, University of New England, Armidale, NSW, Australia
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49
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Magalhães de Oliveira HF, Camargo NF, Hemprich-Bennett DR, Rodríguez-Herrera B, Rossiter SJ, Clare EL. Wing morphology predicts individual niche specialization in Pteronotus mesoamericanus (Mammalia: Chiroptera). PLoS One 2020; 15:e0232601. [PMID: 32392221 PMCID: PMC7213686 DOI: 10.1371/journal.pone.0232601] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 04/17/2020] [Indexed: 12/30/2022] Open
Abstract
Morphological variation between individuals can increase niche segregation and decrease intraspecific competition when heterogeneous individuals explore their environment in different ways. Among bat species, wing shape correlates with flight maneuverability and habitat use, with species that possess broader wings typically foraging in more cluttered habitats. However, few studies have investigated the role of morphological variation in bats for niche partitioning at the individual level. To determine the relationship between wing shape and diet, we studied a population of the insectivorous bat species Pteronotus mesoamericanus in the dry forest of Costa Rica. Individual diet was resolved using DNA metabarcoding, and bat wing shape was assessed using geometric morphometric analysis. Inter-individual variation in wing shape showed a significant relationship with both dietary dissimilarity based on Bray-Curtis estimates, and nestedness derived from an ecological network. Individual bats with broader and more rounded wings were found to feed on a greater diversity of arthropods (less nested) in comparison to individuals with triangular and pointed wings (more nested). We conclude that individual variation in bat wing morphology can impact foraging efficiency leading to the observed overall patterns of diet specialization and differentiation within the population.
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Affiliation(s)
- Hernani Fernandes Magalhães de Oliveira
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, Iowa, United States of America
- School of Biological and Chemical Sciences, Queen Mary University of London, London, England, United Kingdom
| | | | - David R. Hemprich-Bennett
- School of Biological and Chemical Sciences, Queen Mary University of London, London, England, United Kingdom
- Department of Zoology, University of Oxford, Oxford, England, United Kingdom
| | | | - Stephen J. Rossiter
- School of Biological and Chemical Sciences, Queen Mary University of London, London, England, United Kingdom
| | - Elizabeth L. Clare
- School of Biological and Chemical Sciences, Queen Mary University of London, London, England, United Kingdom
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50
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Alberdi A, Razgour O, Aizpurua O, Novella-Fernandez R, Aihartza J, Budinski I, Garin I, Ibáñez C, Izagirre E, Rebelo H, Russo D, Vlaschenko A, Zhelyazkova V, Zrnčić V, Gilbert MTP. DNA metabarcoding and spatial modelling link diet diversification with distribution homogeneity in European bats. Nat Commun 2020; 11:1154. [PMID: 32123172 PMCID: PMC7052159 DOI: 10.1038/s41467-020-14961-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 01/29/2020] [Indexed: 11/09/2022] Open
Abstract
Inferences of the interactions between species' ecological niches and spatial distribution have been historically based on simple metrics such as low-resolution dietary breadth and range size, which might have impeded the identification of meaningful links between niche features and spatial patterns. We analysed the relationship between dietary niche breadth and spatial distribution features of European bats, by combining continent-wide DNA metabarcoding of faecal samples with species distribution modelling. Our results show that while range size is not correlated with dietary features of bats, the homogeneity of the spatial distribution of species exhibits a strong correlation with dietary breadth. We also found that dietary breadth is correlated with bats' hunting flexibility. However, these two patterns only stand when the phylogenetic relations between prey are accounted for when measuring dietary breadth. Our results suggest that the capacity to exploit different prey types enables species to thrive in more distinct environments and therefore exhibit more homogeneous distributions within their ranges.
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Affiliation(s)
- Antton Alberdi
- Centre for Evolutionary Hologenomics, GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353, Copenhagen, Denmark.
| | - Orly Razgour
- Biological Sciences, University of Southampton, Southampton, SO17 1BJ, UK.,Biosciences, University of Exeter, Exeter, EX4 4PY, UK
| | - Ostaizka Aizpurua
- Centre for Evolutionary Hologenomics, GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353, Copenhagen, Denmark
| | | | | | - Ivana Budinski
- Department of Genetic Research, Institute for Biological Research "Siniša Stanković", University of Belgrade, Belgrade, 11060, Serbia
| | - Inazio Garin
- University of the Basque Country UPV/EHU, 48940, Leioa, Spain
| | - Carlos Ibáñez
- Doñana Biological Station, CSIC, 41092, Seville, Spain
| | - Eñaut Izagirre
- University of the Basque Country UPV/EHU, 48940, Leioa, Spain.,Basque Centre for Climate Change BC3, 48940, Leioa, Spain
| | - Hugo Rebelo
- CIBIO-InBIO, Centro de Investigação em Biodiversidade Recursos e Genéticos, Universidade do Porto, Vairão, Portugal.,CIBIO-InBIO, Instituto Superior de Agronomia, Universidade de Lisboa, 1349-017, Lisboa, Portugal
| | - Danilo Russo
- Wildlife Research Unit, Dipartimento di Agraria, Università degli Studi di Napoli Federico II, 80055, Portici, Naples, Italy
| | - Anton Vlaschenko
- Bat Rehabilitation Center of Feldman Ecopark, Kharkiv, 62340, Ukraine
| | - Violeta Zhelyazkova
- National Museum of Natural History, Bulgarian Academy of Sciences, 1 Tsar Osvoboditel Blvd., 1000, Sofia, Bulgaria
| | - Vida Zrnčić
- Croatian Biospeleological Society, HR-10000, Zagreb, Croatia
| | - M Thomas P Gilbert
- Centre for Evolutionary Hologenomics, GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353, Copenhagen, Denmark.,Norwegian University of Science and Technology, University Museum, 7491, Trondheim, Norway
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