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Flo S, Vader A, Præbel K. Brute force prey metabarcoding to explore the diets of small invertebrates. Ecol Evol 2024; 14:e11369. [PMID: 38711484 PMCID: PMC11070772 DOI: 10.1002/ece3.11369] [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: 11/13/2023] [Revised: 04/16/2024] [Accepted: 04/17/2024] [Indexed: 05/08/2024] Open
Abstract
Prey metabarcoding has become a popular tool in molecular ecology for resolving trophic interactions at high resolution, from various sample types and animals. To date, most predator-prey studies of small-sized animals (<1 mm) have met the problem of overabundant predator DNA in dietary samples by adding blocking primers/peptide nucleic acids. These primers aim to limit the PCR amplification and detection of the predator DNA but may introduce bias to the prey composition identified by interacting with sequences that are similar to those of the predator. Here we demonstrate the use of an alternative method to explore the prey of small marine copepods using whole-body DNA extracts and deep, brute force metabarcoding of an 18S rDNA fragment. After processing and curating raw data from two sequencing runs of varying depths (0.4 and 5.4 billion raw reads), we isolated 1.3 and 52.2 million prey reads, with average depths of ~15,900 and ~120,000 prey reads per copepod individual, respectively. While data from both sequencing runs were sufficient to distinguish dietary compositions from disparate seasons, locations, and copepod species, greater sequencing depth led to better separation of clusters. As computation and sequencing are becoming ever more powerful and affordable, we expect the brute force approach to become a general standard for prey metabarcoding, as it offers a simple and affordable solution to consumers that is impractical to dissect or unknown to science.
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Affiliation(s)
- Snorre Flo
- Department of Arctic BiologyThe University Centre in SvalbardLongyearbyen, SvalbardNorway
- Faculty of Biosciences, Fisheries and EconomicsUiT The Arctic University of NorwayTromsøNorway
| | - Anna Vader
- Department of Arctic BiologyThe University Centre in SvalbardLongyearbyen, SvalbardNorway
| | - Kim Præbel
- The Norwegian College of Fishery Science (NFH)UiT The Arctic University of NorwayTromsøNorway
- Department of Forestry and Wildlife ManagementInland Norway University of Applied SciencesElverumNorway
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2
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Thongjued K, Garcia K, Scott D, Gonthier DJ, Dupuis JR. DNA metabarcoding diet analysis in a generalist omnivore: feeding trials reveal the efficacy of extraction kits and a multi-locus approach for identifying diverse diets. Integr Zool 2024. [PMID: 38297429 DOI: 10.1111/1749-4877.12806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2024]
Abstract
Metabarcoding-based diet analysis is a valuable tool for understanding the feeding behavior of a wide range of species. However, many studies using these methods for wild animals assume accuracy and precision without experimental evaluation with known positive control food items. Here, we conducted a feeding trial experiment with a positive control community in pasture-raised chickens and assessed the efficacy of several commonly used DNA extraction kits and primer sets. We hand-fed 22 known food items, including insects and plants, to six backyard laying hens and collected their excreta for eight h. We evaluated the efficacy of three DNA extraction kits, three primer sets for plant identification (targeting rbcL, trnL, and internal transcribed spacer 2 [ITS2]), and three primer sets for arthropod identification (targeting cytochrome oxidase subunit I [COI]). The detection success rate of our positive control food items was highly variable, ranging from 2.04% to 93.88% for all kit/primer combinations and averaging 37.35% and 43.57% for the most effective kit/primer combination for plants and insects, respectively. Extraction kits using bead-based homogenization positively affected the recovery proportion of plant and insect DNA in excreta samples. The minimum time to detect known food items was 44 min post-feeding. Two COI primer sets significantly outperformed the third, and both recovery proportion and taxonomic resolution from ITS2 were significantly higher than those from rbcL and trnL. Taken together, these results display the potential variability that can be inherently present in DNA-based diet analyses and highlight the utility of experimental feeding trials in validating such approaches, particularly for omnivores with diverse diets.
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Affiliation(s)
- Kantima Thongjued
- Department of Entomology, University of Kentucky, Agricultural Science Center, Lexington, Kentucky, USA
| | - Karina Garcia
- Department of Entomology, University of Kentucky, Agricultural Science Center, Lexington, Kentucky, USA
| | - Delia Scott
- Department of Entomology, University of Kentucky, Agricultural Science Center, Lexington, Kentucky, USA
| | - David J Gonthier
- Department of Entomology, University of Kentucky, Agricultural Science Center, Lexington, Kentucky, USA
| | - Julian R Dupuis
- Department of Entomology, University of Kentucky, Agricultural Science Center, Lexington, Kentucky, USA
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3
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Jüds M, Heidemann K, Eitzinger B, Scheu S. Testing the effectiveness of different wash protocols to remove body surface contaminants in invertebrate food web studies. PeerJ 2023; 11:e16018. [PMID: 38025744 PMCID: PMC10668814 DOI: 10.7717/peerj.16018] [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: 05/12/2023] [Accepted: 08/10/2023] [Indexed: 12/01/2023] Open
Abstract
Molecular gut content analysis via diagnostic PCR or high-throughput sequencing (metabarcoding) of consumers allows unravelling of feeding interactions in a wide range of animals. This is of particular advantage for analyzing the diet of small invertebrates living in opaque habitats such as the soil. Due to their small body size, which complicates dissection, microarthropods are subjected to whole-body DNA extraction-step before their gut content is screened for DNA of their food. This poses the problem that body surface contaminants, such as fungal spores may be incorrectly identified as ingested food particles for fungivorous species. We investigated the effectiveness of ten methods for body surface decontamination in litter-dwelling oribatid mites using Steganacarus magnus as model species. Furthermore, we tested for potential adverse effects of the decontamination techniques on the molecular detection of ingested prey organisms. Prior to decontamination, oribatid mites were fed with an oversupply of nematodes (Plectus sp.) and postmortem contaminated with fungal spores (Chaetomium globosum). We used diagnostic PCR with primers specific for C. globosum and Plectus sp. to detect contaminants and prey, respectively. The results suggest that chlorine bleach (sodium hypochloride, NaClO, 5%) is most efficient in removing fungal surface contamination without significantly affecting the detection of prey DNA in the gut. Based on these results, we provide a standard protocol for efficient body surface decontamination allowing to trace the prey spectrum of microarthropods using molecular gut content analysis.
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Affiliation(s)
- Melissa Jüds
- J. F. Blumenbach Institute of Zoology and Anthropology, Georg-August Universität Göttingen, Göttingen, Germany
| | - Kerstin Heidemann
- J. F. Blumenbach Institute of Zoology and Anthropology, Georg-August Universität Göttingen, Göttingen, Germany
| | - Bernhard Eitzinger
- J. F. Blumenbach Institute of Zoology and Anthropology, Georg-August Universität Göttingen, Göttingen, Germany
- iES Landau, Institute for Environmental Sciences, RPTU Kaiserslautern-Landau, Landau in der Pfalz, Germany
| | - Stefan Scheu
- J. F. Blumenbach Institute of Zoology and Anthropology, Georg-August Universität Göttingen, Göttingen, Germany
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Rijal DP, Hanebrekke T, Arneberg P, Johansen T, Sint D, Traugott M, Skern‐Mauritzen M, Westgaard J. Contaminants reach everywhere: Fish dietary samples should be surface decontaminated prior to molecular diet analysis. Ecol Evol 2023; 13:e10187. [PMID: 37342457 PMCID: PMC10277604 DOI: 10.1002/ece3.10187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 05/12/2023] [Accepted: 05/16/2023] [Indexed: 06/23/2023] Open
Abstract
Knowledge of trophic interaction is necessary to understand the dynamics of ecosystems and develop ecosystem-based management. The key data to measure these interactions should come from large-scale diet analyses with good taxonomic resolution. To that end, molecular methods that analyze prey DNA from guts and feces provide high-resolution dietary taxonomic data. However, molecular diet analysis may also produce unreliable results if the samples are contaminated by external sources of DNA. Employing the freshwater European whitefish (Coregonus lavaretus) as a tracer for sample contamination, we studied the possible route of whitefish in beaked redfish (Sebastes mentella) guts sampled in the Barents Sea. We used whitefish-specific COI primers for diagnostic analysis, and fish-specific 12S and metazoa-specific COI primers for metabarcoding analyses of intestine and stomach contents of fish samples that were either not cleaned, water cleaned, or bleach cleaned after being in contact with whitefish. Both the diagnostic and COI metabarcoding revealed clear positive effects of cleaning samples as whitefish were detected in significantly higher numbers of uncleaned samples compared to water or bleach-cleaned samples. Stomachs were more susceptible to contamination than intestines and bleach cleaning reduced the frequency of whitefish contamination. Also, the metabarcoding approach detected significantly more reads of whitefish in the stomach than in intestine samples. The diagnostic analysis and COI metabarcoding detected contaminants in a higher and comparable number of gut samples than the 12S-based approach. Our study underlines thus the importance of surface decontamination of aquatic samples to obtain reliable diet information from molecular data.
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Affiliation(s)
| | | | | | | | - Daniela Sint
- Applied Animal Ecology, Department of ZoologyUniversity of InnsbruckInnsbruckAustria
| | - Michael Traugott
- Applied Animal Ecology, Department of ZoologyUniversity of InnsbruckInnsbruckAustria
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Miller-ter Kuile A, Apigo A, Bui A, Butner K, Childress JN, Copeland S, DiFiore BP, Forbes ES, Klope M, Motta CI, Orr D, Plummer KA, Preston DL, Young HS. Changes in invertebrate food web structure between high- and low-productivity environments are driven by intermediate but not top-predator diet shifts. Biol Lett 2022; 18:20220364. [PMID: 36287142 PMCID: PMC9601239 DOI: 10.1098/rsbl.2022.0364] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 10/06/2022] [Indexed: 12/30/2022] Open
Abstract
Predator-prey interactions shape ecosystem stability and are influenced by changes in ecosystem productivity. However, because multiple biotic and abiotic drivers shape the trophic responses of predators to productivity, we often observe patterns, but not mechanisms, by which productivity drives food web structure. One way to capture mechanisms shaping trophic responses is to quantify trophic interactions among multiple trophic groups and by using complementary metrics of trophic ecology. In this study, we combine two diet-tracing methods: diet DNA and stable isotopes, for two trophic groups (top predators and intermediate predators) in both low- and high-productivity habitats to elucidate where in the food chain trophic structure shifts in response to changes in underlying ecosystem productivity. We demonstrate that while top predators show increases in isotopic trophic position (δ15N) with productivity, neither their isotopic niche size nor their DNA diet composition changes. Conversely, intermediate predators show clear turnover in DNA diet composition towards a more predatory prey base in high-productivity habitats. Taking this multi-trophic approach highlights how predator identity shapes responses in predator-prey interactions across environments with different underlying productivity, building predictive power for understanding the outcomes of ongoing anthropogenic change.
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Affiliation(s)
- Ana Miller-ter Kuile
- Ecology, Evolution, and Marine Biology Department, University of California, Santa Barbara, CA, USA
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ, USA
- USDA Forest Service Rocky Mountain Research Station, Flagstaff, AZ, USA
| | - Austen Apigo
- Ecology, Evolution, and Marine Biology Department, University of California, Santa Barbara, CA, USA
| | - An Bui
- Ecology, Evolution, and Marine Biology Department, University of California, Santa Barbara, CA, USA
| | - Kirsten Butner
- Ecology, Evolution, and Marine Biology Department, University of California, Santa Barbara, CA, USA
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Jasmine N. Childress
- Ecology, Evolution, and Marine Biology Department, University of California, Santa Barbara, CA, USA
| | - Stephanie Copeland
- Ecology, Evolution, and Marine Biology Department, University of California, Santa Barbara, CA, USA
| | - Bartholomew P. DiFiore
- Ecology, Evolution, and Marine Biology Department, University of California, Santa Barbara, CA, USA
| | - Elizabeth S. Forbes
- Ecology, Evolution, and Marine Biology Department, University of California, Santa Barbara, CA, USA
- Yale School of the Environment, Yale University, New Haven, CT, USA
| | - Maggie Klope
- Ecology, Evolution, and Marine Biology Department, University of California, Santa Barbara, CA, USA
| | - Carina I. Motta
- Ecology, Evolution, and Marine Biology Department, University of California, Santa Barbara, CA, USA
- Departamento de Biodiversidade, Universidade Estadual Paulista Júlio de Mesquita Filho, Av. 24 A, 1515 - Bela Vista, Rio Claro, SP, 13506-752, Brasil
| | - Devyn Orr
- Ecology, Evolution, and Marine Biology Department, University of California, Santa Barbara, CA, USA
- USDA ARS Eastern Oregon Agricultural Research Center, Burns, OR, USA
| | | | - Daniel L. Preston
- Department of Fish, Wildlife, and Conservation Biology, Colorado State University, Fort Collins, CO, USA
| | - Hillary S. Young
- Ecology, Evolution, and Marine Biology Department, University of California, Santa Barbara, CA, USA
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Mondino A, Crovadore J, Lefort F, Ursenbacher S. Impact of invading species on biodiversity: Diet study of the green whip snake’s (Hierophis viridiflavus, L. 1789) in Switzerland. Glob Ecol Conserv 2022. [DOI: 10.1016/j.gecco.2022.e02239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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7
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Kuile AM, Apigo A, Bui A, DiFiore B, Forbes ES, Lee M, Orr D, Preston DL, Behm R, Bogar T, Childress J, Dirzo R, Klope M, Lafferty KD, McLaughlin J, Morse M, Motta C, Park K, Plummer K, Weber D, Young R, Young H. Predator–prey interactions of terrestrial invertebrates are determined by predator body size and species identity. Ecology 2022; 103:e3634. [DOI: 10.1002/ecy.3634] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 09/15/2021] [Accepted: 10/18/2021] [Indexed: 11/11/2022]
Affiliation(s)
- Ana Miller‐ter Kuile
- Department of Ecology, Evolution, and Marine Biology University of California, Santa Barbara Santa Barbara California United States
| | - Austen Apigo
- Department of Ecology, Evolution, and Marine Biology University of California, Santa Barbara Santa Barbara California United States
| | - An Bui
- Department of Ecology, Evolution, and Marine Biology University of California, Santa Barbara Santa Barbara California United States
| | - Bartholomew DiFiore
- Department of Ecology, Evolution, and Marine Biology University of California, Santa Barbara Santa Barbara California United States
| | - Elizabeth S. Forbes
- Department of Ecology, Evolution, and Marine Biology University of California, Santa Barbara Santa Barbara California United States
| | - Michelle Lee
- Department of Ecology, Evolution, and Marine Biology University of California, Santa Barbara Santa Barbara California United States
| | - Devyn Orr
- Department of Ecology, Evolution, and Marine Biology University of California, Santa Barbara Santa Barbara California United States
| | - Daniel L. Preston
- Department of Fish, Wildlife, and Conservation Biology Colorado State University Fort Collins Colorado United States
| | - Rachel Behm
- Department of Ecology, Evolution, and Marine Biology University of California, Santa Barbara Santa Barbara California United States
| | - Taylor Bogar
- School of Biological Sciences University of Hong Kong Hong Kong HK
| | - Jasmine Childress
- Department of Ecology, Evolution, and Marine Biology University of California, Santa Barbara Santa Barbara California United States
| | - Rodolfo Dirzo
- Department of Biology Stanford University, Gilbert Biology Building, 371 Jane Stanford Way Stanford California United States
| | - Maggie Klope
- Department of Ecology, Evolution, and Marine Biology University of California, Santa Barbara Santa Barbara California United States
| | - Kevin D. Lafferty
- Western Ecological Research Center U.S. Geological Survey, at Marine Science Institute, University of California Santa Barbara United States
| | - John McLaughlin
- Department of Ecology, Evolution, and Marine Biology University of California, Santa Barbara Santa Barbara California United States
| | - Marisa Morse
- Department of Ecology, Evolution, and Marine Biology University of California, Santa Barbara Santa Barbara California United States
| | - Carina Motta
- Department of Ecology, Evolution, and Marine Biology University of California, Santa Barbara Santa Barbara California United States
| | - Kevin Park
- Department of Ecology, Evolution, and Marine Biology University of California, Santa Barbara Santa Barbara California United States
| | - Katherine Plummer
- Department of Biology Stanford University, Gilbert Biology Building, 371 Jane Stanford Way Stanford California United States
| | - David Weber
- Warnell School of Forestry and Natural Resources University of Georgia Athens Georgia United States
| | - Ronny Young
- Department of Ecology, Evolution, and Marine Biology University of California, Santa Barbara Santa Barbara California United States
| | - Hillary Young
- Department of Ecology, Evolution, and Marine Biology University of California, Santa Barbara Santa Barbara California United States
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Higgins E, Parr TB, Vaughn CC. Mussels and Local Conditions Interact to Influence Microbial Communities in Mussel Beds. Front Microbiol 2022; 12:790554. [PMID: 35095802 PMCID: PMC8793333 DOI: 10.3389/fmicb.2021.790554] [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: 10/06/2021] [Accepted: 11/24/2021] [Indexed: 11/13/2022] Open
Abstract
Microbiomes are increasingly recognized as widespread regulators of function from individual organism to ecosystem scales. However, the manner in which animals influence the structure and function of environmental microbiomes has received considerably less attention. Using a comparative field study, we investigated the relationship between freshwater mussel microbiomes and environmental microbiomes. We used two focal species of unionid mussels, Amblema plicata and Actinonaias ligamentina, with distinct behavioral and physiological characteristics. Mussel microbiomes, those of the shell and biodeposits, were less diverse than both surface and subsurface sediment microbiomes. Mussel abundance was a significant predictor of sediment microbial community composition, but mussel species richness was not. Our data suggest that local habitat conditions which change dynamically along streams, such as discharge, water turnover, and canopy cover, work in tandem to influence environmental microbial community assemblages at discreet rather than landscape scales. Further, mussel burrowing activity and mussel shells may provide habitat for microbial communities critical to nutrient cycling in these systems.
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Affiliation(s)
- Edward Higgins
- Oklahoma Biological Survey and Department of Biology, University of Oklahoma, Norman, OK, United States
- *Correspondence: Edward Higgins,
| | - Thomas B. Parr
- Oklahoma Biological Survey and Department of Biology, University of Oklahoma, Norman, OK, United States
- National Park Service, Great Lakes Inventory and Monitoring Network, Ashland, WI, United States
| | - Caryn C. Vaughn
- Oklahoma Biological Survey and Department of Biology, University of Oklahoma, Norman, OK, United States
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