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Li W, Cheng L, He X, He G, Liu Y, Sang Z, Wang Y, Shao M, Xiong T, Xu H, Zhao J. Gut fungi of black-necked cranes (Grus nigricollis) respond to dietary changes during wintering. BMC Microbiol 2024; 24:232. [PMID: 38951807 PMCID: PMC11218170 DOI: 10.1186/s12866-024-03396-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Accepted: 06/20/2024] [Indexed: 07/03/2024] Open
Abstract
BACKGROUND Migratory birds exhibit heterogeneity in foraging strategies during wintering to cope with environmental and migratory pressures, and gut bacteria respond to changes in host diet. However, less is known about the dynamics of diet and gut fungi during the wintering period in black-necked cranes (Grus nigricollis). RESULTS In this work, we performed amplicon sequencing of the trnL-P6 loop and ITS1 regions to characterize the dietary composition and gut fungal composition of black-necked cranes during wintering. Results indicated that during the wintering period, the plant-based diet of black-necked cranes mainly consisted of families Poaceae, Solanaceae, and Polygonaceae. Among them, the abundance of Solanaceae, Polygonaceae, Fabaceae, and Caryophyllaceae was significantly higher in the late wintering period, which also led to a more even consumption of various food types by black-necked cranes during this period. The diversity of gut fungal communities and the abundance of core fungi were more conserved during the wintering period, primarily dominated by Ascomycota and Basidiomycota. LEfSe analysis (P < 0.05, LDA > 2) found that Pyxidiophora, Pseudopeziza, Sporormiella, Geotrichum, and Papiliotrema were significantly enriched in early winter, Ramularia and Dendryphion were significantly enriched in mid-winter, Barnettozyma was significantly abundant in late winter, and Pleuroascus was significantly abundant in late winter. Finally, mantel test revealed a significant correlation between winter diet and gut fungal. CONCLUSIONS This study revealed the dynamic changes in the food composition and gut fungal community of black-necked cranes during wintering in Dashanbao. In the late wintering period, their response to environmental and migratory pressures was to broaden their diet, increase the intake of non-preferred foods, and promote a more balanced consumption ratio of various foods. Balanced food composition played an important role in stabilizing the structure of the gut fungal community. While gut fungal effectively enhanced the host's food utilization rate, they may also faced potential risks of introducing pathogenic fungi. Additionally, we recongnized the limitations of fecal testing in studying the composition of animal gut fungal, as it cannot effectively distinguished between fungal taxa from food or soil inadvertently ingested and intestines. Future research on functions such as cultivation and metagenomics may further elucidate the role of fungi in the gut ecosystem.
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Affiliation(s)
- Wenhao Li
- College of Agronomy and Life Sciences, Zhaotong University, Zhaotong, 657000, China
- College of Life Science, Sichuan Agricultural University, No. 46, Xinkang Road, Yucheng District, Ya'an, Sichuan, 625014, China
| | - Lijun Cheng
- College of Agronomy and Life Sciences, Zhaotong University, Zhaotong, 657000, China
- Yunnan Key Laboratory of Gastrodia and Fungi Symbiotic Biology, Zhaotong University, Zhaotong, 657000, China
| | - Xin He
- Sichuan Academy of Grassland Sciences, Chengdu, 610000, China
| | - Guiwen He
- College of Agronomy and Life Sciences, Zhaotong University, Zhaotong, 657000, China
- Yunnan Key Laboratory of Gastrodia and Fungi Symbiotic Biology, Zhaotong University, Zhaotong, 657000, China
| | - Yutong Liu
- Sichuan Academy of Grassland Sciences, Chengdu, 610000, China
| | - Zhenglin Sang
- College of Agronomy and Life Sciences, Zhaotong University, Zhaotong, 657000, China
- Yunnan Key Laboratory of Gastrodia and Fungi Symbiotic Biology, Zhaotong University, Zhaotong, 657000, China
| | - Yuanjian Wang
- Management Bureau of Dashanbao Black-Necked Crane National Nature Reserve, Zhaotong, Yunnan Province, 657000, China
| | - Mingcui Shao
- Management Bureau of Dashanbao Black-Necked Crane National Nature Reserve, Zhaotong, Yunnan Province, 657000, China
| | - Tingsong Xiong
- Management Bureau of Dashanbao Black-Necked Crane National Nature Reserve, Zhaotong, Yunnan Province, 657000, China
| | - Huailiang Xu
- College of Life Science, Sichuan Agricultural University, No. 46, Xinkang Road, Yucheng District, Ya'an, Sichuan, 625014, China.
| | - Junsong Zhao
- College of Agronomy and Life Sciences, Zhaotong University, Zhaotong, 657000, China.
- Yunnan Key Laboratory of Gastrodia and Fungi Symbiotic Biology, Zhaotong University, Zhaotong, 657000, China.
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Vescera C, Van Vyve C, Smits Q, Michaux JR. All-you-can-eat buffet: A spider-specialized bat species (Myotis emarginatus) turns into a pest fly eater around cattle. PLoS One 2024; 19:e0302028. [PMID: 38718094 PMCID: PMC11078406 DOI: 10.1371/journal.pone.0302028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 03/26/2024] [Indexed: 05/12/2024] Open
Abstract
Determining the dietary spectrum of European insectivorous bats over time is the cornerstone of their conservation, as it will aid our understanding of foraging behavior plasticity in response to plummeting insect populations. Despite the global decline in insects, a restricted number of arthropod pest species thrive. Yet past research has overlooked the potential of European bats to suppress pests harmful to woodlands or livestock, in spite of their economic relevance. Here we investigated the diet composition, its breeding season variations and pest consumption of an insectivorous bat species (Myotis emarginatus), at the northern edge of its range (Wallonia, Belgium). We also explored the prey ecology to gain insight into the hunting strategies and foraging habitats of this bat species. We used DNA metabarcoding to amplify two COI markers within 195 bat droppings collected in June, July and August, thereby identifying 512 prey taxa predominated by Diptera, Araneae and Lepidoptera. Overall, in 97% of the samples we detected at least one of the 58 potential pest taxa, 41 of which targeting trees. The June samples were marked by a diet rich in orb-weaver spiders, in accordance with the archetypal diet of M. emarginatus bats. However, during the highly energy demanding July-August parturition and lactation period, roughly 55% of the dropping samples contained two cattle fly pests (Stomoxys calcitrans and Musca domestica). Moreover, among the 88 Diptera species preyed upon by M. emarginatus in July and August, these flies accounted for around 50% of the taxa occurrences. This plasticity-the switch from a spider-rich to a fly-rich diet-seems providential considering the dramatic ongoing drop in insect populations but this involves ensuring bat-friendly cattle farming. Our results revealed that bats widely consume pest entomofauna, thereby highlighting their potential role as allies of forest managers and farmers.
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Affiliation(s)
- Chloé Vescera
- Conservation Genetics Laboratory, University of Liège, Liège, Belgium
| | | | - Quentin Smits
- Département de l’Etude du Milieu Naturel et Agricole (DEMNA), Service Public de Wallonie (SPW), Gembloux, Belgium
| | - Johan R. Michaux
- Conservation Genetics Laboratory, University of Liège, Liège, Belgium
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Hernández M, Hereira-Pacheco S, Alberdi A, Díaz DE LA Vega-Pérez AH, Estrada-Torres A, Ancona S, Navarro-Noya YE. DNA metabarcoding reveals seasonal changes in diet composition across four arthropod-eating lizard species (Phrynosomatidae: Sceloporus). Integr Zool 2024; 19:480-495. [PMID: 37550887 DOI: 10.1111/1749-4877.12755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/09/2023]
Abstract
Diet composition and its ecological drivers are rarely investigated in coexisting closely related species. We used a molecular approach to characterize the seasonal variation in diet composition in four spiny lizard species inhabiting a mountainous ecosystem. DNA metabarcoding revealed that the lizards Sceloporus aeneus, S. bicanthalis, S. grammicus, and S. spinosus mostly consumed arthropods of the orders Hemiptera, Araneae, Hymenoptera, and Coleoptera. The terrestrial lizards S. aeneus and S. bicanthalis mostly predated ants and spiders, whereas the arboreal-saxicolous S. grammicus and saxicolous S. spinosus largely consumed grasshoppers and leafhoppers. The taxonomic and phylogenetic diversity of the prey was higher during the dry season than the rainy season, likely because reduced prey availability in the dry season forced lizards to diversify their diets to meet their nutritional demands. Dietary and phylogenetic composition varied seasonally depending on the species, but only dietary composition varied with altitude. Seasonal dietary turnover was greater in S. spinosus than in S. bicanthalis, suggesting site-specific seasonal variability in prey availability; no other differences among species were observed. S. bicanthalis, which lives at the highest altitude in our study site, displayed interseasonal variation in diet breadth. Dietary differences were correlated with the species' feeding strategies and elevational distribution, which likely contributed to the coexistence of these lizard species in the studied geographic area and beyond.
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Affiliation(s)
- Mauricio Hernández
- Doctorado en Ciencias Biológicas, Centro Tlaxcala de Biología de la Conducta, Universidad Autónoma de Tlaxcala, Tlaxcala, Mexico
| | - Stephanie Hereira-Pacheco
- Estación Científica La Malinche, Centro Tlaxcala de Biología de la Conducta, Universidad Autónoma de Tlaxcala, Tlaxcala, Mexico
| | - Antton Alberdi
- Center for Evolutionary Hologenomics, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Aníbal H Díaz DE LA Vega-Pérez
- Consejo Nacional de Ciencia y Tecnología-Centro Tlaxcala de Biología de la Conducta, Universidad Autónoma de Tlaxcala, Tlaxcala, Mexico
| | - Arturo Estrada-Torres
- Estación Científica La Malinche, Centro Tlaxcala de Biología de la Conducta, Universidad Autónoma de Tlaxcala, Tlaxcala, Mexico
| | - Sergio Ancona
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Yendi E Navarro-Noya
- Laboratorio de Interacciones Bióticas, Centro de Investigación en Ciencias Biológicas, Universidad Autónoma de Tlaxcala, San Felipe Ixtacuixtla, Tlaxcala, Mexico
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Li L, Yin X, Wan Q, Rusitanmu D, Han J. Diet Diversity of the Fluviatile Masu Salmon, Oncorhynchus masou (Brevoort 1856) Revealed via Gastrointestinal Environmental DNA Metabarcoding and Morphological Identification of Contents. BIOLOGY 2024; 13:129. [PMID: 38392347 PMCID: PMC10887057 DOI: 10.3390/biology13020129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 02/15/2024] [Accepted: 02/16/2024] [Indexed: 02/24/2024]
Abstract
Masu salmon, Oncorhynchus masou (Brevoort 1856), a commercially important fish species endemic to the North Pacific Ocean, attained national second-level protected animal status in China in 2021. Despite this recognition, knowledge about the trophic ecology of this fish remains limited. This study investigated the diet diversity of fluviatile Masu salmon in the Mijiang River, China, utilizing the gastrointestinal tract environmental DNA (GITeDNA) metabarcoding and morphological identification. The results revealed a diverse prey composition, ranging from terrestrial and aquatic invertebrates to small fishes. The fluviatile Masu salmon in general consumed noteworthily more aquatic prey than terrestrial prey. There were much more prey taxa and a higher diet diversity detected by GITeDNA metabarcoding than by morphological identification. GITeDNA metabarcoding showed that larger and older Masu salmon consumed significantly more terrestrial insects than aquatic prey species did, with 7366 verses 5012 sequences in the group of ≥20 cm, 9098 verses 4743 sequences in the group of ≥100 g and 11,540 verses 729 sequences in the group of age 3+. GITeDNA metabarcoding also showed size- and age-related diet diversity, indicating that the dietary niche breadth and trophic diversity of larger and older Masu salmon increased with food resources expanding to more terrestrial prey. Terrestrial invertebrates of riparian habitats play a vital role in the diet of fluviatile Masu salmon, especially larger individuals, highlighting their importance in connecting aquatic and terrestrial food webs. Conservation plans should prioritize the protection and restoration of riparian habitats. This study advocates the combined use of GITeDNA metabarcoding and morphological observation for a comprehensive understanding of fish diet diversity.
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Affiliation(s)
- Lijuan Li
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, No. 19 Xin Jie Kou Wai Avenue, Beijing 100875, China
| | - Xuwang Yin
- Liaoning Provincial Key Laboratory for Hydrobiology, College of Fisheries and Life Science, Dalian Ocean University, No. 52 Hei Shi Jiao Avenue, Dalian 116000, China
| | - Qianruo Wan
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, No. 19 Xin Jie Kou Wai Avenue, Beijing 100875, China
| | - Dilina Rusitanmu
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, No. 19 Xin Jie Kou Wai Avenue, Beijing 100875, China
| | - Jie Han
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, No. 19 Xin Jie Kou Wai Avenue, Beijing 100875, China
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Curd EE, Gal L, Gallego R, Silliman K, Nielsen S, Gold Z. rCRUX: A Rapid and Versatile Tool for Generating Metabarcoding Reference libraries in R. ENVIRONMENTAL DNA (HOBOKEN, N.J.) 2024; 6:e489. [PMID: 38370872 PMCID: PMC10871694 DOI: 10.1002/edn3.489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 10/19/2023] [Indexed: 02/20/2024]
Abstract
The sequencing revolution requires accurate taxonomic classification of DNA sequences. Key to making accurate taxonomic assignments are curated, comprehensive reference barcode databases. However, the generation and curation of such databases has remained challenging given the large and continuously growing volumes of both DNA sequence data and novel reference barcode targets. Monitoring and research applications require a greater diversity of specialized gene regions and targeted taxa then are currently curated by professional staff. Thus there is a growing need for an easy to implement computational tool that can generate comprehensive metabarcoding reference libraries for any bespoke locus. We address this need by reimagining CRUX from the Anacapa Toolkit and present the rCRUX package in R which, like it's predecessor, relies on sequence homology and PCR primer compatibility instead of keyword-searches to avoid limitations of user-defined metadata. The typical workflow involves searching for plausible seed amplicons (get_seeds_local() or get_seeds_remote()) by simulating in silico PCR to acquire a set of sequences analogous to PCR products containing a user-defined set of primer sequences. Next, these seeds are used to iteratively blast search seed sequences against a local copy of the National Center for Biotechnology Information (NCBI) formatted nt database using a taxonomic-rank based stratified random sampling approach ( blast_seeds() ). This results in a comprehensive set of sequence matches. This database is dereplicated and cleaned (derep_and_clean_db()) by identifying identical reference sequences and collapsing the taxonomic path to the lowest taxonomic agreement across all matching reads. This results in a curated, comprehensive database of primer-specific reference barcode sequences from NCBI. Databases can then be compared (compare_db()) to determine read and taxonomic overlap. We demonstrate that rCRUX provides more comprehensive reference databases for the MiFish Universal Teleost 12S, Taberlet trnl, fungal ITS, and Leray CO1 loci than CRABS, MetaCurator, RESCRIPt, and ecoPCR reference databases. We then further demonstrate the utility of rCRUX by generating 24 reference databases for 20 metabarcoding loci, many of which lack dedicated reference database curation efforts. The rCRUX package provides a simple to use tool for the generation of curated, comprehensive reference databases for user-defined loci, facilitating accurate and effective taxonomic classification of metabarcoding and DNA sequence efforts broadly.
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Affiliation(s)
- Emily E. Curd
- Vermont Biomedical Research Network, University of Vermont, VT, USA
| | - Luna Gal
- Landmark College, VT, USA
- California Cooperative Oceanic Fisheries Investigations (CalCOFI), Scripps Institution of Oceanography, University of California San Diego (UCSD), La Jolla, CA, USA
| | - Ramon Gallego
- Departamento de Biología, Universidad Autónoma de Madrid, Cantoblanco, Madrid, Spain
| | - Katherine Silliman
- Northern Gulf Institute, Mississippi State University, Starkville, MS, USA
- NOAA Atlantic Oceanographic and Meteorological Laboratory, Miami, FL, USA
| | | | - Zachary Gold
- California Cooperative Oceanic Fisheries Investigations (CalCOFI), Scripps Institution of Oceanography, University of California San Diego (UCSD), La Jolla, CA, USA
- NOAA Pacific Marine Environmental Laboratory, Seattle, WA, USA
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6
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Noll NW, Scherber C, Schäffler L. taxalogue: a toolkit to create comprehensive CO1 reference databases. PeerJ 2023; 11:e16253. [PMID: 38077427 PMCID: PMC10702336 DOI: 10.7717/peerj.16253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 09/18/2023] [Indexed: 12/18/2023] Open
Abstract
Background Taxonomic identification through DNA barcodes gained considerable traction through the invention of next-generation sequencing and DNA metabarcoding. Metabarcoding allows for the simultaneous identification of thousands of organisms from bulk samples with high taxonomic resolution. However, reliable identifications can only be achieved with comprehensive and curated reference databases. Therefore, custom reference databases are often created to meet the needs of specific research questions. Due to taxonomic inconsistencies, formatting issues, and technical difficulties, building a custom reference database requires tremendous effort. Here, we present taxalogue, an easy-to-use software for creating comprehensive and customized reference databases that provide clean and taxonomically harmonized records. In combination with extensive geographical filtering options, taxalogue opens up new possibilities for generating and testing evolutionary hypotheses. Methods taxalogue collects DNA sequences from several online sources and combines them into a reference database. Taxonomic incongruencies between the different data sources can be harmonized according to available taxonomies. Dereplication and various filtering options are available regarding sequence quality or metadata information. taxalogue is implemented in the open-source Ruby programming language, and the source code is available at https://github.com/nwnoll/taxalogue. We benchmark four reference databases by sequence identity against eight queries from different localities and trapping devices. Subsamples from each reference database were used to compare how well another one is covered. Results taxalogue produces reference databases with the best coverage at high identities for most tested queries, enabling more accurate, reliable predictions with higher certainty than the other benchmarked reference databases. Additionally, the performance of taxalogue is more consistent while providing good coverage for a variety of habitats, regions, and sampling methods. taxalogue simplifies the creation of reference databases and makes the process reproducible and transparent. Multiple available output formats for commonly used downstream applications facilitate the easy adoption of taxalogue in many different software pipelines. The resulting reference databases improve the taxonomic classification accuracy through high coverage of the query sequences at high identities.
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Affiliation(s)
- Niklas W. Noll
- Centre for Biodiversity Monitoring and Conservation Science, Leibniz Institute for the Analysis of Biodiversity Change, Bonn, North Rhine-Westphalia, Germany
| | - Christoph Scherber
- Centre for Biodiversity Monitoring and Conservation Science, Leibniz Institute for the Analysis of Biodiversity Change, Bonn, North Rhine-Westphalia, Germany
| | - Livia Schäffler
- Centre for Biodiversity Monitoring and Conservation Science, Leibniz Institute for the Analysis of Biodiversity Change, Bonn, North Rhine-Westphalia, Germany
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7
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Westeen EP, Martínez‐Fonseca JG, d'Orgeix CA, Walker FM, Sanchez DE, Wang IJ. Dietary niche partitioning of three Sky Island Sceloporus lizards as revealed through DNA metabarcoding. Ecol Evol 2023; 13:e10461. [PMID: 37693939 PMCID: PMC10485322 DOI: 10.1002/ece3.10461] [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: 05/23/2023] [Revised: 08/04/2023] [Accepted: 08/18/2023] [Indexed: 09/12/2023] Open
Abstract
Lizard diets are highly diverse and have contributed to the diversification, biogeographical distributions, and evolution of novel traits across this global radiation. Many parts of a lizard's ecology-including habitat preferences, foraging modes, predation risks, interspecific competition, and thermal constraints, among others-interact to shape diets, and dietary niche partitioning simultaneously contributes to co-occurrence within communities. We used DNA metabarcoding of fecal samples to identify prey items in the diets of three sympatric Sceloporus lizards in the Madrean Sky Islands of Arizona, USA. We found evidence for dietary niche partitioning between interacting species concomitant with their respective ecologies. We also compared diet composition between populations to understand how conserved or plastic species' diets are between different environments. Our findings suggest that habitat generalists are also diet generalists in this system, while the same may be true for specialists. The identification of prey items to much lower taxonomic levels than previously documented further reveals hidden diversity in the diets of these species and underscores the utility of metabarcoding for understanding the full complexity of lizard diets.
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Affiliation(s)
- Erin P. Westeen
- Department of Environmental Science, Policy, and ManagementUniversity of California, BerkeleyBerkeleyCaliforniaUSA
- Museum of Vertebrate ZoologyUniversity of California BerkeleyBerkeleyCaliforniaUSA
| | | | | | - Faith M. Walker
- School of ForestryNorthern Arizona UniversityFlagstaffArizonaUSA
- Pathogen and Microbiome InstituteNorthern Arizona UniversityFlagstaffArizonaUSA
| | - Daniel E. Sanchez
- School of ForestryNorthern Arizona UniversityFlagstaffArizonaUSA
- Pathogen and Microbiome InstituteNorthern Arizona UniversityFlagstaffArizonaUSA
| | - Ian J. Wang
- Department of Environmental Science, Policy, and ManagementUniversity of California, BerkeleyBerkeleyCaliforniaUSA
- Museum of Vertebrate ZoologyUniversity of California BerkeleyBerkeleyCaliforniaUSA
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8
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Nsengimana O, Walker FM, Webala PW, Twizeyimana I, Dusabe MC, Sanchez DE, Sobek CJ, Ruhagazi D, Iribagiza P, Muvunyi R, Medellin RA. Our good neighbors: Understanding ecosystem services provided by insectivorous bats in Rwanda. PLoS One 2023; 18:e0287536. [PMID: 37352304 PMCID: PMC10289311 DOI: 10.1371/journal.pone.0287536] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 06/07/2023] [Indexed: 06/25/2023] Open
Abstract
Bats are prodigious consumers of agricultural and forest pests, and are, therefore, a natural asset for agricultural productivity, suppressing populations of such pests. This study provides baseline information of diet of 143 bats belonging to eight insectivorous bat species from agricultural areas of Rwanda while evaluating the effectiveness of bats as pest suppressors. Using DNA metabarcoding to analyze bat fecal pellets, 85 different insect species were detected, with 60% (n = 65), 64% (n = 11) and 78% (n = 9) found to be agricultural pests from eastern, northern and western regions, respectively. Given the high percentages of agricultural pests detected, we submit that Rwandan insectivorous bats have the capacity for biocontrol of agricultural pests. Rwandan bat populations should be protected and promoted since they may foster higher crop yields and sustainable livelihoods.
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Affiliation(s)
| | - Faith M. Walker
- Bat Ecology & Genetics Lab, School of Forestry, Northern Arizona University, Flagstaff, Arizona, United States of America
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Paul W. Webala
- Department of Forestry and Wildlife Management, Maasai Mara University, Narok, Kenya
| | | | | | - Daniel E. Sanchez
- Bat Ecology & Genetics Lab, School of Forestry, Northern Arizona University, Flagstaff, Arizona, United States of America
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Colin J. Sobek
- Bat Ecology & Genetics Lab, School of Forestry, Northern Arizona University, Flagstaff, Arizona, United States of America
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Deo Ruhagazi
- Rwanda Wildlife Conservation Association, Kigali, Rwanda
| | | | | | - Rodrigo A. Medellin
- Institute of Ecology, National Autonomous University of Mexico, Mexico City, Mexico
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Curd EE, Gal L, Gallego R, Nielsen S, Gold Z. rCRUX: A Rapid and Versatile Tool for Generating Metabarcoding Reference libraries in R. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.31.543005. [PMID: 37397980 PMCID: PMC10312559 DOI: 10.1101/2023.05.31.543005] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Key to making accurate taxonomic assignments are curated, comprehensive reference barcode databases. However, the generation and curation of such databases has remained challenging given the large and continuously growing volumes of DNA sequence data and novel reference barcode targets. Monitoring and research applications require a greater diversity of specialized gene regions and targeted taxa to meet taxonomic classification goals then are currently curated by professional staff. Thus, there is a growing need for an easy to implement tool that can generate comprehensive metabarcoding reference libraries for any bespoke locus. We address this need by reimagining CRUX from the Anacapa Toolkit and present the rCRUX package in R. The typical workflow involves searching for plausible seed amplicons (get_seeds_local() or get_seeds_remote()) by simulating in silico PCR to acquire seed sequences containing a user-defined primer set. Next these seeds are used to iteratively blast search seed sequences against a local NCBI formatted database using a taxonomic rank based stratified random sampling approach (blast_seeds()) that results in a comprehensive set of sequence matches. This database is dereplicated and cleaned (derep_and_clean_db()) by identifying identical reference sequences and collapsing the taxonomic path to the lowest taxonomic agreement across all matching reads. This results in a curated, comprehensive database of primer specific reference barcode sequences from NCBI. We demonstrate that rCRUX provides more comprehensive reference databases for the MiFish Universal Teleost 12S, Taberlet trnl, and fungal ITS locus than CRABS, METACURATOR, RESCRIPt, and ECOPCR reference databases. We then further demonstrate the utility of rCRUX by generating 16 reference databases for metabarcoding loci that lack dedicated reference database curation efforts. The rCRUX package provides a simple to use tool for the generation of curated, comprehensive reference databases for user-defined loci, facilitating accurate and effective taxonomic classification of metabarcoding and DNA sequence efforts broadly.
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Affiliation(s)
- Emily E. Curd
- Vermont Biomedical Research Network, University of Vermont, VT, USA
| | - Luna Gal
- Landmark College, VT, USA
- California Cooperative Oceanic Fisheries Investigations (CalCOFI), Scripps Institution of Oceanography, University of California San Diego (UCSD), La Jolla, CA, USA
| | - Ramon Gallego
- Universidad Autónoma de Madrid - Unidad de Genética, Spain
| | | | - Zachary Gold
- California Cooperative Oceanic Fisheries Investigations (CalCOFI), Scripps Institution of Oceanography, University of California San Diego (UCSD), La Jolla, CA, USA
- NOAA Pacific Marine Environmental Laboratory, Seattle, WA, USA
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Mayne SJ, King DI, Andersen JC, Elkinton JS. Pest control services on farms vary among bird species on diversified, low-intensity farms. Glob Ecol Conserv 2023. [DOI: 10.1016/j.gecco.2023.e02447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023] Open
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11
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Shim KY, Shin H, Yeo IC, Kim KR, Kwak IS, Jeong CB. Environmental DNA surveillance of biocontamination in a drinking water treatment plant. JOURNAL OF HAZARDOUS MATERIALS 2023; 456:131656. [PMID: 37236104 DOI: 10.1016/j.jhazmat.2023.131656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 05/15/2023] [Accepted: 05/16/2023] [Indexed: 05/28/2023]
Abstract
A clean and adequate supply of drinking water is essential to life and good health. However, despite the risk of biologically derived contamination of drinking water, monitoring of invertebrate outbreaks has relied primarily on naked-eye inspections that are prone to errors. In this study, we applied environmental DNA (eDNA) metabarcoding as a biomonitoring tool at seven different stages of drinking water treatment, from prefiltration to release from household faucets. While the composition of invertebrate eDNA communities reflected the communities of the source water in earlier stages of the treatment, several predominant invertebrate taxa (e.g., rotifer) were shown to be introduced during purification, but most were eliminated in later treatment stages. In addition, the limit of detection/quantification of PCR assay and read capacity of high-throughput sequencing was assessed with further microcosm experiments to estimate the applicability eDNA metabarcoding to the biocontamination surveillance in drinking water treatment plants (DWTPs). Here we propose a novel eDNA-based approach for sensitive and efficient surveillance of invertebrate outbreaks in DWTPs.
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Affiliation(s)
- Kyu-Young Shim
- Department of Marine Science, College of Natural Sciences, Incheon National University, Incheon 22012, Republic of Korea
| | - Heesang Shin
- Department of Marine Science, College of Natural Sciences, Incheon National University, Incheon 22012, Republic of Korea
| | - In-Cheol Yeo
- Department of Marine Science, College of Natural Sciences, Incheon National University, Incheon 22012, Republic of Korea
| | - Kyu Ri Kim
- Hoseo Toxicology Research Center, Hoseo University, Asan 31499, Republic of Korea
| | - Ihn-Sil Kwak
- Department of Ocean Integrated Science, Chonnam National University, Yeosu 59626, Republic of Korea
| | - Chang-Bum Jeong
- Department of Marine Science, College of Natural Sciences, Incheon National University, Incheon 22012, Republic of Korea.
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12
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Swinehart A, Partridge C, Russell A, Thacker A, Kovach J, Moore J. Diet of a threatened rattlesnake (eastern massasauga) revealed by DNA metabarcoding. Ecol Evol 2023; 13:e10029. [PMID: 37122773 PMCID: PMC10131807 DOI: 10.1002/ece3.10029] [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: 01/12/2023] [Revised: 04/04/2023] [Accepted: 04/06/2023] [Indexed: 05/02/2023] Open
Abstract
Characterizing the diet of imperiled species using minimally invasive methods is crucial to understanding their ecology and conservation requirements. Here, we apply a DNA metabarcoding approach to study the diet of the eastern massasauga rattlesnake (Sistrurus catenatus), a Federally Threatened snake found throughout the Great Lakes region. Eighty-three fecal samples collected across 10 different massasauga populations located in Michigan, USA, were sequenced, with 70 samples containing prey DNA. We used universal metazoan primers and developed a host-specific oligonucleotide blocker to characterize their diet. We identified at least 12 different prey species, with eastern massasaugas exhibiting opportunistic feeding and a strong preference towards small mammals. Meadow voles (Microtus pennsylvanicus) were the most common prey item (70% of diet) followed by the northern short-tailed shrew (Blarina brevicauda) and masked shrew (Sorex cinereus; 15.7% of diet each), along with occasional bird and snake prey. Adult individuals exhibited a more generalized diet, consuming a larger number of prey taxa on average. Younger snakes consumed a smaller variety of prey items and tended to consume smaller-sized mammals such as masked shrews (Sorex cinereus) and northern short-tailed shrews (Blarina brevicauda). We conclude that small mammals are a crucial part of eastern massasauga rattlesnake diet and recommend this be taken into consideration when conservation strategies are developed. The methods developed in this study can be applied to other reptile species, providing an accurate, minimally invasive, and thorough diet assessment for at-risk reptile species.
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Affiliation(s)
- Alyssa Swinehart
- Biology DepartmentGrand Valley State UniversityAllendaleMichiganUSA
| | - Charlyn Partridge
- Annis Water Resources InstituteGrand Valley State UniversityMuskegonMichiganUSA
| | - Amy Russell
- Biology DepartmentGrand Valley State UniversityAllendaleMichiganUSA
| | - Arin Thacker
- Biology DepartmentGrand Valley State UniversityAllendaleMichiganUSA
| | - Jennifer Kovach
- Biology DepartmentGrand Valley State UniversityAllendaleMichiganUSA
| | - Jennifer Moore
- Biology DepartmentGrand Valley State UniversityAllendaleMichiganUSA
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13
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Boast AP, Wood JR, Bolstridge N, Perry GLW, Wilmshurst JM. Ancient and modern scats record broken ecological interactions and a decline in dietary breadth of the critically endangered kākāpō parrot (Strigops habroptilus). Front Ecol Evol 2023. [DOI: 10.3389/fevo.2023.1058130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/30/2023] Open
Abstract
Threatened animal taxa are often absent from most of their original habitats, meaning their ecological niche cannot be fully captured by contemporary data alone. Although DNA metabarcoding of scats and coprolites (palaeofaeces) can identify the past and present species interactions of their depositors, the usefulness of coprolites in conservation biology is untested as few endangered taxa have known coprolite records. Here, we perform multilocus metabarcoding sequencing and palynological analysis of dietary plants of >100 coprolites (estimated to date from c. 400–1900 A.D.) and > 100 frozen scats (dating c. 1950 A.D. to present) of the critically endangered, flightless, herbivorous kākāpō (Strigops habroptilus), a species that disappeared from its natural range in Aotearoa-New Zealand (NZ) after the 13th C. A.D. We identify 24 orders, 56 families and 67 native plant genera unrecorded in modern kākāpō diets (increases of 69, 108 and 75% respectively). We found that southern beeches (Nothofagaceae), which are important canopy-forming trees and not an important kākāpō food today, dominated kākāpō diets in upland (c. >900 m elevation) habitats. We also found that kākāpō frequently consumed hemiparasitic mistletoes (Loranthaceae) and the holoparasitic wood rose (Dactylanthus taylorii), taxa which are nutrient rich, and now threatened by mammalian herbivory and a paucity of dispersers and pollinators. No single dataset or gene identified all taxa in our dataset, demonstrating the value of multiproxy or multigene datasets in studies of animal diets. Our results highlight how contemporary data may considerably underestimate the full dietary breadth of threatened species and demonstrate the potential value of coprolite analysis in conservation biology.
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14
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Bourret A, Nozères C, Parent E, Parent GJ. Maximizing the reliability and the number of species assignments in metabarcoding studies using a curated regional library and a public repository. METABARCODING AND METAGENOMICS 2023. [DOI: 10.3897/mbmg.7.98539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023] Open
Abstract
Biodiversity assessments relying on DNA have increased rapidly over the last decade. However, the reliability of taxonomic assignments in metabarcoding studies is variable and affected by the reference databases and the assignment methods used. Species level assignments are usually considered as reliable using regional libraries but unreliable using public repositories. In this study, we aimed to test this assumption for metazoan species detected in the Gulf of St. Lawrence in the Northwest Atlantic. We first created a regional library (GSL-rl) by data mining COI barcode sequences from BOLD, and included a reliability ranking system for species assignments. We then estimated 1) the accuracy and precision of the public repository NCBI-nt for species assignments using sequences from the regional library and 2) compared the detection and reliability of species assignments of a metabarcoding dataset using either NCBI-nt or the regional library and popular assignment methods. With NCBI-nt and sequences from the regional library, the BLAST-LCA (least common ancestor) method was the most precise method for species assignments, but the accuracy was higher with the BLAST-TopHit method (>80% over all taxa, between 70% and 90% amongst taxonomic groups). With the metabarcoding dataset, the reliability of species assignments was greater using GSL-rl compared to NCBI-nt. However, we also observed that the total number of reliable species assignments could be maximized using both GSL-rl and NCBI-nt with different optimized assignment methods. The use of a two-step approach for species assignments, i.e., using a regional library and a public repository, could improve the reliability and the number of detected species in metabarcoding studies.
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15
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L'Ambert G, Gendrot M, Briolant S, Nguyen A, Pages S, Bosio L, Palomo V, Gomez N, Benoit N, Savini H, Pradines B, Durand GA, Leparc-Goffart I, Grard G, Fontaine A. Analysis of trapped mosquito excreta as a noninvasive method to reveal biodiversity and arbovirus circulation. Mol Ecol Resour 2023; 23:410-423. [PMID: 36161270 PMCID: PMC10092573 DOI: 10.1111/1755-0998.13716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 09/02/2022] [Accepted: 09/16/2022] [Indexed: 01/04/2023]
Abstract
Emerging and endemic mosquito-borne viruses can be difficult to detect and monitor because they often cause asymptomatic infections in human or vertebrate animals or cause nonspecific febrile illness with a short recovery waiting period. Some of these pathogens circulate into complex cryptic cycles involving several animal species as reservoir or amplifying hosts. Detection of cases in vertebrate hosts can be complemented by entomological surveillance, but this method is not adapted to low infection rates in mosquito populations that typically occur in low or nonendemic areas. We identified West Nile virus circulation in Camargue, a wetland area in South of France, using a cost-effective xenomonitoring method based on the molecular detection of virus in excreta from trapped mosquitoes. We also succeeded at identifying the mosquito species community on several sampling sites, together with the vertebrate hosts on which they fed prior to being captured using amplicon-based metabarcoding on mosquito excreta without processing any mosquitoes. Mosquito excreta-based virus surveillance can complement standard surveillance methods because it is cost-effective and does not require personnel with a strong background in entomology. This strategy can also be used to noninvasively explore the ecological network underlying arbovirus circulation.
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Affiliation(s)
- Grégory L'Ambert
- Entente Interdépartementale Pour la Démoustication du Littoral Méditerranéen (EID Méditerranée), Montpellier, France
| | - Mathieu Gendrot
- Unité Parasitologie et Entomologie, Département Microbiologie et Maladies Infectieuses, Institut de Recherche Biomédicale des Armées (IRBA), Marseille, France.,IRD, SSA, AP-HM, VITROME, Aix Marseille Univ, Marseille, France.,IHU Méditerranée Infection, Marseille, France
| | - Sébastien Briolant
- Unité Parasitologie et Entomologie, Département Microbiologie et Maladies Infectieuses, Institut de Recherche Biomédicale des Armées (IRBA), Marseille, France.,IRD, SSA, AP-HM, VITROME, Aix Marseille Univ, Marseille, France.,IHU Méditerranée Infection, Marseille, France
| | | | - Sylvain Pages
- Entente Interdépartementale Pour la Démoustication du Littoral Méditerranéen (EID Méditerranée), Montpellier, France
| | - Laurent Bosio
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207), Marseille, France.,Centre National de Référence des Arbovirus, Institut de Recherche Biomédicale des Armées, Marseille, France
| | - Vincent Palomo
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207), Marseille, France.,Centre National de Référence des Arbovirus, Institut de Recherche Biomédicale des Armées, Marseille, France
| | - Nicolas Gomez
- Unité Parasitologie et Entomologie, Département Microbiologie et Maladies Infectieuses, Institut de Recherche Biomédicale des Armées (IRBA), Marseille, France.,IRD, SSA, AP-HM, VITROME, Aix Marseille Univ, Marseille, France.,IHU Méditerranée Infection, Marseille, France
| | - Nicolas Benoit
- Unité Parasitologie et Entomologie, Département Microbiologie et Maladies Infectieuses, Institut de Recherche Biomédicale des Armées (IRBA), Marseille, France.,IRD, SSA, AP-HM, VITROME, Aix Marseille Univ, Marseille, France.,IHU Méditerranée Infection, Marseille, France
| | - Hélène Savini
- IRD, SSA, AP-HM, VITROME, Aix Marseille Univ, Marseille, France.,Service des Maladies Infectieuses, Hôpital d'Instruction des Armées Laveran, Marseille, France
| | - Bruno Pradines
- Unité Parasitologie et Entomologie, Département Microbiologie et Maladies Infectieuses, Institut de Recherche Biomédicale des Armées (IRBA), Marseille, France.,IRD, SSA, AP-HM, VITROME, Aix Marseille Univ, Marseille, France.,IHU Méditerranée Infection, Marseille, France.,Centre National de Référence du Paludisme, Marseille, France
| | - Guillaume André Durand
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207), Marseille, France.,Centre National de Référence des Arbovirus, Institut de Recherche Biomédicale des Armées, Marseille, France
| | - Isabelle Leparc-Goffart
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207), Marseille, France.,Centre National de Référence des Arbovirus, Institut de Recherche Biomédicale des Armées, Marseille, France
| | - Gilda Grard
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207), Marseille, France.,Centre National de Référence des Arbovirus, Institut de Recherche Biomédicale des Armées, Marseille, France
| | - Albin Fontaine
- Unité Parasitologie et Entomologie, Département Microbiologie et Maladies Infectieuses, Institut de Recherche Biomédicale des Armées (IRBA), Marseille, France.,IRD, SSA, AP-HM, VITROME, Aix Marseille Univ, Marseille, France.,IHU Méditerranée Infection, Marseille, France
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16
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VTAM: A robust pipeline for validating metabarcoding data using controls. Comput Struct Biotechnol J 2023; 21:1151-1156. [PMID: 36789260 PMCID: PMC9918390 DOI: 10.1016/j.csbj.2023.01.034] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 01/25/2023] [Accepted: 01/25/2023] [Indexed: 01/29/2023] Open
Abstract
To obtain accurate estimates for biodiversity and ecological studies, metabarcoding studies should be carefully designed to minimize both false positive (FP) and false negative (FN) occurrences. Internal controls (mock samples and negative controls), replicates, and overlapping markers allow controlling metabarcoding errors but current metabarcoding software packages do not explicitly integrate these additional experimental data to optimize filtering. We have developed the metabarcoding analysis software VTAM, which uses explicitly these elements of the experimental design to find optimal parameter settings that minimize FP and FN occurrences. VTAM showed similar sensitivity, but a higher precision compared to two other pipelines using three datasets and two different markers (COI, 16S). The stringent filtering procedure implemented in VTAM aims to produce robust metabarcoding data to obtain accurate ecological estimates and represents an important step towards a non-arbitrary and standardized validation of metabarcoding data for conducting ecological studies. VTAM is implemented in Python and available from: https://github.com/aitgon/vtam. The VTAM benchmark code is available from: https://github.com/aitgon/vtam_benchmark.
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17
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Walker FM, Sanchez DE, Froehlich EM, Federman EL, Lyman JA, Owens M, Lear K. Endangered Nectar-Feeding Bat Detected by Environmental DNA on Flowers. Animals (Basel) 2022; 12:ani12223075. [PMID: 36428303 PMCID: PMC9686659 DOI: 10.3390/ani12223075] [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: 10/17/2022] [Revised: 10/30/2022] [Accepted: 11/03/2022] [Indexed: 11/11/2022] Open
Abstract
Leptonycteris nivalis (the Mexican long-nosed bat) is an endangered nectar-feeding bat species that follows "nectar corridors" as it migrates from Mexico to the southwestern United States. Locating these nectar corridors is key to their conservation and may be possible using environmental DNA (eDNA) from these bats. Hence, we developed and tested DNA metabarcoding and qPCR eDNA assays to determine whether L. nivalis could be detected by sampling the agave flowers on which it feeds. We sampled plants with known bat visitations in the Sierra Madre Oriental in Laguna de Sanchez (LS), Nuevo León, Mexico, and in the Chisos Mountains in Big Bend National Park, TX, USA (CB). A total of 13 samples included both swabs of agave umbels and cuttings of individual flowers. DNA metabarcoding was performed as a PCR multiplex that targeted bats (SFF-COI), arthropods (ANML-COI), and plants (ITS2 and rbcL). We targeted arthropods and plants in parallel with bats because future metabarcoding studies may wish to examine all the pollinators and plants within the nectar corridor. We developed and tested the sensitivity and specificity of two qPCR assays. We found that both DNA metabarcoding and qPCR were highly successful at detecting L. nivalis (11 of 13 for DNA metabarcoding and 12 of 13 for qPCR). Swabs and flower cuttings and both qPCR assays detected the species over four replicates. We suggest that L. nivalis leaves substantial DNA behind as it forages for nectar. We also suggest that future studies examine the time since sampling to determine its effect on detection success. The DNA metabarcoding multiplex will be useful for parallel questions regarding pollination ecology, while, with further testing, the qPCR assays will be effective for large-scale sampling for the detection of migration corridors and foraging areas. This work may be relevant to other nectar-feeding bat species, which can likely be detected with similar methodologies.
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Affiliation(s)
- Faith M. Walker
- Bat Ecology & Genetics Lab, School of Forestry, Northern Arizona University, Flagstaff, AZ 86011, USA
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011, USA
- Correspondence:
| | - Daniel E. Sanchez
- Bat Ecology & Genetics Lab, School of Forestry, Northern Arizona University, Flagstaff, AZ 86011, USA
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Emma M. Froehlich
- Bat Ecology & Genetics Lab, School of Forestry, Northern Arizona University, Flagstaff, AZ 86011, USA
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Emma L. Federman
- Bat Ecology & Genetics Lab, School of Forestry, Northern Arizona University, Flagstaff, AZ 86011, USA
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Jacque A. Lyman
- Bat Ecology & Genetics Lab, School of Forestry, Northern Arizona University, Flagstaff, AZ 86011, USA
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Meagan Owens
- Bat Ecology & Genetics Lab, School of Forestry, Northern Arizona University, Flagstaff, AZ 86011, USA
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Kristen Lear
- Integrative Conservation and Forestry & Natural Resources, University of Georgia, Athens, GA 30602, USA
- Bat Conservation International, Austin, TX 78746, USA
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18
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Villsen K, Corse E, Meglécz E, Archambaud‐Suard G, Vignes H, Ereskovsky AV, Chappaz R, Dubut V. DNA metabarcoding suggests adaptive seasonal variation of individual trophic traits in a critically endangered fish. Mol Ecol 2022; 31:5889-5908. [PMID: 36125278 PMCID: PMC9828795 DOI: 10.1111/mec.16698] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 09/12/2022] [Accepted: 09/15/2022] [Indexed: 01/13/2023]
Abstract
Dietary studies are critical for understanding foraging strategies and have important applications in conservation and habitat management. We applied a robust metabarcoding protocol to characterize the diet of the critically endangered freshwater fish Zingel asper (the Rhone streber). We conducted modelling and simulation analyses to identify and characterize some of the drivers of individual trophic trait variation in this species. We found that population density and ontogeny had minor effects on the trophic niche of Z. asper. Instead, our results suggest that the majority of trophic niche variation was driven by seasonal variation in ecological opportunity. The total trophic niche width of Z. asper seasonally expanded to include a broader range of prey. Furthermore, null model simulations revealed that the increase of between-individual variation in autumn indicates that Z. asper become more opportunistic relative to summer and spring, rather than being associated with a seasonal specialization of individuals. Overall, our results suggest an adaptive variation of individual trophic traits in Z. asper: the species mainly consumes a few ephemeropteran taxa (Baetis fuscatus and Ecdyonurus) but seems to be capable of adapting its foraging strategy to maintain its body condition. This study illustrates how metabarcoding data obtained from faeces can be validated and combined with individual-based modelling and simulation approaches to explore inter- and intrapopulational individual trophic traits variation and to test hypotheses in the conventional analytic framework of trophic ecology.
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Affiliation(s)
- Kurt Villsen
- Aix Marseille Université, CNRS, IRDAvignon Université, IMBEMarseilleFrance
| | - Emmanuel Corse
- Aix Marseille Université, CNRS, IRDAvignon Université, IMBEMarseilleFrance,Centre Universitaire de Formation et de Recherche de Mayotte (CUFR)DembeniFrance,MARBEC, University of Montpellier, CNRS, Ifremer, IRDMontpellierFrance
| | - Emese Meglécz
- Aix Marseille Université, CNRS, IRDAvignon Université, IMBEMarseilleFrance
| | | | - Hélène Vignes
- CIRAD, University of Montpellier, INRAE, Montpellier SupAgro, AGAPMontpellierFrance
| | - Alexander V. Ereskovsky
- Aix Marseille Université, CNRS, IRDAvignon Université, IMBEMarseilleFrance,St. Petersburg State UniversitySt. PetersburgRussia,Koltzov Institute of Developmental Biology of Russian Academy of SciencesMoscowRussia
| | - Rémi Chappaz
- INRAE, Aix Marseille Université, RECOVERAix‐en‐ProvenceFrance
| | - Vincent Dubut
- Aix Marseille Université, CNRS, IRDAvignon Université, IMBEMarseilleFrance
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19
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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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20
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Kimble M, Allers S, Campbell K, Chen C, Jackson LM, King BL, Silverbrand S, York G, Beard K. medna-metadata: an open-source data management system for tracking environmental DNA samples and metadata. Bioinformatics 2022; 38:4589-4597. [PMID: 35960154 PMCID: PMC9524998 DOI: 10.1093/bioinformatics/btac556] [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: 05/09/2022] [Revised: 07/23/2022] [Accepted: 08/09/2022] [Indexed: 12/24/2022] Open
Abstract
MOTIVATION Environmental DNA (eDNA), as a rapidly expanding research field, stands to benefit from shared resources including sampling protocols, study designs, discovered sequences, and taxonomic assignments to sequences. High-quality community shareable eDNA resources rely heavily on comprehensive metadata documentation that captures the complex workflows covering field sampling, molecular biology lab work, and bioinformatic analyses. There are limited sources that provide documentation of database development on comprehensive metadata for eDNA and these workflows and no open-source software. RESULTS We present medna-metadata, an open-source, modular system that aligns with Findable, Accessible, Interoperable, and Reusable guiding principles that support scholarly data reuse and the database and application development of a standardized metadata collection structure that encapsulates critical aspects of field data collection, wet lab processing, and bioinformatic analysis. Medna-metadata is showcased with metabarcoding data from the Gulf of Maine (Polinski et al., 2019). AVAILABILITY AND IMPLEMENTATION The source code of the medna-metadata web application is hosted on GitHub (https://github.com/Maine-eDNA/medna-metadata). Medna-metadata is a docker-compose installable package. Documentation can be found at https://medna-metadata.readthedocs.io/en/latest/?badge=latest. The application is implemented in Python, PostgreSQL and PostGIS, RabbitMQ, and NGINX, with all major browsers supported. A demo can be found at https://demo.metadata.maine-edna.org/. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- M Kimble
- To whom correspondence should be addressed.
| | - S Allers
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, ME 04469, USA
| | - K Campbell
- School of Computing and Information Science, University of Maine, Orono, ME 04469, USA
| | - C Chen
- School of Computing and Information Science, University of Maine, Orono, ME 04469, USA
| | - L M Jackson
- Advanced Research Computing, Security and Information Management, University of Maine, Orono, ME 04469, USA,Maine EPSCoR, University of Maine, Orono, ME 04469, USA
| | - B L King
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, ME 04469, USA
| | - S Silverbrand
- School of Marine Sciences, University of Maine, Orono, ME 04469, USA
| | - G York
- Environmental DNA Laboratory, Coordinated Operating Research Entities, University of Maine, Orono, ME 04469, USA
| | - K Beard
- School of Computing and Information Science, University of Maine, Orono, ME 04469, USA
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Klure DM, Greenhalgh R, Dearing MD. Addressing nontarget amplification in DNA metabarcoding studies of arthropod-feeding rodents. MAMMAL RES 2022; 67:499-509. [PMID: 36968646 PMCID: PMC10035264 DOI: 10.1007/s13364-022-00646-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Abstract
High-throughput sequencing approaches have revolutionized how we study animal diets by enabling the detection of dietary components from the metabarcoding of DNA in excrement. Mitochondrial cytochrome oxidase C subunit I (mtCOI) DNA metabarcoding is commonly used to study the diets of arthropod-feeding animals; however, this approach is susceptible to nontarget amplification of the consumer species mtCOI locus. Nontarget amplification is often an unforeseen complication that can drastically reduce the quality and utility of the results generated by high-throughput amplicon sequencing. By interrogating the diets of new world rodents in the genus Neotoma (woodrats) in both natural and captive settings, we demonstrate that nontarget amplification can drastically reduce the total read abundance of detected arthropod taxa in fecal samples and inhibit downstream analyses of dietary diversity and composition metrics. Using the results from these investigations, we offer a guide on how to identify concerns for nontarget amplification when selecting degenerate primers for DNA metabarcoding studies and recommend several approaches that can reduce or eliminate nontarget amplification. Lastly, for the community interested in investigating the diets of arthropod-feeding rodents, we generated a database containing the degree of mismatch between publicly available Rodentia mtCOI sequences and four common universal mtCOI primer sets to be used as a resource for inferring the relative risk of nontarget amplification when designing arthropod metabarcoding studies in rodent systems. This guide will be especially useful for researchers working with consumer species that have not previously been studied.
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Aylward CM, Statham MJ, Barthman‐Thompson L, Kelt DA, Sacks BN. Dietary characterization of the endangered salt marsh harvest mouse and sympatric rodents using DNA metabarcoding. Ecol Evol 2022; 12:e9121. [PMID: 35866012 PMCID: PMC9289124 DOI: 10.1002/ece3.9121] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 06/22/2022] [Accepted: 06/27/2022] [Indexed: 11/05/2022] Open
Abstract
The salt marsh harvest mouse (Reithrodontomys raviventris; RERA) is an endangered species endemic to the coastal wetlands of the San Francisco Estuary, California. RERA are specialized to saline coastal wetlands, and their historical range has been severely impacted by landscape conversion and the introduction of non-native plant and rodent species. A better understanding of their diet is needed to assess habitat quality, particularly in relation to potential competitors. We investigated three questions using DNA metabarcoding with ITS2 and trnL markers: (1) Do RERA specialize on the native plant, pickleweed (Salicornia pacifica), (2) Do RERA consume non-native plants, and (3) What is the dietary niche breadth and overlap with three sympatric native and non-native rodents? RERA diet was dominated by two plants, native Salicornia and non-native salt bush (Atriplex spp.), but included 48 plant genera. RERA diet breadth was narrowest in fall, when they consumed the highest frequencies of Salicornia and Atriplex, and broadest in spring, when the frequencies of these two plants were lowest. Diet breadth was slightly lower for RERA than for co-occurring species in pairwise comparisons. All four species consumed similarly high frequencies of wetland plants, but RERA consumed fewer grasses and upland plants, suggesting that it may be less suited to fragmented habitat than sympatric rodents. Diet overlap was lowest between RERA and the native California vole (Microtis californicus). In contrast, RERA diet overlapped substantially with the native western harvest mouse (R. megalotis) and non-native house mouse (Mus musculus), suggesting potential for competition if these species become sufficiently abundant.
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Affiliation(s)
- Cody M. Aylward
- Department of Wildlife, Fish, and ConservationUniversity of California, DavisDavisCaliforniaUSA
- Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory, School of Veterinary MedicineUniversity of California, DavisDavisCaliforniaUSA
| | - Mark J. Statham
- Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory, School of Veterinary MedicineUniversity of California, DavisDavisCaliforniaUSA
| | | | - Douglas A. Kelt
- Department of Wildlife, Fish, and ConservationUniversity of California, DavisDavisCaliforniaUSA
| | - Benjamin N. Sacks
- Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory, School of Veterinary MedicineUniversity of California, DavisDavisCaliforniaUSA
- Department of Population Health and Reproduction, School of Veterinary MedicineUniversity of California, DavisDavisCaliforniaUSA
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RESCRIPt: Reproducible sequence taxonomy reference database management. PLoS Comput Biol 2021; 17:e1009581. [PMID: 34748542 PMCID: PMC8601625 DOI: 10.1371/journal.pcbi.1009581] [Citation(s) in RCA: 236] [Impact Index Per Article: 78.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 11/18/2021] [Accepted: 10/21/2021] [Indexed: 12/22/2022] Open
Abstract
Nucleotide sequence and taxonomy reference databases are critical resources for widespread applications including marker-gene and metagenome sequencing for microbiome analysis, diet metabarcoding, and environmental DNA (eDNA) surveys. Reproducibly generating, managing, using, and evaluating nucleotide sequence and taxonomy reference databases creates a significant bottleneck for researchers aiming to generate custom sequence databases. Furthermore, database composition drastically influences results, and lack of standardization limits cross-study comparisons. To address these challenges, we developed RESCRIPt, a Python 3 software package and QIIME 2 plugin for reproducible generation and management of reference sequence taxonomy databases, including dedicated functions that streamline creating databases from popular sources, and functions for evaluating, comparing, and interactively exploring qualitative and quantitative characteristics across reference databases. To highlight the breadth and capabilities of RESCRIPt, we provide several examples for working with popular databases for microbiome profiling (SILVA, Greengenes, NCBI-RefSeq, GTDB), eDNA and diet metabarcoding surveys (BOLD, GenBank), as well as for genome comparison. We show that bigger is not always better, and reference databases with standardized taxonomies and those that focus on type strains have quantitative advantages, though may not be appropriate for all use cases. Most databases appear to benefit from some curation (quality filtering), though sequence clustering appears detrimental to database quality. Finally, we demonstrate the breadth and extensibility of RESCRIPt for reproducible workflows with a comparison of global hepatitis genomes. RESCRIPt provides tools to democratize the process of reference database acquisition and management, enabling researchers to reproducibly and transparently create reference materials for diverse research applications. RESCRIPt is released under a permissive BSD-3 license at https://github.com/bokulich-lab/RESCRIPt. Generating and managing sequence and taxonomy reference data presents a bottleneck to many researchers, whether they are generating custom databases or attempting to format existing, curated reference databases for use with standard sequence analysis tools. Evaluating database quality and choosing the “best” database can be an equally formidable challenge. We developed RESCRIPt to alleviate this bottleneck, supporting reproducible, streamlined generation, curation, and evaluation of reference sequence databases. RESCRIPt uses QIIME 2 artifact file formats, which store all processing steps as data provenance within each file, allowing researchers to retrace the computational steps used to generate any given file. We used RESCRIPt to benchmark several commonly used marker-gene sequence databases for 16S rRNA genes, ITS, and COI sequences, demonstrating both the utility of RESCRIPt to streamline use of these databases, but also to evaluate several qualitative and quantitative characteristics of each database. We show that larger databases are not always best, and curation steps to reduce redundancy and filter out noisy sequences may be beneficial for some applications. We anticipate that RESCRIPt will streamline the use, management, and evaluation/selection of reference database materials for microbiomics, diet metabarcoding, eDNA, and other diverse applications.
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Perez-Muñoz ME, Sugden S, Harmsen HJM, 't Hart BA, Laman JD, Walter J. Nutritional and ecological perspectives of the interrelationships between diet and the gut microbiome in multiple sclerosis: Insights from marmosets. iScience 2021; 24:102709. [PMID: 34296070 PMCID: PMC8282968 DOI: 10.1016/j.isci.2021.102709] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Studies in experimental autoimmune encephalomyelitis (EAE), the animal model of multiple sclerosis, have shown potential links between diet components, microbiome composition, and modulation of immune responses. In this review, we reanalyze and discuss findings in an outbred marmoset EAE model in which a yogurt-based dietary supplement decreased disease frequency and severity. We show that although diet has detectable effects on the fecal microbiome, microbiome changes are more strongly associated with the EAE development. Using an ecological framework, we further show that the dominant factors influencing the gut microbiota were marmoset sibling pair and experimental time point. These findings emphasize challenges in assigning cause-and-effect relationships in studies of diet-microbiome-host interactions and differentiating the diet effects from other environmental, stochastic, and host-related factors. We advocate for animal experiments to be designed to allow causal inferences of the microbiota's role in pathology while considering the complex ecological processes that shape microbial communities.
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Affiliation(s)
- Maria Elisa Perez-Muñoz
- Department of Agricultural, Nutritional and Food Science, University of Alberta, Edmonton, AB T6G 2P5, Canada
| | - Scott Sugden
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Hermie J M Harmsen
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen 9700AE, The Netherlands
| | - Bert A 't Hart
- Department of Biomedical Sciences of Cells and Systems, Section of Molecular Neurobiology, University of Groningen, University Medical Center Groningen 9700AE, Groningen, The Netherlands.,Department Anatomy and Neuroscience, Amsterdam University Medical Center, Amsterdam 1081HV, The Netherlands
| | - Jon D Laman
- Department of Biomedical Sciences of Cells and Systems, Section of Molecular Neurobiology, University of Groningen, University Medical Center Groningen 9700AE, Groningen, The Netherlands.,Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen 9700AE, The Netherlands
| | - Jens Walter
- Department of Agricultural, Nutritional and Food Science, University of Alberta, Edmonton, AB T6G 2P5, Canada.,Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada.,APC Microbiome Ireland, School of Microbiology, and Department of Medicine, University College Cork - National University of Ireland, Cork T12 YT20, Ireland
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Antich A, Palacin C, Wangensteen OS, Turon X. To denoise or to cluster, that is not the question: optimizing pipelines for COI metabarcoding and metaphylogeography. BMC Bioinformatics 2021; 22:177. [PMID: 33820526 PMCID: PMC8020537 DOI: 10.1186/s12859-021-04115-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Accepted: 03/30/2021] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND The recent blooming of metabarcoding applications to biodiversity studies comes with some relevant methodological debates. One such issue concerns the treatment of reads by denoising or by clustering methods, which have been wrongly presented as alternatives. It has also been suggested that denoised sequence variants should replace clusters as the basic unit of metabarcoding analyses, missing the fact that sequence clusters are a proxy for species-level entities, the basic unit in biodiversity studies. We argue here that methods developed and tested for ribosomal markers have been uncritically applied to highly variable markers such as cytochrome oxidase I (COI) without conceptual or operational (e.g., parameter setting) adjustment. COI has a naturally high intraspecies variability that should be assessed and reported, as it is a source of highly valuable information. We contend that denoising and clustering are not alternatives. Rather, they are complementary and both should be used together in COI metabarcoding pipelines. RESULTS Using a COI dataset from benthic marine communities, we compared two denoising procedures (based on the UNOISE3 and the DADA2 algorithms), set suitable parameters for denoising and clustering, and applied these steps in different orders. Our results indicated that the UNOISE3 algorithm preserved a higher intra-cluster variability. We introduce the program DnoisE to implement the UNOISE3 algorithm taking into account the natural variability (measured as entropy) of each codon position in protein-coding genes. This correction increased the number of sequences retained by 88%. The order of the steps (denoising and clustering) had little influence on the final outcome. CONCLUSIONS We highlight the need for combining denoising and clustering, with adequate choice of stringency parameters, in COI metabarcoding. We present a program that uses the coding properties of this marker to improve the denoising step. We recommend researchers to report their results in terms of both denoised sequences (a proxy for haplotypes) and clusters formed (a proxy for species), and to avoid collapsing the sequences of the latter into a single representative. This will allow studies at the cluster (ideally equating species-level diversity) and at the intra-cluster level, and will ease additivity and comparability between studies.
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Affiliation(s)
- Adrià Antich
- Department of Marine Ecology, Centre for Advanced Studies of Blanes (CEAB-CSIC), Blanes (Girona), Catalonia, Spain
| | - Creu Palacin
- Department of Evolutionary Biology, Ecology and Environmental Sciences, University of Barcelona and Research Institute of Biodiversity (IRBIO), Barcelona, Catalonia, Spain
| | - Owen S Wangensteen
- Norwegian College of Fishery Science, UiT The Arctic University of Norway, Tromsö, Norway.
| | - Xavier Turon
- Department of Marine Ecology, Centre for Advanced Studies of Blanes (CEAB-CSIC), Blanes (Girona), Catalonia, Spain.
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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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