1
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Vargovčík O, Čiamporová-Zaťovičová Z, Beracko P, Kopáček J, Macko P, Tuhrinová K, Čiampor F. Environmental gradients and optimal fixation time revealed with DNA metabarcoding of benthic sample fixative. Sci Rep 2024; 14:18396. [PMID: 39117754 PMCID: PMC11310421 DOI: 10.1038/s41598-024-68939-x] [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: 02/01/2024] [Accepted: 07/30/2024] [Indexed: 08/10/2024] Open
Abstract
Assessments of biodiversity and ecosystem status can benefit from DNA metabarcoding as a means to streamline sample processing and specimen identification. Moreover, processing the fixation medium instead of the precious material introduces straightforward protocols that allow subsequent focus on certain organisms detected among the preserved specimens. In this study, we present a proof of concept via the analysis of freshwater invertebrate samples from the Tatra Mountain lakes (Slovakia). Besides highlighting a match between the lake-specific environmental conditions and the results of our fixative DNA metabarcoding, we observed an option to fine-tune the fixation time: to prefer two weeks over a day or a month. This effect emerged from the presence/absence of individual taxa rather than from coarse per-sample records of taxonomic richness, demonstrating that metabarcoding studies-and efforts to optimize their protocols-can use the robust metrics to explore even subtle trends. We also provide evidence that fixative DNA might better capture large freshwater species than terrestrial or meiofauna.
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Affiliation(s)
- Ondrej Vargovčík
- Department of Ecology, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, 842 15, Slovakia
- Department of Biodiversity and Ecology, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, Bratislava, 845 23, Slovakia
| | - Zuzana Čiamporová-Zaťovičová
- Department of Ecology, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, 842 15, Slovakia.
- Department of Biodiversity and Ecology, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, Bratislava, 845 23, Slovakia.
| | - Pavel Beracko
- Department of Ecology, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, 842 15, Slovakia
| | - Jiří Kopáček
- Institute of Hydrobiology, Biology Centre CAS, České Budějovice, 370 05, Czech Republic
| | - Patrik Macko
- Department of Ecology, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, 842 15, Slovakia
| | - Kornélia Tuhrinová
- Department of Ecology, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, 842 15, Slovakia
- Department of Biodiversity and Ecology, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, Bratislava, 845 23, Slovakia
| | - Fedor Čiampor
- Department of Biodiversity and Ecology, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, Bratislava, 845 23, Slovakia
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2
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Chai Z, Liu Y, Jia S, Li F, Hu Z, Deng Y, Yue C, Tang YZ. DNA and RNA Stability of Marine Microalgae in Cold-Stored Sediments and Its Implications in Metabarcoding Analyses. Int J Mol Sci 2024; 25:1724. [PMID: 38339002 PMCID: PMC10855355 DOI: 10.3390/ijms25031724] [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: 12/15/2023] [Revised: 01/24/2024] [Accepted: 01/25/2024] [Indexed: 02/12/2024] Open
Abstract
The ever-increasing applications of metabarcoding analyses for environmental samples demand a well-designed assessment of the stability of DNA and RNA contained in cells that are deposited or buried in marine sediments. We thus conducted a qPCR quantification of the DNA and RNA in the vegetative cells of three microalgae entrapped in facsimile marine sediments and found that >90% of DNA and up to 99% of RNA for all microalgal species were degraded within 60 days at 4 °C. A further examination of the potential interference of the relic DNA of the vegetative cells with resting cyst detection in sediments was performed via a metabarcoding analysis in artificial marine sediments spiked with the vegetative cells of two Kareniaceae dinoflagellates and the resting cysts of another three dinoflagellates. The results demonstrated a dramatic decrease in the relative abundances of the two Kareniaceae dinoflagellates in 120 days, while those of the three resting cysts increased dramatically. Together, our results suggest that a positive detection of microalgae via metabarcoding analysis in DNA or RNA extracted from marine sediments strongly indicates the presence of intact or viable cysts or spores due to the rapid decay of relic DNA/RNA. This study provides a solid basis for the data interpretation of metabarcoding surveys, particularly in resting cyst detection.
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Affiliation(s)
- Zhaoyang Chai
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (Z.C.); (Y.L.); (F.L.); (Z.H.); (Y.D.); (C.Y.)
- Laoshan Laboratory, Qingdao 266237, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Yuyang Liu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (Z.C.); (Y.L.); (F.L.); (Z.H.); (Y.D.); (C.Y.)
- Laoshan Laboratory, Qingdao 266237, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Siyang Jia
- Yellow Sea and East Sea Buoy Observation Station, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China;
| | - Fengting Li
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (Z.C.); (Y.L.); (F.L.); (Z.H.); (Y.D.); (C.Y.)
- Laoshan Laboratory, Qingdao 266237, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Zhangxi Hu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (Z.C.); (Y.L.); (F.L.); (Z.H.); (Y.D.); (C.Y.)
- Laoshan Laboratory, Qingdao 266237, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Yunyan Deng
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (Z.C.); (Y.L.); (F.L.); (Z.H.); (Y.D.); (C.Y.)
- Laoshan Laboratory, Qingdao 266237, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Caixia Yue
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (Z.C.); (Y.L.); (F.L.); (Z.H.); (Y.D.); (C.Y.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ying-Zhong Tang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (Z.C.); (Y.L.); (F.L.); (Z.H.); (Y.D.); (C.Y.)
- Laoshan Laboratory, Qingdao 266237, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
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3
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Haas-Renninger M, Schwabe NLA, Moser M, Krogmann L. Black gold rush - Evaluating the efficiency of the Fractionator in separating Hymenoptera families in a meadow ecosystem over a two week period. Biodivers Data J 2023; 11:e107051. [PMID: 37915314 PMCID: PMC10616778 DOI: 10.3897/bdj.11.e107051] [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: 05/26/2023] [Accepted: 08/16/2023] [Indexed: 11/03/2023] Open
Abstract
In the face of insect decline, monitoring projects are launched widely to assess trends of insect populations. Collecting over long time periods results in large numbers of samples with thousands of individuals that are often just stored in freezers waiting to be further processed. As the time-consuming process of sorting and identifying specimens prevents taxonomists from working on mass samples, important information on species composition remains unknown and taxonomically neglected species remain undiagnosed. Size fractioning of bulk samples can improve sample handling and, thus, can help to overcome the taxonomic impediment. In this paper, we evaluate the efficiency of the fractionator in separating Hymenoptera families from a Malaise trap sample of a meadow ecosystem over a two week interval to make them available for further morphological identification. The fractionator system by Buffington and Gates (2008) was used to separate the sample in two size classes - a large (macro) and a small (micro) fraction - and Hymenoptera specimens were then counted and identified on family level. In total, 2,449 Hymenoptera specimens were found in the macro fraction and 3,016 in the micro fraction (5,465 specimens in total). For 24 out of 34 Hymenoptera families (71%), separation was significant. This study illustrates the efficiency of the fractionator and its potential to improve workflows dealing with specimen-rich Malaise trap samples.
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Affiliation(s)
- Maura Haas-Renninger
- State Museum of Natural History Stuttgart, Stuttgart, GermanyState Museum of Natural History StuttgartStuttgartGermany
- University of Hohenheim, Stuttgart, GermanyUniversity of HohenheimStuttgartGermany
| | - Noa L. A. Schwabe
- University of Hohenheim, Stuttgart, GermanyUniversity of HohenheimStuttgartGermany
| | - Marina Moser
- State Museum of Natural History Stuttgart, Stuttgart, GermanyState Museum of Natural History StuttgartStuttgartGermany
- University of Hohenheim, Stuttgart, GermanyUniversity of HohenheimStuttgartGermany
| | - Lars Krogmann
- State Museum of Natural History Stuttgart, Stuttgart, GermanyState Museum of Natural History StuttgartStuttgartGermany
- University of Hohenheim, Stuttgart, GermanyUniversity of HohenheimStuttgartGermany
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4
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Cock PJA, Cooke DEL, Thorpe P, Pritchard L. THAPBI PICT-a fast, cautious, and accurate metabarcoding analysis pipeline. PeerJ 2023; 11:e15648. [PMID: 37609440 PMCID: PMC10441533 DOI: 10.7717/peerj.15648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 06/06/2023] [Indexed: 08/24/2023] Open
Abstract
THAPBI PICT is an open source software pipeline for metabarcoding analysis of Illumina paired-end reads, including cases of multiplexing where more than one amplicon is amplified per DNA sample. Initially a Phytophthora ITS1 Classification Tool (PICT), we demonstrate using worked examples with our own and public data sets how, with appropriate primer settings and a custom database, it can be applied to other amplicons and organisms, and used for reanalysis of existing datasets. The core dataflow of the implementation is (i) data reduction to unique marker sequences, often called amplicon sequence variants (ASVs), (ii) dynamic thresholds for discarding low abundance sequences to remove noise and artifacts (rather than error correction by default), before (iii) classification using a curated reference database. The default classifier assigns a label to each query sequence based on a database match that is either perfect, or a single base pair edit away (substitution, deletion or insertion). Abundance thresholds for inclusion can be set by the user or automatically using per-batch negative or synthetic control samples. Output is designed for practical interpretation by non-specialists and includes a read report (ASVs with classification and counts per sample), sample report (samples with counts per species classification), and a topological graph of ASVs as nodes with short edit distances as edges. Source code available from https://github.com/peterjc/thapbi-pict/ with documentation including installation instructions.
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Affiliation(s)
- Peter J. A. Cock
- Information and Computational Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - David E. L. Cooke
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Peter Thorpe
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
- The Data Analysis Group, School of Life Sciences, The University of Dundee, Dundee, United Kingdom
| | - Leighton Pritchard
- Information and Computational Sciences, The James Hutton Institute, Dundee, United Kingdom
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, United Kingdom
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5
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Stenhouse EH, Bellamy P, Kirby W, Vaughan IP, Symondson WOC, Orozco-terWengel P. Herbivorous dietary selection shown by hawfinch ( Coccothraustes coccothraustes) within mixed woodland habitats. ROYAL SOCIETY OPEN SCIENCE 2023; 10:230156. [PMID: 37181798 PMCID: PMC10170347 DOI: 10.1098/rsos.230156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 04/23/2023] [Indexed: 05/16/2023]
Abstract
Knowledge of diet and dietary selectivity is vital, especially for the conservation of declining species. Accurately obtaining this information, however, is difficult, especially if the study species feeds on a wide range of food items within heterogeneous and inaccessible environments, such as the tree canopy. Hawfinches (Coccothraustes coccothraustes), like many woodland birds, are declining for reasons that are unclear. We investigated the possible role that dietary selection may have in these declines in the UK. Here, we used a combination of high-throughput sequencing of 261 hawfinch faecal samples assessed against tree occurrence data from quadrats sampled in three hawfinch population strongholds in the UK to test for evidence of selective foraging. This revealed that hawfinches show selective feeding and consume certain tree genera disproportionally to availability. Positive selection was shown for beech (Fagus), cherry (Prunus), hornbeam (Carpinus), maples (Acer) and oak (Quercus), while Hawfinch avoided ash (Fraxinus), birch (Betula), chestnut (Castanea), fir (Abies), hazel (Corylus), rowan (Sorbus) and lime (Tilia). This approach provided detailed information on hawfinch dietary choice and may be used to predict the effects of changing food resources on other declining passerines populations in the future.
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Affiliation(s)
- Ewan H. Stenhouse
- School of Biosciences, Cardiff University, Cardiff CF10 3AT, Wales, UK
- RSPB Centre for Conservation Science, The Lodge, Sandy SG19 2DL, UK
| | - Paul Bellamy
- RSPB Centre for Conservation Science, The Lodge, Sandy SG19 2DL, UK
| | - Will Kirby
- RSPB Centre for Conservation Science, The Lodge, Sandy SG19 2DL, UK
| | - Ian P. Vaughan
- School of Biosciences, Cardiff University, Cardiff CF10 3AT, Wales, UK
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6
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Li M, Lei T, Wang G, Zhang D, Liu H, Zhang Z. Monitoring insect biodiversity and comparison of sampling strategies using metabarcoding: A case study in the Yanshan Mountains, China. Ecol Evol 2023; 13:e10031. [PMID: 37091562 PMCID: PMC10121320 DOI: 10.1002/ece3.10031] [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: 07/26/2022] [Revised: 03/31/2023] [Accepted: 04/07/2023] [Indexed: 04/25/2023] Open
Abstract
Insects are the richest and most diverse group of animals and yet there remains a lack, not only of systematic research into their distribution across some key regions of the planet, but of standardized sampling strategies for their study. The Yanshan Mountains, being the boundary range between the Inner Mongolian Plateau and the North China Plain, present an indispensable piece of the insect biodiversity puzzle: both requiring systematic study and offering opportunities for the development of standardized methodologies. This is the first use of DNA metabarcoding to survey the insect biodiversity of the Yanshan Mountains. The study focuses on differences of community composition among samples collected via different methods and from different habitat types. In total, 74 bulk samples were collected from five habitat types (scrubland, woodland, wetland, farmland and grassland) using three collection methods (sweep netting, Malaise traps and light traps). After DNA extraction, PCR amplification, sequencing and diversity analysis were performed, a total of 7427 Operational Taxonomic Units (OTUs) at ≥97% sequence similarity level were delimited, of which 7083 OTUs were identified as belonging to Insecta. Orthoptera, Diptera, Coleoptera and Hemiptera were found to be the dominant orders according to community composition analysis. Nonmetric multidimensional scaling (NMDS) analysis based on Bray-Curtis distances revealed highly divergent estimates of insect community composition among samples differentiated by the collection method (R = .524802, p = .001), but nonsignificant difference among samples differentiated according to habitat (R = .051102, p = .078). The study therefore appears to indicate that the concurrent use of varied collection methods is essential to the accurate monitoring of insect biodiversity.
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Affiliation(s)
- Min Li
- College of Biological Science and TechnologyTaiyuan Normal UniversityJinzhongChina
| | - Ting Lei
- College of Biological Science and TechnologyTaiyuan Normal UniversityJinzhongChina
| | - Guobin Wang
- College of Biological Science and TechnologyTaiyuan Normal UniversityJinzhongChina
| | - Danli Zhang
- College of Biological Science and TechnologyTaiyuan Normal UniversityJinzhongChina
| | - Huaxi Liu
- Department of Life SciencesNatural History MuseumLondonUK
| | - Zhiwei Zhang
- College of Forestry, Shanxi Agricultural UniversityJinzhongChina
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7
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Nguyen N, Pawłowska J, Angeles IB, Zajaczkowski M, Pawłowski J. Metabarcoding reveals high diversity of benthic foraminifera linked to water masses circulation at coastal Svalbard. GEOBIOLOGY 2023; 21:133-150. [PMID: 36259453 PMCID: PMC10092302 DOI: 10.1111/gbi.12530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 07/05/2022] [Accepted: 09/19/2022] [Indexed: 06/16/2023]
Abstract
Arctic marine biodiversity is undergoing rapid changes due to global warming and modifications of oceanic water masses circulation. These changes have been demonstrated in the case of mega- and macrofauna, but much less is known about their impact on the biodiversity of smaller size organisms, such as foraminifera that represent a main component of meiofauna in the Arctic. Several studies analyzed the distribution and diversity of Arctic foraminifera. However, all these studies are based exclusively on the morphological identification of specimens sorted from sediment samples. Here, we present the first assessment of Arctic foraminifera diversity based on metabarcoding of sediment DNA samples collected in fjords and open sea areas in the Svalbard Archipelago. We obtained a total of 5,968,786 reads that represented 1384 amplicon sequence variants (ASVs). More than half of the ASVs (51.7%) could not be assigned to any group in the reference database suggesting a high genetic novelty of Svalbard foraminifera. The sieved and unsieved samples resolved comparable communities, sharing 1023 ASVs, comprising over 97% of reads. Our analyses show that the foraminiferal assemblage differs between the localities, with communities distinctly separated between fjord and open sea stations. Each locality was characterized by a specific assemblage, with only a small overlap in the case of open sea areas. Our study demonstrates a clear pattern of the influence of water masses on the structure of foraminiferal communities. The stations situated on the western coast of Svalbard that are strongly influenced by warm and salty Atlantic water (AW) are characterized by much higher diversity than stations in the northern and eastern part, where the impact of AW is less pronounced. This high diversity and specificity of Svalbard foraminifera associated with water mass distribution indicate that the foraminiferal metabarcoding data can be very useful for inferring present and past environmental conditions in the Arctic.
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Affiliation(s)
- Ngoc‐Loi Nguyen
- Institute of Oceanology Polish Academy of SciencesSopotPoland
| | | | - Inès Barrenechea Angeles
- Department of Earth SciencesUniversity of GenevaGenevaSwitzerland
- Department of Genetics and EvolutionUniversity of GenevaGenevaSwitzerland
| | | | - Jan Pawłowski
- Institute of Oceanology Polish Academy of SciencesSopotPoland
- Department of Genetics and EvolutionUniversity of GenevaGenevaSwitzerland
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8
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Designing a surveillance program for early detection of alien plants and insects in Norway. Biol Invasions 2022. [DOI: 10.1007/s10530-022-02957-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
AbstractNaturalized species of alien plants and animals comprise < 3% of biodiversity recorded in Norway but have had major impacts on natural ecosystems through displacement of native species. Encroachment of alien species has been especially problematic for coastal sites close to transport facilities and urban areas with high density housing. The goal of our field project was to design and test a surveillance program for early detection of alien species of vascular plants and terrestrial insects at the first phase of establishment in natural areas. In our 3-year project (2018–2020), we sampled 60 study plots in three counties in the Oslofjord region of southern Norway. Study plots (6.25 ha) were selected by two criteria: manual selection based on expert opinion (27 plots) or by random selection based on weights from a hotspot analysis of occurrence of alien species (33 plots). Vascular plants were surveyed by two experienced botanists who found a total of 239 alien species of vascular plants in 95 rounds of surveys. Insects and other invertebrates were captured with a single Malaise trap per site, with 3–4 rounds of repeated sampling. We used DNA-metabarcoding to identify invertebrates based on DNA extractions from crushed insects or from the preservative media. Over 3500 invertebrate taxa were detected in 255 rounds of sampling. We recorded 20 alien species of known risk, and 115 species that were new to Norway, including several ‘doorknocker’ species identified by previous risk assessments. We modeled the probabilities of occupancy (ψ) and detection (p) with occupancy models with repeated visits by multiple observers (vascular plants) or multiple rounds of sampling (insects). The two probabilities covaried with risk category for alien organisms and both were low for species categorized as no known or low risk (range = 0.052–0.326) but were higher for species categorized as severe risk (range = 0.318–0.651). Selecting sites at random or manually did not improve the probability of finding novel alien species, but occupancy had a weak positive relationship with housing density for some categories of alien plants and insects. We used our empirical estimates to test alternative sampling designs that would minimize the combined variance of occupancy and detection (A-optimality criterion). Sampling designs with 8–10 visits per site were best for surveillance of new alien species if the probabilities of occupancy and detection were both low, and provided low conditional probabilities of site occupancy ($$\hat{\psi }_{condl}$$
ψ
^
condl
≤ 0.032) and a high probabilities of cumulative detection ($$\hat{p}*$$
p
^
∗
≥ 0.943). Our field results demonstrate that early detection is feasible as a key component of a national surveillance program based on early detection and rapid response.
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9
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Rogers AD, Appeltans W, Assis J, Ballance LT, Cury P, Duarte C, Favoretto F, Hynes LA, Kumagai JA, Lovelock CE, Miloslavich P, Niamir A, Obura D, O'Leary BC, Ramirez-Llodra E, Reygondeau G, Roberts C, Sadovy Y, Steeds O, Sutton T, Tittensor DP, Velarde E, Woodall L, Aburto-Oropeza O. Discovering marine biodiversity in the 21st century. ADVANCES IN MARINE BIOLOGY 2022; 93:23-115. [PMID: 36435592 DOI: 10.1016/bs.amb.2022.09.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
We review the current knowledge of the biodiversity of the ocean as well as the levels of decline and threat for species and habitats. The lack of understanding of the distribution of life in the ocean is identified as a significant barrier to restoring its biodiversity and health. We explore why the science of taxonomy has failed to deliver knowledge of what species are present in the ocean, how they are distributed and how they are responding to global and regional to local anthropogenic pressures. This failure prevents nations from meeting their international commitments to conserve marine biodiversity with the results that investment in taxonomy has declined in many countries. We explore a range of new technologies and approaches for discovery of marine species and their detection and monitoring. These include: imaging methods, molecular approaches, active and passive acoustics, the use of interconnected databases and citizen science. Whilst no one method is suitable for discovering or detecting all groups of organisms many are complementary and have been combined to give a more complete picture of biodiversity in marine ecosystems. We conclude that integrated approaches represent the best way forwards for accelerating species discovery, description and biodiversity assessment. Examples of integrated taxonomic approaches are identified from terrestrial ecosystems. Such integrated taxonomic approaches require the adoption of cybertaxonomy approaches and will be boosted by new autonomous sampling platforms and development of machine-speed exchange of digital information between databases.
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Affiliation(s)
- Alex D Rogers
- REV Ocean, Lysaker, Norway; Nekton Foundation, Begbroke Science Park, Oxford, United Kingdom.
| | - Ward Appeltans
- Intergovernmental Oceanographic Commission of UNESCO, Oostende, Belgium
| | - Jorge Assis
- Centre of Marine Sciences, University of Algarve, Faro, Portugal
| | - Lisa T Ballance
- Marine Mammal Institute, Oregon State University, Newport, OR, United States
| | | | - Carlos Duarte
- King Abdullah University of Science and Technology (KAUST), Red Sea Research Center (RSRC) and Computational Bioscience Research Center (CBRC), Thuwal, Kingdom of Saudi Arabia
| | - Fabio Favoretto
- Autonomous University of Baja California Sur, La Paz, Baja California Sur, Mexico
| | - Lisa A Hynes
- Nekton Foundation, Begbroke Science Park, Oxford, United Kingdom
| | - Joy A Kumagai
- Senckenberg Biodiversity and Climate Research Institute, Frankfurt am Main, Germany
| | - Catherine E Lovelock
- School of Biological Sciences, The University of Queensland, St Lucia, QLD, Australia
| | - Patricia Miloslavich
- Scientific Committee on Oceanic Research (SCOR), College of Earth, Ocean and Environment, University of Delaware, Newark, DE, United States; Departamento de Estudios Ambientales, Universidad Simón Bolívar, Venezuela & Scientific Committee for Oceanic Research (SCOR), Newark, DE, United States
| | - Aidin Niamir
- Senckenberg Biodiversity and Climate Research Institute, Frankfurt am Main, Germany
| | | | - Bethan C O'Leary
- Centre for Ecology & Conservation, College of Life and Environmental Sciences, University of Exeter, Penryn, United Kingdom; Department of Environment and Geography, University of York, York, United Kingdom
| | - Eva Ramirez-Llodra
- REV Ocean, Lysaker, Norway; Nekton Foundation, Begbroke Science Park, Oxford, United Kingdom
| | - Gabriel Reygondeau
- Yale Center for Biodiversity Movement and Global Change, Yale University, New Haven, CT, United States; Nippon Foundation-Nereus Program, Institute for the Oceans and Fisheries, University of British Columbia, Vancouver, BC, Canada
| | - Callum Roberts
- Centre for Ecology & Conservation, College of Life and Environmental Sciences, University of Exeter, Penryn, United Kingdom
| | - Yvonne Sadovy
- School of Biological Sciences, Swire Institute of Marine Science, The University of Hong Kong, Hong Kong
| | - Oliver Steeds
- Nekton Foundation, Begbroke Science Park, Oxford, United Kingdom
| | - Tracey Sutton
- Nova Southeastern University, Halmos College of Natural Sciences and Oceanography, Dania Beach, FL, United States
| | | | - Enriqueta Velarde
- Instituto de Ciencias Marinas y Pesquerías, Universidad Veracruzana, Veracruz, Mexico
| | - Lucy Woodall
- Nekton Foundation, Begbroke Science Park, Oxford, United Kingdom; Department of Zoology, University of Oxford, Oxford, United Kingdom
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10
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Fluctuating insect diversity, abundance and biomass across agricultural landscapes. Sci Rep 2022; 12:17706. [PMID: 36271271 PMCID: PMC9587014 DOI: 10.1038/s41598-022-20989-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 09/21/2022] [Indexed: 01/18/2023] Open
Abstract
Habitat destruction and deterioration of habitat quality caused a severe decline of biodiversity, such as insect diversity. In this study, we analyze insect diversity and biomass across agro-environments. We collected flying insects with 20 malaise traps across a landscape mosaic consisting of organic (eight traps) and conventional (four traps) farmland, as well as across agricultural land that has been recently converted from conventional to organic farming (eight traps). Sampling was conducted over 2 years, in 2019 and 2020, with in total 340 sampling events. We measured the dry weight of the captured organisms and identified species diversity by analyzing Operational Taxonomic Units (OTUs) and Barcode Index Numbers (BINs) via metabarcoding. The results obtained show temporal dynamics. The number of OTUs were always higher than the number of BINs. OTUs and BINs were moderately to highly correlated, while the number of OTUs and BINs were only moderately positively correlated with dry biomass. OTUs and BINs as well as biomass were highest in the recently transformed farmland if compared with pure organic and conventional farmland sites, which showed no significant differences in respect of insect diversity. OTU and BIN numbers but not the OTU/BIN ratio significantly decreased with increasing distance from the nearest forest fringe. The numbers of OTUs, BINs and the OTU/BIN proportion, as well as OTU and BIN/biomass proportions varied strongly over seasons, irrespective of agricultural practice. Based on our findings, we suggest to combine data on insect species richness and biomass measured over a period of time, to derive a largely complete and meaningful assessment of biodiversity for a specific region.
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11
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Arribas P, Andújar C, Bohmann K, deWaard JR, Economo EP, Elbrecht V, Geisen S, Goberna M, Krehenwinkel H, Novotny V, Zinger L, Creedy TJ, Meramveliotakis E, Noguerales V, Overcast I, Morlon H, Papadopoulou A, Vogler AP, Emerson BC. Toward global integration of biodiversity big data: a harmonized metabarcode data generation module for terrestrial arthropods. Gigascience 2022; 11:6646445. [PMID: 35852418 PMCID: PMC9295367 DOI: 10.1093/gigascience/giac065] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 05/04/2022] [Accepted: 06/02/2022] [Indexed: 11/12/2022] Open
Abstract
Metazoan metabarcoding is emerging as an essential strategy for inventorying biodiversity, with diverse projects currently generating massive quantities of community-level data. The potential for integrating across such data sets offers new opportunities to better understand biodiversity and how it might respond to global change. However, large-scale syntheses may be compromised if metabarcoding workflows differ from each other. There are ongoing efforts to improve standardization for the reporting of inventory data. However, harmonization at the stage of generating metabarcode data has yet to be addressed. A modular framework for harmonized data generation offers a pathway to navigate the complex structure of terrestrial metazoan biodiversity. Here, through our collective expertise as practitioners, method developers, and researchers leading metabarcoding initiatives to inventory terrestrial biodiversity, we seek to initiate a harmonized framework for metabarcode data generation, with a terrestrial arthropod module. We develop an initial set of submodules covering the 5 main steps of metabarcode data generation: (i) sample acquisition; (ii) sample processing; (iii) DNA extraction; (iv) polymerase chain reaction amplification, library preparation, and sequencing; and (v) DNA sequence and metadata deposition, providing a backbone for a terrestrial arthropod module. To achieve this, we (i) identified key points for harmonization, (ii) reviewed the current state of the art, and (iii) distilled existing knowledge within submodules, thus promoting best practice by providing guidelines and recommendations to reduce the universe of methodological options. We advocate the adoption and further development of the terrestrial arthropod module. We further encourage the development of modules for other biodiversity fractions as an essential step toward large-scale biodiversity synthesis through harmonization.
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Affiliation(s)
- Paula Arribas
- Island Ecology and Evolution Research Group, Institute of Natural Products and Agrobiology (IPNA-CSIC), 38206 San Cristóbal de la Laguna, Spain
| | - Carmelo Andújar
- Island Ecology and Evolution Research Group, Institute of Natural Products and Agrobiology (IPNA-CSIC), 38206 San Cristóbal de la Laguna, Spain
| | - Kristine Bohmann
- Section for Evolutionary Genomics, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark
| | - Jeremy R deWaard
- Centre for Biodiversity Genomics, University of Guelph, N1G2W1 Guelph, Canada.,School of Environmental Sciences, University of Guelph, N1G2W1 Guelph, Canada
| | - Evan P Economo
- Biodiversity and Biocomplexity Unit, Okinawa Institute of Science and Technology Graduate University, 904-0495 Japan
| | - Vasco Elbrecht
- Centre for Biodiversity Monitoring (ZBM), Zoological Research Museum Alexander Koenig,D-53113 Bonn, Germany
| | - Stefan Geisen
- Laboratory of Nematology, Department of Plant Sciences, Wageningen University and Research, 6708PB Wageningen, The Netherlands
| | - Marta Goberna
- Department of Environment and Agronomy, INIA-CSIC, 28040 Madrid, Spain
| | | | - Vojtech Novotny
- Biology Centre, Czech Academy of Sciences, Institute of Entomology, 37005 Ceske Budejovice, Czech Republic.,Faculty of Science, University of South Bohemia, 37005 Ceske Budejovice, Czech Republic
| | - Lucie Zinger
- Institut de Biologie de l'ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France.,Naturalis Biodiversity Center, 2300 RA Leiden, The Netherlands
| | - Thomas J Creedy
- Department of Life Sciences, Natural History Museum, SW7 5BD London, UK
| | | | - Víctor Noguerales
- Island Ecology and Evolution Research Group, Institute of Natural Products and Agrobiology (IPNA-CSIC), 38206 San Cristóbal de la Laguna, Spain
| | - Isaac Overcast
- Institut de Biologie de l'ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
| | - Hélène Morlon
- Institut de Biologie de l'ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
| | - Anna Papadopoulou
- Department of Biological Sciences, University of Cyprus, 1678 Nicosia, Cyprus
| | - Alfried P Vogler
- Department of Life Sciences, Natural History Museum, SW7 5BD London, UK.,Department of Life Sciences, Imperial College London, SW7 2AZ London, UK
| | - Brent C Emerson
- Island Ecology and Evolution Research Group, Institute of Natural Products and Agrobiology (IPNA-CSIC), 38206 San Cristóbal de la Laguna, Spain
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12
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Marquina D, Roslin T, Łukasik P, Ronquist F. Evaluation of non-destructive DNA extraction protocols for insect metabarcoding: gentler and shorter is better. METABARCODING AND METAGENOMICS 2022. [DOI: 10.3897/mbmg.6.78871] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
DNA metabarcoding can accelerate research on insect diversity, as it is cheap and fast compared to manual sorting and identification. Most metabarcoding protocols require homogenisation of the sample, preventing further work on the specimens. Mild digestion of the tissue by incubation in a lysis buffer has been proposed as an alternative, and, although some mild lysis protocols have already been presented, they have so far not been evaluated against each other. Here, we analyse how two mild lysis buffers (one more aggressive, one gentler in terms of tissue degradation), two different incubation times, and two DNA purification methods (a manual precipitation and an automated protocol) affect the accuracy of retrieving the true composition of mock communities using two mitochondrial markers (COI and 16S). We found that protocol-specific variation in concentration and purity of the DNA extracts produced had little effect on the recovery of species. However, the two lysis treatments differed in quantification of species abundances. Digestion in the gentler buffer and for a shorter time yielded better representation of original sample composition. Digestion in a more aggressive buffer or longer incubation time yielded lower alpha diversity values and increased differences between metabarcoding results and the true species-abundance distribution. We conclude that the details of non-destructive protocols can have a significant effect on metabarcoding performance. A short and mild lysis treatment appears the best choice for recovering the true composition of the sample. This not only improves accuracy, but also comes with a faster processing time than the other treatments.
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13
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Egeter B, Veríssimo J, Lopes-Lima M, Chaves C, Pinto J, Riccardi N, Beja P, Fonseca NA. Speeding up the detection of invasive bivalve species using environmental DNA: a Nanopore and Illumina sequencing comparison. Mol Ecol Resour 2022; 22:2232-2247. [PMID: 35305077 DOI: 10.1111/1755-0998.13610] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 02/09/2022] [Accepted: 03/02/2022] [Indexed: 11/30/2022]
Abstract
Traditional detection of aquatic invasive species via morphological identification is often time-consuming and can require a high level of taxonomic expertise, leading to delayed mitigation responses. Environmental DNA (eDNA) detection approaches of multiple species using Illumina-based sequencing technology have been used to overcome these hindrances, but sample processing is often lengthy. More recently, portable nanopore sequencing technology has become available, which has the potential to make molecular detection of invasive species more widely accessible and substantially decrease sample turnaround times. However, nanopore-sequenced reads have a much higher error rate than those produced by Illumina platforms, which has so far hindered the adoption of this technology. We provide a detailed laboratory protocol and bioinformatic tools (msi package) to increase the reliability of nanopore sequencing to detect invasive species, and we test its application using invasive bivalves while comparing it with Illumina-based sequencing. We sampled water from sites with pre-existing bivalve occurrence and abundance data, and contrasting bivalve communities, in Italy and Portugal. Samples were extracted, amplified, and sequenced by the two platforms. The mean agreement between sequencing methods was 69% and the difference between methods was non-significant. The lack of detections of some species at some sites could be explained by their known low abundances. This is the first reported use of MinION to detect aquatic invasive species from eDNA samples.
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Affiliation(s)
- Bastian Egeter
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661, Vairão, Portugal.,NatureMetrics, Bakeham Lane, Egham, Surrey, TW20 9TY, U.K
| | - Joana Veríssimo
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661, Vairão, Portugal.,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | - Manuel Lopes-Lima
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661, Vairão, Portugal.,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal.,IUCN SSC Mollusc Specialist Group, c/o 219 Huntingdon Road, Cambridge, CB3 0DL, U.K
| | - Cátia Chaves
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661, Vairão, Portugal.,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal
| | - Joana Pinto
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661, Vairão, Portugal.,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal
| | | | - Pedro Beja
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661, Vairão, Portugal.,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal.,CIBIO/InBIO, Instituto Superior de Agronomia, Universidade de Lisboa, Lisboa, Portugal
| | - Nuno A Fonseca
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661, Vairão, Portugal.,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal
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14
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Martoni F, Piper AM, Rodoni BC, Blacket MJ. Disentangling bias for non-destructive insect metabarcoding. PeerJ 2022; 10:e12981. [PMID: 35228909 PMCID: PMC8881911 DOI: 10.7717/peerj.12981] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 02/01/2022] [Indexed: 01/11/2023] Open
Abstract
A fast and reliable method for obtaining a species-level identification is a fundamental requirement for a wide range of activities, from plant protection and invasive species management to biodiversity assessments and ecological studies. For insects, novel molecular techniques such as DNA metabarcoding have emerged as a rapid alternative to traditional morphological identification, reducing the dependence on limited taxonomic experts. Until recently, molecular techniques have required a destructive DNA extraction, precluding the possibility of preserving voucher specimens for future studies, or species descriptions. Here we paired insect metabarcoding with two recent non-destructive DNA extraction protocols, to obtain a rapid and high-throughput taxonomic identification of diverse insect taxa while retaining a physical voucher specimen. The aim of this work was to explore how non-destructive extraction protocols impact the semi-quantitative nature of metabarcoding, which alongside species presence/absence also provides a quantitative, but biased, representation of their relative abundances. By using a series of mock communities representing each stage of a typical metabarcoding workflow we were able to determine how different morphological (i.e., insect biomass and exoskeleton hardness) and molecular traits (i.e., primer mismatch and amplicon GC%), interact with different protocol steps to introduce quantitative bias into non-destructive metabarcoding results. We discuss the relevance of taxonomic bias to metabarcoding identification of insects and potential approaches to account for it.
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Affiliation(s)
- Francesco Martoni
- Agriculture Victoria Research, AgriBio Centre for AgriBioscience, State Government Victoria, Bundoora, Victoria, Australia
| | - Alexander M. Piper
- Agriculture Victoria Research, AgriBio Centre for AgriBioscience, State Government Victoria, Bundoora, Victoria, Australia,School of Applied Systems Biology, La Trobe University, Bundoora, Victoria, Australia
| | - Brendan C. Rodoni
- Agriculture Victoria Research, AgriBio Centre for AgriBioscience, State Government Victoria, Bundoora, Victoria, Australia,School of Applied Systems Biology, La Trobe University, Bundoora, Victoria, Australia
| | - Mark J. Blacket
- Agriculture Victoria Research, AgriBio Centre for AgriBioscience, State Government Victoria, Bundoora, Victoria, Australia
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15
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Aquatic Ecological Risk of Heavy-Metal Pollution Associated with Degraded Mining Landscapes of the Southern Africa River Basins: A Review. MINERALS 2022. [DOI: 10.3390/min12020225] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Africa accounts for nearly 30% of the discovered world’s mineral reserves, with half of the world’s platinum group metals deposits, 36% of gold, and 20% of cobalt being in Southern Africa (SA). The intensification of heavy-metal production in the SA region has exacerbated negative human and environmental health impacts. In recent years, mining waste generated from industrial and artisanal mining has significantly affected the ecological integrity of SA aquatic ecosystems due to the accelerated introduction and deposition of heavy metals. However, the extent to which heavy-metal pollution associated with mining has impacted the aquatic ecosystems has not been adequately documented, particularly during bioassessments. This review explores the current aquatic ecological impacts on the heavily mined river basins of SA. It also discusses the approaches to assessing the ecological risks, inherent challenges, and potential for developing an integrated ecological risk assessment protocol for aquatic systems in the region. Progress has been made in developing rapid bioassessment schemes (RBS) for SA aquatic ecosystems. Nevertheless, method integration, which also involves heavy-metal pollution monitoring and molecular technology, is necessary to overcome the current challenges of the standardisation of RBS protocols. Citizenry science will also encourage community and stakeholder involvement in sustainable environmental management in SA.
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16
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Young MR, Hebert PDN. Unearthing soil arthropod diversity through DNA metabarcoding. PeerJ 2022; 10:e12845. [PMID: 35178296 PMCID: PMC8815377 DOI: 10.7717/peerj.12845] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 01/06/2022] [Indexed: 01/10/2023] Open
Abstract
DNA metabarcoding has the potential to greatly advance understanding of soil biodiversity, but this approach has seen limited application for the most abundant and species-rich group of soil fauna-the arthropods. This study begins to address this gap by comparing information on species composition recovered from metabarcoding two types of bulk samples (specimens, soil) from a temperate zone site and from bulk soil samples collected at eight sites in the Arctic. Analysis of 22 samples (3 specimen, 19 soil) revealed 410 arthropod OTUs belonging to 112 families, 25 orders, and nine classes. Studies at the temperate zone site revealed little overlap in species composition between soil and specimen samples, but more overlap at higher taxonomic levels (families, orders) and congruent patterns of α- and β-diversity. Expansion of soil analyses to the Arctic revealed locally rich, highly dissimilar, and spatially structured assemblages compatible with dispersal limited and environmentally driven assembly. The current study demonstrates that DNA metabarcoding of bulk soil enables rapid, large-scale assessments of soil arthropod diversity. However, deep sequence coverage is required to adequately capture the species present in these samples, and expansion of the DNA barcode reference library is necessary to improve taxonomic resolution of the sequences recovered through this approach.
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Affiliation(s)
- Monica R. Young
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada,Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
| | - Paul D. N. Hebert
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada,Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
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17
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van der Heyde M, Bunce M, Dixon KW, Fernandes K, Majer J, Wardell-Johnson G, White NE, Nevill P. Evaluating restoration trajectories using DNA metabarcoding of ground-dwelling and airborne invertebrates and associated plant communities. Mol Ecol 2022; 31:2172-2188. [PMID: 35092102 PMCID: PMC9304231 DOI: 10.1111/mec.16375] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 12/05/2021] [Accepted: 01/19/2022] [Indexed: 11/26/2022]
Abstract
Invertebrates are important for restoration processes as they are key drivers of many landscape‐scale ecosystem functions; including pollination, nutrient cycling and soil formation. However, invertebrates are often overlooked in restoration monitoring because they are highly diverse, poorly described, and time‐consuming to survey, and require increasingly scarce taxonomic expertise to enable identification. DNA metabarcoding is a relatively new tool for rapid survey that is able to address some of these concerns, and provide information about the taxa with which invertebrates are interacting via food webs and habitat. Here, we evaluate how invertebrate communities may be used to determine ecosystem trajectories during restoration. We collected ground‐dwelling and airborne invertebrates across chronosequences of mine‐site restoration in three ecologically disparate locations in Western Australia and identified invertebrate and plant communities using DNA metabarcoding. Ground‐dwelling invertebrates showed the clearest restoration signals, with communities becoming more similar to reference communities over time. These patterns were weaker in airborne invertebrates, which have higher dispersal abilities and therefore less local fidelity to environmental conditions. Although we detected directional changes in community composition indicative of invertebrate recovery, patterns observed were inconsistent between study locations. The inclusion of plant assays allowed identification of plant species, as well as potential food sources and habitat. We demonstrate that DNA metabarcoding of invertebrate communities can be used to evaluate restoration trajectories. Testing and incorporating new monitoring techniques such as DNA metabarcoding is critical to improving restoration outcomes.
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Affiliation(s)
- M van der Heyde
- ARC Centre for Mine Site Restoration, School of Molecular and Life Sciences, Curtin University, Bentley, GPP Box U1987, Perth, Western Australia, 6845, Australia.,Trace and Environmental DNA Laboratory, School of Life and Molecular Sciences, Curtin University, GPP Box U1987, Perth, Western Australia, 6845, Australia
| | - M Bunce
- Trace and Environmental DNA Laboratory, School of Life and Molecular Sciences, Curtin University, GPP Box U1987, Perth, Western Australia, 6845, Australia.,Institute of Environmental Science and Research (ESR), Kenepuru, Porirua, 5022, New Zealand
| | - K W Dixon
- ARC Centre for Mine Site Restoration, School of Molecular and Life Sciences, Curtin University, Bentley, GPP Box U1987, Perth, Western Australia, 6845, Australia
| | - K Fernandes
- Trace and Environmental DNA Laboratory, School of Life and Molecular Sciences, Curtin University, GPP Box U1987, Perth, Western Australia, 6845, Australia
| | - J Majer
- ARC Centre for Mine Site Restoration, School of Molecular and Life Sciences, Curtin University, Bentley, GPP Box U1987, Perth, Western Australia, 6845, Australia
| | - G Wardell-Johnson
- ARC Centre for Mine Site Restoration, School of Molecular and Life Sciences, Curtin University, Bentley, GPP Box U1987, Perth, Western Australia, 6845, Australia
| | - N E White
- Trace and Environmental DNA Laboratory, School of Life and Molecular Sciences, Curtin University, GPP Box U1987, Perth, Western Australia, 6845, Australia
| | - P Nevill
- ARC Centre for Mine Site Restoration, School of Molecular and Life Sciences, Curtin University, Bentley, GPP Box U1987, Perth, Western Australia, 6845, Australia.,Trace and Environmental DNA Laboratory, School of Life and Molecular Sciences, Curtin University, GPP Box U1987, Perth, Western Australia, 6845, Australia
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18
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Hu J, Pentinsaari M, Hebert PD. Measuring mass: variation among 3,161 species of Canadian Coleoptera and the prospects of a mass registry for all insects. PeerJ 2022; 10:e12799. [PMID: 35116199 PMCID: PMC8785658 DOI: 10.7717/peerj.12799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 12/24/2021] [Indexed: 01/10/2023] Open
Abstract
Although biomass values are critical for diverse ecological and evolutionary analyses, they are unavailable for most insect species. Museum specimens have the potential to address this gap, but the variation introduced by sampling and preservation methods is uncertain. This study quantifies species-level variation in the body mass of Canadian Coleoptera based on the analysis of 3,744 specimens representing 3,161 Barcode Index Number (BIN) clusters. Employing the BIN system as a proxy for species allows the inclusion of groups where the taxonomic impediment prevents the assignment of specimens to a Linnaean species. By validating the reproducibility of measurements and evaluating the error introduced by operational complexities such as curatorial practice and the loss of body parts, this study demonstrates that museum specimens can speed the assembly of a mass registry. The results further indicate that congeneric species of Coleoptera generally have limited variation in mass, so a genus-level identification allows prediction of the body mass of species that have not been weighed or measured. Building on the present results, the construction of a mass registry for all insects is feasible.
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Affiliation(s)
- Jingchan Hu
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada,Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
| | - Mikko Pentinsaari
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Paul D.N. Hebert
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada,Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
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19
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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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20
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Sire L, Yáñez PS, Wang C, Bézier A, Courtial B, Cours J, Fontaneto D, Larrieu L, Bouget C, Thorn S, Müller J, Yu DW, Monaghan MT, Herniou EA, Lopez-Vaamonde C. Climate-induced forest dieback drives compositional changes in insect communities that are more pronounced for rare species. Commun Biol 2022; 5:57. [PMID: 35042989 PMCID: PMC8766456 DOI: 10.1038/s42003-021-02968-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Accepted: 12/07/2021] [Indexed: 12/26/2022] Open
Abstract
Species richness, abundance and biomass of insects have recently undergone marked declines in Europe. We metabarcoded 211 Malaise-trap samples to investigate whether drought-induced forest dieback and subsequent salvage logging had an impact on ca. 3000 species of flying insects in silver fir Pyrenean forests. While forest dieback had no measurable impact on species richness, there were significant changes in community composition that were consistent with those observed during natural forest succession. Importantly, most observed changes were driven by rare species. Variation was explained primarily by canopy openness at the local scale, and the tree-related microhabitat diversity and deadwood amount at landscape scales. The levels of salvage logging in our study did not explain compositional changes. We conclude that forest dieback drives changes in species assemblages that mimic natural forest succession, and markedly increases the risk of catastrophic loss of rare species through homogenization of environmental conditions.
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Affiliation(s)
- Lucas Sire
- Institut de Recherche sur la Biologie de l'Insecte (IRBI), UMR 7261, CNRS-Université de Tours, Tours, France.
| | - Paul Schmidt Yáñez
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Müggelseedamm 301, 12587, Berlin, Germany
| | - Cai Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
- Kunming College of Life Sciences, University of Chinese Academy of Sciences, Kunming, China
| | - Annie Bézier
- Institut de Recherche sur la Biologie de l'Insecte (IRBI), UMR 7261, CNRS-Université de Tours, Tours, France
| | | | - Jérémy Cours
- INRAE 'Forest Ecosystems' Research Unit - Biodiversity team Domaine des Barres, F-45290, Nogent-sur-Vernisson, France
| | - Diego Fontaneto
- Water Research Institute, National Research Council of Italy, CNR-IRSA, Largo Tonolli 50, 28922, Verbania Pallanza, Italy
| | - Laurent Larrieu
- Université de Toulouse, INRAE, UMR DYNAFOR, Castanet-Tolosan, France
- CRPF Occitanie, Tarbes, France
| | - Christophe Bouget
- INRAE 'Forest Ecosystems' Research Unit - Biodiversity team Domaine des Barres, F-45290, Nogent-sur-Vernisson, France
| | - Simon Thorn
- Field Station Fabrikschleichach, Department of Animal Ecology and Tropical Biology, Biocenter, University of Würzburg, Glashüttenstraße 5, 96181, Rauhenebrach, Germany
| | - Jörg Müller
- Field Station Fabrikschleichach, Department of Animal Ecology and Tropical Biology, Biocenter, University of Würzburg, Glashüttenstraße 5, 96181, Rauhenebrach, Germany
- Bavarian Forest National Park, Freyunger Str. 2, 94481, Grafenau, Germany
| | - Douglas W Yu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk, NR47TJ, UK
| | - Michael T Monaghan
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Müggelseedamm 301, 12587, Berlin, Germany
- Institut für Biologie, Freie Universität Berlin, Königin-Luise-Straße. 1-3, 12489, Berlin, Germany
| | - Elisabeth A Herniou
- Institut de Recherche sur la Biologie de l'Insecte (IRBI), UMR 7261, CNRS-Université de Tours, Tours, France
| | - Carlos Lopez-Vaamonde
- Institut de Recherche sur la Biologie de l'Insecte (IRBI), UMR 7261, CNRS-Université de Tours, Tours, France
- INRAE, Zoologie Forestière, F-45075, Orléans, France
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21
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Leroy BML, Seibold S, Morinière J, Bozicevic V, Jaworek J, Roth N, Vogel S, Zytynska S, Petercord R, Eichel P, Weisser WW. Metabarcoding of canopy arthropods reveals negative impacts of forestry insecticides on community structure across multiple taxa. J Appl Ecol 2022. [DOI: 10.1111/1365-2664.14110] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Benjamin M. L. Leroy
- Terrestrial Ecology Research Group School of Life Sciences Weihenstephan, Technical University of Munich Freising Germany
| | - Sebastian Seibold
- Terrestrial Ecology Research Group School of Life Sciences Weihenstephan, Technical University of Munich Freising Germany
- Ecosystem Dynamics and Forest Management Research Group School of Life Sciences Weihenstephan, Technical University of Munich Freising Germany
| | | | | | - Jessica Jaworek
- Terrestrial Ecology Research Group School of Life Sciences Weihenstephan, Technical University of Munich Freising Germany
| | - Nicolas Roth
- Department of Animal Ecology and Tropical Biology University of Würzburg Würzburg Germany
- School of Agricultural Forest and Food Sciences Bern University of Applied Sciences Zollikofen Switzerland
- Forest Entomology Swiss Federal Research Institute WSL Birmensdorf Switzerland
| | - Sebastian Vogel
- Department of Animal Ecology and Tropical Biology University of Würzburg Würzburg Germany
| | - Sharon Zytynska
- Terrestrial Ecology Research Group School of Life Sciences Weihenstephan, Technical University of Munich Freising Germany
- Institute of Infection, Veterinary and Ecological Sciences Department of Evolution, Ecology and Behaviour, University of Liverpool Liverpool United Kingdom
| | - Ralf Petercord
- Forest Protection Bavarian State Institute for Forests and Silviculture Freising Germany
| | - Peter Eichel
- Forest Protection Bavarian State Institute for Forests and Silviculture Freising Germany
| | - Wolfgang W. Weisser
- Terrestrial Ecology Research Group School of Life Sciences Weihenstephan, Technical University of Munich Freising Germany
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22
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Huang J, Miao X, Wang Q, Menzel F, Tang P, Yang D, Wu H, Vogler AP. Metabarcoding reveals massive species diversity of Diptera in a subtropical ecosystem. Ecol Evol 2022; 12:e8535. [PMID: 35127039 PMCID: PMC8796913 DOI: 10.1002/ece3.8535] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 12/08/2021] [Accepted: 12/22/2021] [Indexed: 11/07/2022] Open
Abstract
Diptera is often considered to be the richest insect group due to its great species diversity and broad ecological versatility. However, data on dipteran diversity from subtropical ecosystems have hitherto been scarce, due to the lack of studies conducted at an appropriate large scale. We investigated the diversity and composition of Diptera communities on Tianmu Mountain, Zhejiang, China, using DNA metabarcoding technology, and evaluated their dynamic responses to the effects of slope aspect, season, and altitudinal zone. A total of 5,092 operational taxonomic units (OTUs) were discovered and tentatively assigned to 72 dipteran families, including 2 family records new for China and 30 family records new for the locality. Cecidomyiidae, Sciaridae, and Phoridae were the predominant families, representing 53.6% of total OTUs, while 52 families include >95% unidentified and presumed undescribed species. We found that the community structure of Diptera was significantly affected by aspect, seasonality (month) and elevation, with richer diversity harbored in north-facing than south-facing slopes, and seasonality a more profound driver of community structure and diversity than elevation. Overall, massive species diversity of Diptera communities was discovered in this subtropical ecosystem of east China. The huge diversity of potentially undescribed species only revealed by metabarcoding now requires more detailed taxonomic study, as a step toward an evolutionary integration that accumulates information on species' geographic ranges, ecological traits, functional roles, and species interactions, and thus places the local communities in the context of the growing knowledge base of global biodiversity and its response to environmental change.
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Affiliation(s)
- Junhao Huang
- Department of Forestry ProtectionSchool of Forestry and BiotechnologyZhejiang A&F UniversityHangzhouChina
| | - Xiaoqian Miao
- Department of Forestry ProtectionSchool of Forestry and BiotechnologyZhejiang A&F UniversityHangzhouChina
| | - Qingyun Wang
- Department of Forestry ProtectionSchool of Forestry and BiotechnologyZhejiang A&F UniversityHangzhouChina
| | - Frank Menzel
- Senckenberg Deutsches Entomologisches InstitutMünchebergGermany
| | - Pu Tang
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Laboratory of Agricultural EntomologyInstitute of Insect SciencesZhejiang UniversityHangzhouChina
| | - Ding Yang
- College of Plant ProtectionChina Agricultural UniversityBeijingChina
| | - Hong Wu
- Department of Forestry ProtectionSchool of Forestry and BiotechnologyZhejiang A&F UniversityHangzhouChina
| | - Alfried P. Vogler
- Department of Life SciencesNatural History MuseumLondonUK
- Department of Life SciencesImperial College LondonAscotUK
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23
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Fayram AH, Wood JS, Swigle B. A comparison of genetically and morphometrically identified macroinvertebrate community index scores with implications for aquatic life use attainment. ENVIRONMENTAL MONITORING AND ASSESSMENT 2021; 194:18. [PMID: 34888736 DOI: 10.1007/s10661-021-09525-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 10/08/2021] [Indexed: 06/13/2023]
Abstract
Measures of aquatic macroinvertebrate communities are often used to characterize water quality and indicate whether waterbodies are meeting management expectations. The accuracy of these measures depends on the skill and experience of the person identifying the macroinvertebrates, and obtaining these measures can be relatively expensive due to the time necessary for identification. Utilizing genetic identification of macroinvertebrate taxa has the potential to reduce the time of sample processing, identify a greater number of taxa, and increase the resolution of identification. We compared Colorado multi-metric index (MMI) scores from seven locations in the Big Thompson River, CO, based on genetic and morphometric identification and estimated the ability of MMI scores based on genetic identification to characterize aquatic life use attainment management thresholds. We found a significant linear relationship (p = 0.002, R2 = 0.87) between MMI scores generated by genetic and morphological identification. MMIs support the following aquatic life use designations as defined by the Colorado Water Quality Control Commission: Impaired < 40, Attaining > 48, and Ambiguous 40-48. These values correspond to MMIs based on genetic identification as Impaired < 20, Attaining > 64, and Ambiguous = 21-63 based on the prediction interval of the regression equation. Our results suggest that using genetically identified macroinvertebrates to estimate MMI scores can provide some degree of certainty regarding aquatic life use designations, and while it may be inappropriate at the current time to entirely replace morphologically based biotic integrity measures with those based on molecular identification, there are opportunities in their use.
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Affiliation(s)
- Andrew H Fayram
- Loveland Water and Power, 902 S. Boise Ave, Loveland, CO, 80537, USA.
| | - John S Wood
- Pisces Molecular, 1600 Range Street, Suite 201, Boulder, CO, 80301, USA
| | - Benjamin Swigle
- Colorado Parks and Wildlife, 317 W Prospect Rd, Fort Collins, CO, 80526, USA
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24
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Lim JY, Patiño J, Noriyuki S, Cayetano L, Gillespie RG, Krehenwinkel H. Semi-quantitative metabarcoding reveals how climate shapes arthropod community assembly along elevation gradients on Hawaii Island. Mol Ecol 2021; 31:1416-1429. [PMID: 34882855 DOI: 10.1111/mec.16323] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 11/29/2021] [Accepted: 12/03/2021] [Indexed: 11/28/2022]
Abstract
Spatial variation in climatic conditions along elevation gradients provides an important backdrop by which communities assemble and diversify. Lowland habitats tend to be connected through time, whereas highlands can be continuously or periodically isolated, conditions that have been hypothesized to promote high levels of species endemism. This tendency is expected to be accentuated among taxa that show niche conservatism within a given climatic envelope. While species distribution modeling approaches have allowed extensive exploration of niche conservatism among target taxa, a broad understanding of the phenomenon requires sampling of entire communities. Species-rich groups such as arthropods are ideal case studies for understanding ecological and biodiversity dynamics along elevational gradients given their important functional role in many ecosystems, but community-level studies have been limited due to their tremendous diversity. Here, we develop a novel semi-quantitative metabarcoding approach that combines specimen counts and size-sorting to characterize arthropod community-level diversity patterns along elevational transects on two different volcanoes of the island of Hawai'i. We found that arthropod communities between the two transects became increasingly distinct compositionally at higher elevations. Resistance surface approaches suggest that climatic differences between sampling localities are an important driver in shaping beta-diversity patterns, though the relative importance of climate varies across taxonomic groups. Nevertheless, the climatic niche position of OTUs between transects was highly correlated, suggesting that climatic filters shape the colonization between adjacent volcanoes. Taken together, our results highlight climatic niche conservatism as an important factor shaping ecological assembly along elevational gradients and suggest topographic complexity as an important driver of diversification.
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Affiliation(s)
- Jun Ying Lim
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Jairo Patiño
- Island Ecology and Evolution Research Group, Institute of Natural Products and Agrobiology (IPNA-CSIC), La Laguna, Spain.,Department of Botany, Ecology and Plant Physiology, University of La Laguna, La Laguna, Spain
| | - Suzuki Noriyuki
- Faculty of Agriculture and Marine Science, Kochi University, Kochi, Japan
| | - Luis Cayetano
- Biology Department, Merced College, Merced, California, USA
| | - Rosemary G Gillespie
- Department of Environmental Science, Policy and Management, University of California, Berkeley, Berkeley, California, USA
| | - Henrik Krehenwinkel
- Department of Biogeography, Faculty of Regional and Environmental Sciences, Trier University, Trier, Germany
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25
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Martins FMS, Feio MJ, Porto M, Filipe AF, Bonin A, Serra SRQ, Alves PC, Taberlet P, Beja P. Assessing changes in stream macroinvertebrate communities across ecological gradients using morphological versus DNA metabarcoding approaches. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 797:149030. [PMID: 34311381 DOI: 10.1016/j.scitotenv.2021.149030] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 07/09/2021] [Accepted: 07/09/2021] [Indexed: 06/13/2023]
Abstract
Freshwater macroinvertebrates provide valuable indicators for biomonitoring ecosystem change in relation to natural and anthropogenic drivers. DNA metabarcoding is an efficient approach for estimating such indicators, but its results may differ from morphotaxonomic approaches traditionally used in biomonitoring. Here we test the hypothesis that despite differences in the number and identity of taxa recorded, both approaches may retrieve comparable patterns of community change, and detect similar ecological gradients influencing such changes. We compared results obtained with morphological identification at family level of macroinvertebrates collected at 80 streams under a Water Framework Directive biomonitoring program in Portugal, with results obtained with metabarcoding from the ethanol preserving the bulk samples, using either single (COI-M19BR2, 16S-Inse01, 18S-Euka02) or multiple markers. Metabarcoding recorded less families and different communities compared to morphotaxonomy, but community sensitivities to disturbance estimated with the IASPT index were more similar across approaches. Spatial variation in local community metrics and the factors influencing such variation were significantly correlated between morphotaxonomy and metabarcoding. After reducing random noise in the dissimilarity matrices, the spatial variation in community composition was also significantly correlated across methods. A dominant gradient of community change was consistently retrieved, and all methods identified a largely similar set of anthropogenic stressors strongly influencing such gradient. Overall, results confirm our initial hypothesis, suggesting that morphotaxonomy and metabarcoding can estimate consistent spatial patterns of community variation and their main drivers. These results are encouraging for macroinvertebrate biomonitoring using metabarcoding approaches, suggesting that they can be intercalibrated with morphotaxonomic approaches to recover equivalent spatial and temporal gradients of ecological change.
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Affiliation(s)
- Filipa M S Martins
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal; CIBIO/InBio, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus de Vairão, Vila do Conde, Portugal.
| | - Maria J Feio
- Universidade de Coimbra, MARE, Centro de Ciências do Mar e do Ambiente, Departamento de Ciência da Vida, Coimbra, Portugal
| | - Miguel Porto
- CIBIO/InBio, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus de Vairão, Vila do Conde, Portugal; CIBIO/InBio, Centro de Investigação em Biodiversidade e Recursos Genéticos, Instituto Superior de Agronomia, Universidade de Lisboa, Lisboa, Portugal
| | - Ana F Filipe
- CIBIO/InBio, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus de Vairão, Vila do Conde, Portugal; CIBIO/InBio, Centro de Investigação em Biodiversidade e Recursos Genéticos, Instituto Superior de Agronomia, Universidade de Lisboa, Lisboa, Portugal
| | - Aurélie Bonin
- Université Grenoble Alpes, CNRS, Laboratoire d'Ecologie Alpine (LECA), Grenoble, France
| | - Sónia R Q Serra
- Universidade de Coimbra, MARE, Centro de Ciências do Mar e do Ambiente, Departamento de Ciência da Vida, Coimbra, Portugal
| | - Paulo C Alves
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal; CIBIO/InBio, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus de Vairão, Vila do Conde, Portugal
| | - Pierre Taberlet
- Université Grenoble Alpes, CNRS, Laboratoire d'Ecologie Alpine (LECA), Grenoble, France; UiT - The Arctic University of Norway, Tromsø Museum, Tromsø, Norway
| | - Pedro Beja
- CIBIO/InBio, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus de Vairão, Vila do Conde, Portugal; CIBIO/InBio, Centro de Investigação em Biodiversidade e Recursos Genéticos, Instituto Superior de Agronomia, Universidade de Lisboa, Lisboa, Portugal
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26
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Elbrecht V, Bourlat SJ, Hörren T, Lindner A, Mordente A, Noll NW, Schäffler L, Sorg M, Zizka VMA. Pooling size sorted Malaise trap fractions to maximize taxon recovery with metabarcoding. PeerJ 2021; 9:e12177. [PMID: 34707928 PMCID: PMC8500090 DOI: 10.7717/peerj.12177] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 08/29/2021] [Indexed: 12/22/2022] Open
Abstract
Background Small and rare specimens can remain undetected when metabarcoding is applied on bulk samples with a high specimen size heterogeneity. This is especially critical for Malaise trap samples, where most of the biodiversity is contributed by small taxa with low biomass. The separation of samples in different size fractions for downstream analysis is one possibility to increase detection of small and rare taxa. However, experiments systematically testing different size sorting approaches and subsequent proportional pooling of fractions are lacking, but would provide important information for the optimization of metabarcoding protocols. We set out to find a size sorting strategy for Malaise trap samples that maximizes taxonomic recovery but remains scalable and time efficient. Methods Three Malaise trap samples were sorted into four size classes using dry sieving. Each fraction was homogenized and lysed. The corresponding lysates were pooled to simulate unsorted samples. Pooling was additionally conducted in equal proportions and in four different proportions enriching the small size fraction of samples. DNA from the individual size classes as well as the pooled fractions was extracted and metabarcoded using the FwhF2 and Fol-degen-rev primer set. Additionally, alternative wet sieving strategies were explored. Results The small size fractions harboured the highest diversity and were best represented when pooling in favour of small specimens. Metabarcoding of unsorted samples decreases taxon recovery compared to size sorted samples. A size separation into only two fractions (below 4 mm and above) can double taxon recovery compared to not size sorting. However, increasing the sequencing depth 3- to 4-fold can also increase taxon recovery to levels comparable with size sorting, but remains biased towards biomass rich taxa in the sample. Conclusion We demonstrate that size fractionation of Malaise trap bulk samples can increase taxon recovery. While results show distinct patterns, the lack of statistical support due to the limited number of samples processed is a limitation. Due to increased speed and lower risk of cross-contamination as well as specimen damage we recommend wet sieving and proportional pooling of the lysates in favour of the small size fraction (80–90% volume). However, for large-scale projects with time constraints, increasing sequencing depth is an alternative solution.
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Affiliation(s)
- Vasco Elbrecht
- Centre for Biodiversity Monitoring, Zoological Research Museum Alexander Koenig, Bonn, Germany.,SimplexDNA AG, Winterthur, Switzerland
| | - Sarah J Bourlat
- Centre for Biodiversity Monitoring, Zoological Research Museum Alexander Koenig, Bonn, Germany
| | | | - Angie Lindner
- Centre for Biodiversity Monitoring, Zoological Research Museum Alexander Koenig, Bonn, Germany
| | - Adriana Mordente
- Centre for Biodiversity Monitoring, Zoological Research Museum Alexander Koenig, Bonn, Germany
| | - Niklas W Noll
- Centre for Biodiversity Monitoring, Zoological Research Museum Alexander Koenig, Bonn, Germany
| | - Livia Schäffler
- Centre for Biodiversity Monitoring, Zoological Research Museum Alexander Koenig, Bonn, Germany
| | - Martin Sorg
- Entomological Society Krefeld, Krefeld, Germany
| | - Vera M A Zizka
- Centre for Biodiversity Monitoring, Zoological Research Museum Alexander Koenig, Bonn, Germany
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27
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Klunder L, van Bleijswijk JDL, Kleine Schaars L, van der Veer HW, Luttikhuizen PC, Bijleveld AI. Quantification of marine benthic communities with metabarcoding. Mol Ecol Resour 2021; 22:1043-1054. [PMID: 34687591 PMCID: PMC9298412 DOI: 10.1111/1755-0998.13536] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 10/12/2021] [Indexed: 01/02/2023]
Abstract
DNA metabarcoding methods have been implemented in studies aimed at detecting and quantifying marine benthic biodiversity. In such surveys, universal barcodes are amplified and sequenced from environmental DNA. To quantify biodiversity with DNA metabarcoding, a relation between the number of DNA sequences of a species and its biomass and/or the abundance is required. However, this relationship is complicated by many factors, and it is often unknown. In this study, we validate estimates of biomass and abundance from molecular approaches with those from the traditional morphological approach. Abundance and biomass were quantified from 126 samples of benthic intertidal mudflat using traditional morphological approaches and compared with frequency of occurrence and relative read abundance estimates from a molecular approach. A relationship between biomass and relative read abundance was found for two widely dispersed annelid taxa (Pygospio and Scoloplos). None of the other taxons, however, showed such a relationship. We discuss how quantification of abundance and biomass using molecular approaches are hampered by the ecology of DNA i.e. all the processes that determine the amount of DNA in the environment, including the ecology of the benthic species as well as the compositional nature of sequencing data.
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Affiliation(s)
- Lise Klunder
- Department of Coastal Systems, NIOZ Royal Netherlands Institute for Sea Research, AB Den Burg Texel, The Netherlands.,Marine Evolution and Conservation, Groningen Institute of Life Sciences, University of Groningen, CC Groningen, The Netherlands
| | - Judith D L van Bleijswijk
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, AB Den Burg Texel, The Netherlands
| | - Loran Kleine Schaars
- Department of Coastal Systems, NIOZ Royal Netherlands Institute for Sea Research, AB Den Burg Texel, The Netherlands
| | - Henk W van der Veer
- Department of Coastal Systems, NIOZ Royal Netherlands Institute for Sea Research, AB Den Burg Texel, The Netherlands
| | - Pieternella C Luttikhuizen
- Department of Coastal Systems, NIOZ Royal Netherlands Institute for Sea Research, AB Den Burg Texel, The Netherlands
| | - Allert I Bijleveld
- Department of Coastal Systems, NIOZ Royal Netherlands Institute for Sea Research, AB Den Burg Texel, The Netherlands
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28
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Uhler J, Redlich S, Zhang J, Hothorn T, Tobisch C, Ewald J, Thorn S, Seibold S, Mitesser O, Morinière J, Bozicevic V, Benjamin CS, Englmeier J, Fricke U, Ganuza C, Haensel M, Riebl R, Rojas-Botero S, Rummler T, Uphus L, Schmidt S, Steffan-Dewenter I, Müller J. Relationship of insect biomass and richness with land use along a climate gradient. Nat Commun 2021; 12:5946. [PMID: 34642336 PMCID: PMC8511018 DOI: 10.1038/s41467-021-26181-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 09/17/2021] [Indexed: 11/09/2022] Open
Abstract
Recently reported insect declines have raised both political and social concern. Although the declines have been attributed to land use and climate change, supporting evidence suffers from low taxonomic resolution, short time series, a focus on local scales, and the collinearity of the identified drivers. In this study, we conducted a systematic assessment of insect populations in southern Germany, which showed that differences in insect biomass and richness are highly context dependent. We found the largest difference in biomass between semi-natural and urban environments (-42%), whereas differences in total richness (-29%) and the richness of threatened species (-56%) were largest from semi-natural to agricultural environments. These results point to urbanization and agriculture as major drivers of decline. We also found that richness and biomass increase monotonously with increasing temperature, independent of habitat. The contrasting patterns of insect biomass and richness question the use of these indicators as mutual surrogates. Our study provides support for the implementation of more comprehensive measures aimed at habitat restoration in order to halt insect declines.
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Affiliation(s)
- Johannes Uhler
- Field Station Fabrikschleichach, Department of Animal Ecology and Tropical Biology, Julius-Maximilians-University Würzburg, Würzburg, Germany
| | - Sarah Redlich
- Department of Animal Ecology and Tropical Biology, Julius-Maximilians-University Würzburg, Würzburg, Germany
| | - Jie Zhang
- Department of Animal Ecology and Tropical Biology, Julius-Maximilians-University Würzburg, Würzburg, Germany
| | - Torsten Hothorn
- Epidemiology, Biostatistics and Prevention Institute, University Zürich, Zürich, Switzerland
| | - Cynthia Tobisch
- Institute of Ecology and Landscape, Weihenstephan-Triesdorf University of Applied Sciences, Freising, Germany
| | - Jörg Ewald
- Botany & Vegetation Science, Faculty of Forestry, Weihenstephan-Triesdorf University of Applied Sciences, Freising, Germany
| | - Simon Thorn
- Field Station Fabrikschleichach, Department of Animal Ecology and Tropical Biology, Julius-Maximilians-University Würzburg, Würzburg, Germany
| | - Sebastian Seibold
- Ecosystem Dynamics and Forest management Group, Technical University of Munich, Freising, Germany.,Berchtesgaden National Park, Berchtesgaden, Germany
| | - Oliver Mitesser
- Field Station Fabrikschleichach, Department of Animal Ecology and Tropical Biology, Julius-Maximilians-University Würzburg, Würzburg, Germany
| | | | | | - Caryl S Benjamin
- TUM School of Life Sciences, Ecoclimatology, Technical University of Munich, Freising, Germany
| | - Jana Englmeier
- Field Station Fabrikschleichach, Department of Animal Ecology and Tropical Biology, Julius-Maximilians-University Würzburg, Würzburg, Germany
| | - Ute Fricke
- Department of Animal Ecology and Tropical Biology, Julius-Maximilians-University Würzburg, Würzburg, Germany
| | - Cristina Ganuza
- Department of Animal Ecology and Tropical Biology, Julius-Maximilians-University Würzburg, Würzburg, Germany
| | - Maria Haensel
- Professorship of Ecological Services, Bayreuth Centre of Ecology and Environmental Research (BayCEER), University of Bayreuth, Bayreuth, Germany
| | - Rebekka Riebl
- Professorship of Ecological Services, Bayreuth Centre of Ecology and Environmental Research (BayCEER), University of Bayreuth, Bayreuth, Germany
| | - Sandra Rojas-Botero
- Chair of Restoration Ecology, Technical University of Munich, Freising, Germany
| | - Thomas Rummler
- Institute of Geography, University of Augsburg, Augsburg, Germany
| | - Lars Uphus
- TUM School of Life Sciences, Ecoclimatology, Technical University of Munich, Freising, Germany
| | - Stefan Schmidt
- SNSB-Zoologische Staatssammlung Muenchen, Munich, Germany
| | - Ingolf Steffan-Dewenter
- Department of Animal Ecology and Tropical Biology, Julius-Maximilians-University Würzburg, Würzburg, Germany
| | - Jörg Müller
- Field Station Fabrikschleichach, Department of Animal Ecology and Tropical Biology, Julius-Maximilians-University Würzburg, Würzburg, Germany. .,Bavarian Forest National Park, Grafenau, Germany.
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Buchner D, Macher TH, Beermann AJ, Werner MT, Leese F. Standardized high-throughput biomonitoring using DNA metabarcoding: Strategies for the adoption of automated liquid handlers. ENVIRONMENTAL SCIENCE AND ECOTECHNOLOGY 2021; 8:100122. [PMID: 36156998 PMCID: PMC9488008 DOI: 10.1016/j.ese.2021.100122] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 08/26/2021] [Accepted: 08/26/2021] [Indexed: 05/11/2023]
Abstract
Reliable and comprehensive monitoring data are required to trace and counteract biodiversity loss. High-throughput metabarcoding using DNA extracted from community samples (bulk) or from water or sediment (environmental DNA) has revolutionized biomonitoring, given the capability to assess biodiversity across the tree of life rapidly with feasible effort and at a modest price. DNA metabarcoding can be upscaled to process hundreds of samples in parallel. However, while automated high-throughput analysis workflows are well-established in the medical sector, manual sample processing still predominates in biomonitoring laboratory workflows limiting the upscaling and standardization for routine monitoring applications. Here we present an automated, scalable, and reproducible metabarcoding workflow to extract DNA from bulk samples, perform PCR and library preparation on a liquid handler. Key features are the independent sample replication throughout the workflow and the use of many negative controls for quality assurance and quality control. We generated two datasets: i) a validation dataset consisting of 42 individual arthropod specimens of different species, and ii) a routine monitoring dataset consisting of 60 stream macroinvertebrate bulk samples. As a marker, we used the mitochondrial COI gene. Our results show that the developed single-deck workflow is free of laboratory-derived contamination and produces highly consistent results. Minor deviations between replicates are mostly due to stochastic differences for low abundant OTUs. Thus, we successfully demonstrated that robotic liquid handling can be used reliably from DNA extraction to final library preparation on a single deck, thereby substantially increasing throughput, reducing costs, and increasing data robustness for biodiversity assessments and monitoring.
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Affiliation(s)
- Dominik Buchner
- University of Duisburg-Essen, Aquatic Ecosystem Research, Universitätsstr. 5, 45141, Essen, Germany
| | - Till-Hendrik Macher
- University of Duisburg-Essen, Aquatic Ecosystem Research, Universitätsstr. 5, 45141, Essen, Germany
| | - Arne J. Beermann
- University of Duisburg-Essen, Aquatic Ecosystem Research, Universitätsstr. 5, 45141, Essen, Germany
- University of Duisburg-Essen, Centre for Water and Environmental Research (ZWU), Universitätsstr. 3, 45141, Essen, Germany
| | - Marie-Thérése Werner
- University of Duisburg-Essen, Aquatic Ecosystem Research, Universitätsstr. 5, 45141, Essen, Germany
| | - Florian Leese
- University of Duisburg-Essen, Aquatic Ecosystem Research, Universitätsstr. 5, 45141, Essen, Germany
- University of Duisburg-Essen, Centre for Water and Environmental Research (ZWU), Universitätsstr. 3, 45141, Essen, Germany
- Corresponding author. University of Duisburg-Essen, Aquatic Ecosystem Research, Universitätsstr. 5, 45141 Essen, Germany.
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30
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Anslan S, Mikryukov V, Armolaitis K, Ankuda J, Lazdina D, Makovskis K, Vesterdal L, Schmidt IK, Tedersoo L. Highly comparable metabarcoding results from MGI-Tech and Illumina sequencing platforms. PeerJ 2021; 9:e12254. [PMID: 34703674 PMCID: PMC8491618 DOI: 10.7717/peerj.12254] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 09/14/2021] [Indexed: 01/04/2023] Open
Abstract
With the developments in DNA nanoball sequencing technologies and the emergence of new platforms, there is an increasing interest in their performance in comparison with the widely used sequencing-by-synthesis methods. Here, we test the consistency of metabarcoding results from DNBSEQ-G400RS (DNA nanoball sequencing platform by MGI-Tech) and NovaSeq 6000 (sequencing-by-synthesis platform by Illumina) platforms using technical replicates of DNA libraries that consist of COI gene amplicons from 120 soil DNA samples. By subjecting raw sequencing data from both platforms to a uniform bioinformatics processing, we found that the proportion of high-quality reads passing through the filtering steps was similar in both datasets. Per-sample operational taxonomic unit (OTU) and amplicon sequence variant (ASV) richness patterns were highly correlated, but sequencing data from DNBSEQ-G400RS harbored a higher number of OTUs. This may be related to the lower dominance of most common OTUs in DNBSEQ data set (thus revealing higher richness by detecting rare taxa) and/or to a lower effective read quality leading to generation of spurious OTUs. However, there was no statistical difference in the ASV and post-clustered ASV richness between platforms, suggesting that additional denoising step in the ASV workflow had effectively removed the 'noisy' reads. Both OTU-based and ASV-based composition were strongly correlated between the sequencing platforms, with essentially interchangeable results. Therefore, we conclude that DNBSEQ-G400RS and NovaSeq 6000 are both equally efficient high-throughput sequencing platforms to be utilized in studies aiming to apply the metabarcoding approach, but the main benefit of the former is related to lower sequencing cost.
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Affiliation(s)
- Sten Anslan
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Tartumaa, Estonia
- Mycology and Microbiology Center, University of Tartu, Tartu, Tartumaa, Estonia
| | - Vladimir Mikryukov
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Tartumaa, Estonia
- Mycology and Microbiology Center, University of Tartu, Tartu, Tartumaa, Estonia
| | - Kęstutis Armolaitis
- Department of Ecology, Institute of Forestry of Lithuanian Research Centre for Agriculture and Forestry (LAMMC), Kaunas, Lithuania
| | - Jelena Ankuda
- Department of Ecology, Institute of Forestry of Lithuanian Research Centre for Agriculture and Forestry (LAMMC), Kaunas, Lithuania
| | - Dagnija Lazdina
- Latvian State Forest Research Institute SILAVA, Riga, Latvia
| | | | - Lars Vesterdal
- Department of Geosciences and Natural Resource Management, University of Copenhagen, Copenhagen, Denmark
| | - Inger Kappel Schmidt
- Department of Geosciences and Natural Resource Management, University of Copenhagen, Copenhagen, Denmark
| | - Leho Tedersoo
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Tartumaa, Estonia
- Mycology and Microbiology Center, University of Tartu, Tartu, Tartumaa, Estonia
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31
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Gálvez-Reyes N, Arribas P, Andújar C, Emerson BC, Piñero D, Mastretta-Yanes A. Dispersal limitations and long-term persistence drive differentiation from haplotypes to communities within a tropical sky-island: Evidence from community metabarcoding. Mol Ecol 2021; 30:6611-6626. [PMID: 34564919 DOI: 10.1111/mec.16195] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Revised: 09/09/2021] [Accepted: 09/13/2021] [Indexed: 01/04/2023]
Abstract
Neutral theory proposes that dispersal stochasticity is one of the main drivers of local diversity. Haplotypes-level genetic variation can now be efficiently sampled from across whole communities, thus making it possible to test neutral predictions from the genetic to species-level diversity, and higher. However, empirical data is still limited, with the few studies to date coming from temperate latitudes. Here, we focus on a tropical mountain within the Transmexican Volcanic Belt to evaluate spatially fine-scale patterns of arthropod community assembly to understand the role of dispersal limitation and landscape features as drivers of diversity. We sampled whole-communities of arthropods for eight orders at a spatial scale ranging from 50 m to 19 km, using whole community metabarcoding. We explored multiple hierarchical levels, from individual haplotypes to lineages at 0.5, 1.5, 3, 5, and 7.5% similarity thresholds, to evaluate patterns of richness, turnover, and distance decay of similarity with isolation-by-distance and isolation-by-resistance (costs to dispersal given by landscape features) approaches. Our results showed that distance and altitude influence distance decay of similarity at all hierarchical levels. This holds for arthropod groups of contrasting dispersal abilities, but with different strength depending on the spatial scale. Our results support a model where local-scale differentiation mediated by dispersal constraints, combined with long-term persistence of lineages, is an important driver of diversity within tropical sky islands.
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Affiliation(s)
- Nancy Gálvez-Reyes
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, CDMX, Mexico.,Programa de Doctorado en Ciencias Biomédicas, Universidad Nacional Autónoma de México, CDMX, Mexico
| | - Paula Arribas
- Island Ecology and Evolution Research Group, Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), Santa Cruz de Tenerife, Spain
| | - Carmelo Andújar
- Island Ecology and Evolution Research Group, Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), Santa Cruz de Tenerife, Spain
| | - Brent C Emerson
- Island Ecology and Evolution Research Group, Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), Santa Cruz de Tenerife, Spain
| | - Daniel Piñero
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, CDMX, Mexico
| | - Alicia Mastretta-Yanes
- Comisión Nacional para el Conocimiento y Uso de la Biodiversidad (CONABIO), CDMX, Mexico.,Consejo Nacional de Ciencia y Tecnología, Benito Juárez (CONACYT), CDMX, Mexico
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32
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Miller‐ter Kuile A, Apigo A, Young HS. Effects of consumer surface sterilization on diet DNA metabarcoding data of terrestrial invertebrates in natural environments and feeding trials. Ecol Evol 2021; 11:12025-12034. [PMID: 34522358 PMCID: PMC8427582 DOI: 10.1002/ece3.7968] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 07/14/2021] [Accepted: 07/16/2021] [Indexed: 01/04/2023] Open
Abstract
DNA metabarcoding is an emerging tool used to quantify diet in environments and consumer groups where traditional approaches are unviable, including small-bodied invertebrate taxa. However, metabarcoding of small taxa often requires DNA extraction from full body parts (without dissection), and it is unclear whether surface contamination from body parts alters presumed diet presence or diversity.We examined four different measures of diet (presence, rarefied read abundance, richness, and species composition) for a terrestrial invertebrate consumer (the spider Heteropoda venatoria) both collected in its natural environment and fed an offered diet item in contained feeding trials using DNA metabarcoding of full body parts (opisthosomas). We compared diet from consumer individuals surface sterilized to remove contaminants in 10% commercial bleach solution followed by deionized water with a set of unsterilized individuals.We found that surface sterilization did not significantly alter any measure of diet for consumers in either a natural environment or feeding trials. The best-fitting model predicting diet detection in feeding trial consumers included surface sterilization, but this term was not statistically significant (β = -2.3, p-value = .07).Our results suggest that surface contamination does not seem to be a significant concern in this DNA diet metabarcoding study for consumers in either a natural terrestrial environment or feeding trials. As the field of diet DNA metabarcoding continues to progress into new environmental contexts with various molecular approaches, we suggest ongoing context-specific consideration of the possibility of surface contamination.
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Affiliation(s)
- Ana Miller‐ter Kuile
- Department of Ecology, Evolution, and Marine BiologyUniversity of California Santa BarbaraSanta BarbaraCAUSA
| | - Austen Apigo
- Department of Ecology, Evolution, and Marine BiologyUniversity of California Santa BarbaraSanta BarbaraCAUSA
| | - Hillary S. Young
- Department of Ecology, Evolution, and Marine BiologyUniversity of California Santa BarbaraSanta BarbaraCAUSA
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33
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Neby M, Kamenova S, Devineau O, Ims RA, Soininen EM. Issues of under-representation in quantitative DNA metabarcoding weaken the inference about diet of the tundra vole Microtus oeconomus. PeerJ 2021; 9:e11936. [PMID: 34527438 PMCID: PMC8403475 DOI: 10.7717/peerj.11936] [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] [Received: 03/01/2021] [Accepted: 07/19/2021] [Indexed: 11/29/2022] Open
Abstract
During the last decade, methods based on high-throughput sequencing such as DNA metabarcoding have opened up for a range of new questions in animal dietary studies. One of the major advantages of dietary metabarcoding resides in the potential to infer a quantitative relationship between sequence read proportions and biomass of ingested food. However, this relationship's robustness is highly dependent on the system under study, calling for case-specific assessments. Herbivorous small rodents often play important roles in the ecosystem, and the use of DNA metabarcoding for analyses of rodent diets is increasing. However, there has been no direct validation of the quantitative reliability of DNA metabarcoding for small rodents. Therefore, we used an experimental approach to assess the relationship between input plant biomass and sequence reads proportions from DNA metabarcoding in the tundra vole Microtus oeconomus. We found a weakly positive relationship between the number of high-throughput DNA sequences and the expected biomass proportions of food plants. The weak relationship was possibly caused by a systematic under-amplification of one of the three plant taxa fed. Generally, our results add to the growing evidence that case-specific validation studies are required to reliably make use of sequence read abundance as a proxy of relative food proportions in the diet.
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Affiliation(s)
- Magne Neby
- Department of Applied Ecology, Inland Norway University of Applied Sciences, Koppang, Norway
| | | | - Olivier Devineau
- Department of Applied Ecology, Inland Norway University of Applied Sciences, Koppang, Norway
| | - Rolf A. Ims
- Department of Arctic and Marine Biology, UiT—the Arctic University of Norway, Tromsø, Norway
| | - Eeva M. Soininen
- Department of Arctic and Marine Biology, UiT—the Arctic University of Norway, Tromsø, Norway
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34
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Turunen J, Mykrä H, Elbrecht V, Steinke D, Braukmann T, Aroviita J. The power of metabarcoding: Can we improve bioassessment and biodiversity surveys of stream macroinvertebrate communities? METABARCODING AND METAGENOMICS 2021. [DOI: 10.3897/mbmg.5.68938] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Most stream bioassessment and biodiversity surveys are currently based on morphological identification of communities. However, DNA metabarcoding is emerging as a fast and cost-effective alternative for species identification. We compared both methods in a survey of benthic macroinvertebrate communities across 36 stream sites in northern Finland. We identified 291 taxa of which 62% were identified only by DNA metabarcoding. DNA metabarcoding produced extensive species level inventories for groups (Oligochaeta, Chironomidae, Simuliidae, Limoniidae and Limnephilidae), for which morphological identification was not feasible due to the high level of expertise needed. Metabarcoding also provided more insightful taxonomic information on the occurrence of three red-listed vulnerable or data deficient species, the discovery of two likely cryptic and potentially new species to Finland and species information of insect genera at an early larval stage that could not be separated morphologically. However, it systematically failed to reliably detect the occurrence of gastropods that were easily identified morphologically. The impact of mining on community structure could only be shown using DNA metabarcoding data which suggests that the finer taxonomic detail can improve detection of subtle impacts. Both methods generally exhibited similar strength of community-environment relationships, but DNA metabarcoding showed better performance with presence/absence data than with relative DNA sequence abundances. Our results suggest that DNA metabarcoding holds a promise for future anthropogenic impact assessments, although, in our case, the performance did not improve much from the morphological species identification. The key advantage of DNA metabarcoding lies in efficient biodiversity surveys, taxonomical studies and applications in conservation biology.
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35
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Elbrecht V, Lindner A, Manerus L, Steinke D. A bright idea-metabarcoding arthropods from light fixtures. PeerJ 2021; 9:e11841. [PMID: 34395083 PMCID: PMC8320520 DOI: 10.7717/peerj.11841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 07/01/2021] [Indexed: 11/28/2022] Open
Abstract
Arthropod communities in buildings have not been extensively studied, although humans have always shared their homes with them. In this study we explored if arthropod DNA can be retrieved and metabarcoded from indoor environments through the collection of dead specimens in light fixtures to better understand what shapes arthropod diversity in our homes. Insects were collected from 45 light fixtures at the Centre for Biodiversity Genomics (CBG, Guelph, Canada), and by community scientists at 12 different residential homes in Southern Ontario. The CBG ground floor of the CBG showed the greatest arthropod diversity, especially in light fixtures that were continuously illuminated. The community scientist samples varied strongly by light fixture type, lightbulb used, time passed since lamp was last cleaned, and specimen size. In all cases, the majority of OTUs was not shared between samples even within the same building. This study demonstrates that light fixtures might be a useful resource to determine arthropod diversity in our homes, but individual samples are likely not representative of the full diversity.
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Affiliation(s)
- Vasco Elbrecht
- Department of Environmental Systems Science Institute of Biogeochemistry and Pollutant Dynamics (IBP), ETH Zurich, Zurich, Switzerland
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Angie Lindner
- Centre for Biodiversity Monitoring, Zoological Research Museum Alexander Koenig, Bonn, Germany
| | - Laura Manerus
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Dirk Steinke
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
- Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
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36
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Shum P, Palumbi SR. Testing small-scale ecological gradients and intraspecific differentiation for hundreds of kelp forest species using haplotypes from metabarcoding. Mol Ecol 2021; 30:3355-3373. [PMID: 33682164 DOI: 10.1111/mec.15851] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 01/27/2021] [Accepted: 02/10/2021] [Indexed: 12/25/2022]
Abstract
DNA metabarcoding has been increasingly used to detail distributions of hundreds of species. Most analyses focus on creating molecular operational taxonomic units (MOTUs) from complex mixtures of DNA sequences, but much less common is use of the sequence diversity within these MOTUs. Here we use the diversity of COI haplotypes within MOTUs from a California kelp forest to infer patterns of population abundance, dispersal and population history from 527 species of animals and algae from 106 samples of benthic habitats in Monterey Bay. Using haplotypes as a unit we show fine-grained differences of abundance across locations for 15 species, and marked aggregation from sample to sample for most of the common species of plants and animals. Previous analyses could not distinguish these patterns from artefacts of amplification or sequence bias. Our haplotype data also reveal strong population genetic differentiation over small spatial scales for 48 species of red algae, sponges and Bryozoa. Last, phylogenetic analysis of mismatch frequencies among haplotypes show a wide variety of demographic histories from recent expansions to long, stable population sizes. These analyses show that abundant, small-bodied marine species that are often overlooked in ecological surveys can have strikingly different patterns of ecological and genetic structure leading to population, ecological and perhaps adaptive differences between habitats. MOTU diversity data from the same sequencing efforts that generate species-level analyses can greatly increase the scope and value of metabarcoding studies.
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Affiliation(s)
- Peter Shum
- School of Biological and Environmental Sciences, Liverpool John Moores University, Liverpool, UK
- Hopkins Marine Station, Department of Biology, Stanford University, Pacific Grove, CA, USA
| | - Stephen R Palumbi
- Hopkins Marine Station, Department of Biology, Stanford University, Pacific Grove, CA, USA
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37
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van der Loos LM, Nijland R. Biases in bulk: DNA metabarcoding of marine communities and the methodology involved. Mol Ecol 2021; 30:3270-3288. [PMID: 32779312 PMCID: PMC8359149 DOI: 10.1111/mec.15592] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Accepted: 07/28/2020] [Indexed: 12/22/2022]
Abstract
With the growing anthropogenic pressure on marine ecosystems, the need for efficient monitoring of biodiversity grows stronger. DNA metabarcoding of bulk samples is increasingly being implemented in ecosystem assessments and is more cost-efficient and less time-consuming than monitoring based on morphology. However, before raw sequences are obtained from bulk samples, a profound number of methodological choices must be made. Here, we critically review the recent methods used for metabarcoding of marine bulk samples (including benthic, plankton and diet samples) and indicate how potential biases can be introduced throughout sampling, preprocessing, DNA extraction, marker and primer selection, PCR amplification and sequencing. From a total of 64 studies evaluated, our recommendations for best practices include to (a) consider DESS as a fixative instead of ethanol, (b) use the DNeasy PowerSoil kit for any samples containing traces of sediment, (c) not limit the marker selection to COI only, but preferably include multiple markers for higher taxonomic resolution, (d) avoid touchdown PCR profiles, (e) use a fixed annealing temperature for each primer pair when comparing across studies or institutes, (f) use a minimum of three PCR replicates, and (g) include both negative and positive controls. Although the implementation of DNA metabarcoding still faces several technical complexities, we foresee wide-ranging advances in the near future, including improved bioinformatics for taxonomic assignment, sequencing of longer fragments and the use of whole-genome information. Despite the bulk of biases involved in metabarcoding of bulk samples, if appropriate controls are included along the data generation process, it is clear that DNA metabarcoding provides a valuable tool in ecosystem assessments.
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Affiliation(s)
- Luna M. van der Loos
- Marine Animal Ecology GroupWageningen UniversityWageningenThe Netherlands
- Present address:
Department of BiologyPhycology Research GroupGhent UniversityGhentBelgium
| | - Reindert Nijland
- Marine Animal Ecology GroupWageningen UniversityWageningenThe Netherlands
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38
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Buchner D, Beermann AJ, Leese F, Weiss M. Cooking small and large portions of “biodiversity‐soup”: Miniaturized DNA metabarcoding PCRs perform as good as large‐volume PCRs. Ecol Evol 2021. [DOI: 10.1002/ece3.7753] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Affiliation(s)
- Dominik Buchner
- Aquatic Ecosystem Research University of Duisburg‐Essen Essen Germany
| | - Arne J. Beermann
- Aquatic Ecosystem Research University of Duisburg‐Essen Essen Germany
- Centre for Water and Environmental Research (ZWU) University of Duisburg‐Essen Essen Germany
| | - Florian Leese
- Aquatic Ecosystem Research University of Duisburg‐Essen Essen Germany
- Centre for Water and Environmental Research (ZWU) University of Duisburg‐Essen Essen Germany
| | - Martina Weiss
- Aquatic Ecosystem Research University of Duisburg‐Essen Essen Germany
- Centre for Water and Environmental Research (ZWU) University of Duisburg‐Essen Essen Germany
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39
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Kirse A, Bourlat SJ, Langen K, Fonseca VG. Unearthing the Potential of Soil eDNA Metabarcoding—Towards Best Practice Advice for Invertebrate Biodiversity Assessment. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.630560] [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
Metabarcoding has proven to be a powerful tool to assess ecological patterns and diversity from different habitats. Terrestrial invertebrate diversity is frequently based on bulk samples, which require comparatively high sampling effort. With environmental DNA (eDNA) metabarcoding, field sampling effort can be reduced while increasing the number of recovered organism groups. However, a proof of concept is missing for several invertebrate groups, hampering the development of best-practice advice for these groups. This study aims to provide recommendations on key aspects for the processing of soil samples, from sampling effort to choice of DNA extraction method and marker genes. This study uses eDNA metabarcoding as a tool for assessing invertebrate biodiversity in soil samples, specifically comparing two DNA extraction methods (with and without a lysis step) and two genes, 18S and COI markers. The results show that the choice of marker and DNA extraction method (including a lysis step) significantly affect species detection rates and concomitantly observed invertebrate community composition. Combining methods, by using larger amounts of starting material and including a lysis step resulted in an increase of invertebrate species numbers. Together, these methods improved the detection of species with known lower population densities and allowed the assessment of temporary mesofauna. Furthermore, the choice of marker significantly influenced the diversity levels found. The 18S marker allowed the detection of a higher number of annelid and nematode OTUs, while the COI marker was more suitable for detecting changes in arthropod community structure, especially at the species level. This study makes significant advances to the field of invertebrate biodiversity assessment, particularly using metabarcoding tools by addressing several methodological considerations that are key for accurate ecological appraisals.
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40
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Kirse A, Bourlat SJ, Langen K, Fonseca VG. Metabarcoding Malaise traps and soil eDNA reveals seasonal and local arthropod diversity shifts. Sci Rep 2021; 11:10498. [PMID: 34006991 PMCID: PMC8131643 DOI: 10.1038/s41598-021-89950-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 04/23/2021] [Indexed: 02/03/2023] Open
Abstract
Forest habitats host enormous diversity, but little is known about the seasonal turnover of arthropod species between the above- and below ground forest layers. In this study, we used metabarcoding approaches to uncover arthropod diversity in different forest types and seasons. Our study shows that metabarcoding soil eDNA and Malaise trap bulk samples can provide valuable insights into the phenology and life cycles of arthropods. We found major differences in arthropod species diversity between soil samples and Malaise traps, with only 11.8% species overlap. Higher diversity levels were found in Malaise traps in summer whereas soil samples showed a diversity peak in winter, highlighting the seasonal habitat preferences and life strategies of arthropods. We conclude that collecting time series of bulk arthropod samples and eDNA in the same locations provides a more complete picture of local arthropod diversity and turnover rates and may provide valuable information on climate induced phenological shifts for long-term monitoring.
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Affiliation(s)
- Ameli Kirse
- Centre for Biodiversity Monitoring, Zoological Research Museum Alexander Koenig, Adenauerallee 160, 53113, Bonn, Germany.
| | - Sarah J Bourlat
- Centre for Biodiversity Monitoring, Zoological Research Museum Alexander Koenig, Adenauerallee 160, 53113, Bonn, Germany
| | - Kathrin Langen
- Centre for Biodiversity Monitoring, Zoological Research Museum Alexander Koenig, Adenauerallee 160, 53113, Bonn, Germany
| | - Vera G Fonseca
- Centre for Biodiversity Monitoring, Zoological Research Museum Alexander Koenig, Adenauerallee 160, 53113, Bonn, Germany.
- Centre for Environment, Fisheries and Aquaculture Science (Cefas), Barrack Road, The Nothe, Weymouth, Dorset, DT4 8UB, UK.
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41
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Yang C, Bohmann K, Wang X, Cai W, Wales N, Ding Z, Gopalakrishnan S, Yu DW. Biodiversity Soup II: A bulk‐sample metabarcoding pipeline emphasizing error reduction. Methods Ecol Evol 2021. [DOI: 10.1111/2041-210x.13602] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Chunyan Yang
- State Key Laboratory of Genetic Resources and Evolution Kunming Institute of ZoologyChinese Academy of Sciences Kunming China
| | - Kristine Bohmann
- Section for Evolutionary Genomics Globe Institute Faculty of Health and Medical Sciences University of Copenhagen Copenhagen Denmark
| | - Xiaoyang Wang
- State Key Laboratory of Genetic Resources and Evolution Kunming Institute of ZoologyChinese Academy of Sciences Kunming China
| | - Wang Cai
- State Key Laboratory of Genetic Resources and Evolution Kunming Institute of ZoologyChinese Academy of Sciences Kunming China
| | - Nathan Wales
- Section for Evolutionary Genomics Globe Institute Faculty of Health and Medical Sciences University of Copenhagen Copenhagen Denmark
- Department of Archaeology University of York York UK
| | - Zhaoli Ding
- Biodiversity Genomics Center Kunming Institute of Zoology Chinese Academy of Sciences Kunming China
| | - Shyam Gopalakrishnan
- Section for Evolutionary Genomics Globe Institute Faculty of Health and Medical Sciences University of Copenhagen Copenhagen Denmark
| | - Douglas W. Yu
- State Key Laboratory of Genetic Resources and Evolution Kunming Institute of ZoologyChinese Academy of Sciences Kunming China
- School of Biological Sciences University of East AngliaNorwich Research Park Norwich UK
- Center for Excellence in Animal Evolution and Genetics Chinese Academy of Sciences Kunming China
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42
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Brandt MI, Pradillon F, Trouche B, Henry N, Liautard-Haag C, Cambon-Bonavita MA, Cueff-Gauchard V, Wincker P, Belser C, Poulain J, Arnaud-Haond S, Zeppilli D. Evaluating sediment and water sampling methods for the estimation of deep-sea biodiversity using environmental DNA. Sci Rep 2021; 11:7856. [PMID: 33846371 PMCID: PMC8041860 DOI: 10.1038/s41598-021-86396-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 03/15/2021] [Indexed: 02/07/2023] Open
Abstract
Despite representing one of the largest biomes on earth, biodiversity of the deep seafloor is still poorly known. Environmental DNA metabarcoding offers prospects for fast inventories and surveys, yet requires standardized sampling approaches and careful choice of environmental substrate. Here, we aimed to optimize the genetic assessment of prokaryote (16S), protistan (18S V4), and metazoan (18S V1-V2, COI) communities, by evaluating sampling strategies for sediment and aboveground water, deployed simultaneously at one deep-sea site. For sediment, while size-class sorting through sieving had no significant effect on total detected alpha diversity and resolved similar taxonomic compositions at the phylum level for all markers studied, it effectively increased the detection of meiofauna phyla. For water, large volumes obtained from an in situ pump (~ 6000 L) detected significantly more metazoan diversity than 7.5 L collected in sampling boxes. However, the pump being limited by larger mesh sizes (> 20 µm), only captured a fraction of microbial diversity, while sampling boxes allowed access to the pico- and nanoplankton. More importantly, communities characterized by aboveground water samples significantly differed from those characterized by sediment, whatever volume used, and both sample types only shared between 3 and 8% of molecular units. Together, these results underline that sediment sieving may be recommended when targeting metazoans, and aboveground water does not represent an alternative to sediment sampling for inventories of benthic diversity.
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Affiliation(s)
- Miriam I. Brandt
- grid.121334.60000 0001 2097 0141MARBEC, IFREMER, IRD, CNRS, Univ Montpellier, Sète, France
| | - Florence Pradillon
- grid.4825.b0000 0004 0641 9240Centre Brest, Laboratoire Environnement Profond (REM/EEP/LEP), IFREMER, CS10070, 29280 Plouzané, France
| | - Blandine Trouche
- grid.4825.b0000 0004 0641 9240IFREMER, CNRS, Laboratoire de Microbiologie Des Environnements Extrêmes (LM2E), Univ Brest, Plouzané, France
| | - Nicolas Henry
- grid.462844.80000 0001 2308 1657CNRS, Station Biologique de Roscoff, AD2M, UMR 7144, Sorbonne University, 29680 Roscoff, France
| | - Cathy Liautard-Haag
- grid.121334.60000 0001 2097 0141MARBEC, IFREMER, IRD, CNRS, Univ Montpellier, Sète, France
| | - Marie-Anne Cambon-Bonavita
- grid.4825.b0000 0004 0641 9240IFREMER, CNRS, Laboratoire de Microbiologie Des Environnements Extrêmes (LM2E), Univ Brest, Plouzané, France
| | - Valérie Cueff-Gauchard
- grid.4825.b0000 0004 0641 9240IFREMER, CNRS, Laboratoire de Microbiologie Des Environnements Extrêmes (LM2E), Univ Brest, Plouzané, France
| | - Patrick Wincker
- grid.434728.e0000 0004 0641 2997Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ of Évry, Paris-Saclay University, 91057 Evry, France
| | - Caroline Belser
- grid.434728.e0000 0004 0641 2997Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ of Évry, Paris-Saclay University, 91057 Evry, France
| | - Julie Poulain
- grid.434728.e0000 0004 0641 2997Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ of Évry, Paris-Saclay University, 91057 Evry, France
| | - Sophie Arnaud-Haond
- grid.121334.60000 0001 2097 0141MARBEC, IFREMER, IRD, CNRS, Univ Montpellier, Sète, France
| | - Daniela Zeppilli
- grid.4825.b0000 0004 0641 9240Centre Brest, Laboratoire Environnement Profond (REM/EEP/LEP), IFREMER, CS10070, 29280 Plouzané, France
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43
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Ratcliffe FC, Uren Webster TM, Rodriguez-Barreto D, O'Rorke R, Garcia de Leaniz C, Consuegra S. Quantitative assessment of fish larvae community composition in spawning areas using metabarcoding of bulk samples. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2021; 31:e02284. [PMID: 33415761 DOI: 10.1002/eap.2284] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 08/10/2020] [Accepted: 10/05/2020] [Indexed: 06/12/2023]
Abstract
Accurate assessment of larval community composition in spawning areas is essential for fisheries management and conservation but is often hampered by the cryptic nature of many larvae, which renders them difficult to identify morphologically. Metabarcoding is a rapid and cost-effective method to monitor early life stages for management and environmental impact assessment purposes but its quantitative capability is under discussion. We compared metabarcoding with traditional morphological identification to evaluate taxonomic precision and reliability of abundance estimates, using 332 fish larvae from multinet hauls (0-50 m depth) collected at 14 offshore sampling sites in the Irish and Celtic seas. To improve quantification accuracy (relative abundance estimates), the amount of tissue for each specimen was standardized and mitochondrial primers (12S gene) with conserved binding sites were used. Relative family abundance estimated from metabarcoding reads and morphological assessment were positively correlated, as well as taxon richness (RS = 0.81, P = 0.007) and diversity (RS = 0.90, P = 0.002). Spatial patterns of community composition did not differ significantly between metabarcoding and morphological assessments. Our results show that DNA metabarcoding of bulk tissue samples can be used to monitor changes in fish larvae abundance and community composition. This represents a feasible, efficient, and faster alternative to morphological methods that can be applied to terrestrial and aquatic habitats.
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Affiliation(s)
- Frances C Ratcliffe
- Department of Biosciences, College of Science, Swansea University, Swansea, SA2 8PP, UK
| | - Tamsyn M Uren Webster
- Department of Biosciences, College of Science, Swansea University, Swansea, SA2 8PP, UK
| | | | - Richard O'Rorke
- Department of Biosciences, College of Science, Swansea University, Swansea, SA2 8PP, UK
| | | | - Sofia Consuegra
- Department of Biosciences, College of Science, Swansea University, Swansea, SA2 8PP, UK
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44
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Macher TH, Beermann AJ, Leese F. TaxonTableTools: A comprehensive, platform-independent graphical user interface software to explore and visualise DNA metabarcoding data. Mol Ecol Resour 2021; 21:1705-1714. [PMID: 33590697 DOI: 10.1111/1755-0998.13358] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 02/09/2021] [Indexed: 01/04/2023]
Abstract
DNA metabarcoding is increasingly used as a tool to assess biodiversity in research and environmental management. Powerful analysis software exists to process raw data. However, the translation of sequence read data into biological information and downstream analyses may be difficult for end users with limited expertise in bioinformatics. Thus, there is a growing need for easy-to-use, graphical user interface (GUI) software to analyse and visualise DNA metabarcoding data. Here, we present TaxonTableTools (TTT), a new platform-independent GUI that aims to fill this gap by providing simple, reproducible analysis and visualisation workflows. At its base, TTT uses a "TaXon table", which is a data format that can be generated easily within TTT from two input files: a read table and a taxonomy table obtained using various published metabarcoding pipelines. TTT analysis and visualisation modules include Venn diagrams to compare taxon overlap among replicates, samples, or analysis methods. TTT analyses and visualises basic statistics, such as read proportion per taxon, as well as more sophisticated visualisations, such as interactive Krona charts for taxonomic data exploration. Various ecological analyses can be produced directly, including alpha or beta diversity estimates, and rarefaction analysis ordination plots. Metabarcoding data can be converted into formats required for traditional, taxonomy-based analyses performed by regulatory bioassessment programs. In addition, TTT is able to produce html-based interactive graphics that can be analysed in any web browser. The software comes with a manual and tutorial, is free and publicly available through GitHub (https://github.com/TillMacher/TaxonTableTools) or the Python package index (https://pypi.org/project/taxontabletools/).
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Affiliation(s)
| | - Arne J Beermann
- Aquatic Ecosystem Research, University of Duisburg-Essen, Essen, Germany
| | - Florian Leese
- Aquatic Ecosystem Research, University of Duisburg-Essen, Essen, Germany
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45
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Integration of DNA-Based Approaches in Aquatic Ecological Assessment Using Benthic Macroinvertebrates. WATER 2021. [DOI: 10.3390/w13030331] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Benthic macroinvertebrates are among the most used biological quality elements for assessing the condition of all types of aquatic ecosystems worldwide (i.e., fresh water, transitional, and marine). Current morphology-based assessments have several limitations that may be circumvented by using DNA-based approaches. Here, we present a comprehensive review of 90 publications on the use of DNA metabarcoding of benthic macroinvertebrates in aquatic ecosystems bioassessments. Metabarcoding of bulk macrozoobenthos has been preferentially used in fresh waters, whereas in marine waters, environmental DNA (eDNA) from sediment and bulk communities from deployed artificial structures has been favored. DNA extraction has been done predominantly through commercial kits, and cytochrome c oxidase subunit I (COI) has been, by far, the most used marker, occasionally combined with others, namely, the 18S rRNA gene. Current limitations include the lack of standardized protocols and broad-coverage primers, the incompleteness of reference libraries, and the inability to reliably extrapolate abundance data. In addition, morphology versus DNA benchmarking of ecological status and biotic indexes are required to allow general worldwide implementation and higher end-user confidence. The increased sensitivity, high throughput, and faster execution of DNA metabarcoding can provide much higher spatial and temporal data resolution on aquatic ecological status, thereby being more responsive to immediate management needs.
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46
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Behrens-Chapuis S, Herder F, Geiger MF. Adding DNA barcoding to stream monitoring protocols - What's the additional value and congruence between morphological and molecular identification approaches? PLoS One 2021; 16:e0244598. [PMID: 33395693 PMCID: PMC7781668 DOI: 10.1371/journal.pone.0244598] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 12/14/2020] [Indexed: 11/25/2022] Open
Abstract
Although aquatic macroinvertebrates and freshwater fishes are important indicators for freshwater quality assessments, the morphological identification to species-level is often impossible and thus especially in many invertebrate taxa not mandatory during Water Framework Directive monitoring, a pragmatism that potentially leads to information loss. Here, we focus on the freshwater fauna of the River Sieg (Germany) to test congruence and additional value in taxa detection and taxonomic resolution of DNA barcoding vs. morphology-based identification in monitoring routines. Prior generated morphological identifications of juvenile fishes and aquatic macroinvertebrates were directly compared to species assignments using the identification engine of the Barcode of Life Data System. In 18% of the invertebrates morphology allowed only assignments to higher systematic entities, but DNA barcoding lead to species-level assignment. Dissimilarities between the two approaches occurred in 7% of the invertebrates and in 1% of the fishes. The 18 fish species were assigned to 20 molecular barcode index numbers, the 104 aquatic invertebrate taxa to 113 molecular entities. Although the cost-benefit analysis of both methods showed that DNA barcoding is still more expensive (5.30–8.60€ per sample) and time consuming (12.5h), the results emphasize the potential to increase taxonomic resolution and gain a more complete profile of biodiversity, especially in invertebrates. The provided reference DNA barcodes help building the foundation for metabarcoding approaches, which provide faster sample processing and more cost-efficient ecological status determination.
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Affiliation(s)
| | - Fabian Herder
- Zoologisches Forschungsmuseum Alexander Koenig, Bonn, Germany
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47
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Harper LR, Lawson Handley L, Sayer CD, Read DS, Benucci M, Blackman RC, Hill MJ, Hänfling B. Assessing the impact of the threatened crucian carp (Carassius carassius) on pond invertebrate diversity: A comparison of conventional and molecular tools. Mol Ecol 2020; 30:3252-3269. [PMID: 33002225 DOI: 10.1111/mec.15670] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 08/20/2020] [Accepted: 09/23/2020] [Indexed: 12/12/2022]
Abstract
Fishes stocked for recreation and angling can damage freshwater habitats and negatively impact biodiversity. The pond-associated crucian carp (Carassius carassius) is rare across Europe and is stocked for conservation management in England, but its impacts on pond biota are understudied. Freshwater invertebrates contribute substantially to aquatic biodiversity, encompassing many rare and endemic species, but their small size and high abundance complicate their assessment. Practitioners have employed sweep-netting and kick-sampling with microscopy (morphotaxonomy), but specimen size/quality and experience can bias identification. DNA and environmental DNA (eDNA) metabarcoding offer alternative means of invertebrate assessment. We compared invertebrate diversity in ponds (N = 18) with and without crucian carp using morphotaxonomic identification, DNA metabarcoding and eDNA metabarcoding. Five 2 L water samples and 3 min sweep-net samples were collected at each pond. Inventories produced by morphotaxonomic identification of netted samples, DNA metabarcoding of bulk tissue samples and eDNA metabarcoding of water samples were compared. Alpha diversity was greatest with DNA or eDNA metabarcoding, depending on whether standard or unbiased methods were considered. DNA metabarcoding reflected morphotaxonomic identification, whereas eDNA metabarcoding produced markedly different communities. These complementary tools should be combined for comprehensive invertebrate assessment. Crucian carp presence minimally reduced alpha diversity in ponds, but positively influenced beta diversity through taxon turnover (i.e., ponds with crucian carp contained different invertebrates to fishless ponds). Crucian carp presence contributes to landscape-scale invertebrate diversity, supporting continued conservation management in England. Our results show that molecular tools can enhance freshwater invertebrate assessment and facilitate development of more accurate and ecologically effective pond management strategies.
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Affiliation(s)
- Lynsey R Harper
- Department of Biological and Marine Sciences, University of Hull, Hull, UK.,Illinois Natural History Survey, Prairie Research Institute, University of Illinois at Urbana-Champaign, Champaign, IL, USA.,School of Biological and Environmental Sciences, Liverpool John Moores University, Liverpool, UK
| | | | - Carl D Sayer
- Pond Restoration Research Group, Environmental Change Research Centre, Department of Geography, University College London, London, UK
| | - Daniel S Read
- Centre for Ecology & Hydrology (CEH), Wallingford, Oxfordshire, UK
| | - Marco Benucci
- Department of Biological and Marine Sciences, University of Hull, Hull, UK
| | - Rosetta C Blackman
- Department of Biological and Marine Sciences, University of Hull, Hull, UK.,Department of Aquatic Ecology, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland.,Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Matthew J Hill
- School of Applied Sciences, University of Huddersfield, Huddersfield, UK
| | - Bernd Hänfling
- Department of Biological and Marine Sciences, University of Hull, Hull, UK
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48
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Martins FMS, Porto M, Feio MJ, Egeter B, Bonin A, Serra SRQ, Taberlet P, Beja P. Modelling technical and biological biases in macroinvertebrate community assessment from bulk preservative using multiple metabarcoding markers. Mol Ecol 2020; 30:3221-3238. [PMID: 32860303 PMCID: PMC8359330 DOI: 10.1111/mec.15620] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Revised: 07/29/2020] [Accepted: 08/05/2020] [Indexed: 01/05/2023]
Abstract
DNA metabarcoding from the ethanol used to store macroinvertebrate bulk samples is a convenient methodological option in molecular biodiversity assessment and biomonitoring of aquatic ecosystems, as it preserves specimens and reduces problems associated with sample sorting. However, this method may be affected by errors and biases, which need to be thoroughly quantified before it can be mainstreamed into biomonitoring programmes. Here, we used 80 unsorted macroinvertebrate samples collected in Portugal under a Water Framework Directive monitoring programme, to compare community diversity and taxonomic composition metrics estimated through morphotaxonomy versus metabarcoding from storage ethanol using three markers (COI‐M19BR2, 16S‐Inse01 and 18S‐Euka02) and a multimarker approach. A preliminary in silico analysis showed that the three markers were adequate for the target taxa, with detection failures related primarily to the lack of adequate barcodes in public databases. Metabarcoding of ethanol samples retrieved far less taxa per site (alpha diversity) than morphotaxonomy, albeit with smaller differences for COI‐M19BR2 and the multimarker approach, while estimates of taxa turnover (beta diversity) among sites were similar across methods. Using generalized linear mixed models, we found that after controlling for differences in read coverage across samples, the probability of detection of a taxon was positively related to its proportional abundance, and negatively so to the presence of heavily sclerotized exoskeleton (e.g., Coleoptera). Overall, using our experimental protocol with different template dilutions, the COI marker showed the best performance, but we recommend the use of a multimarker approach to detect a wider range of taxa in freshwater macroinvertebrate samples. Further methodological development and optimization efforts are needed to reduce biases associated with body armouring and rarity in some macroinvertebrate taxa.
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Affiliation(s)
- Filipa M S Martins
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal.,CIBIO/InBio, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vila do Conde, Portugal
| | - Miguel Porto
- CIBIO/InBio, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vila do Conde, Portugal.,CIBIO/InBio, Centro de Investigação em Biodiversidade e Recursos Genéticos, Instituto Superior de Agronomia, Universidade de Lisboa, Lisboa, Portugal
| | - Maria J Feio
- Departamento de Ciência da Vida, Centro de Ciências do Mar e do Ambiente, MARE, Universidade de Coimbra, Coimbra, Portugal
| | - Bastian Egeter
- CIBIO/InBio, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vila do Conde, Portugal
| | - Aurélie Bonin
- Laboratoire d'Ecologie Alpine (LECA), CNRS, Université Grenoble Alpes, Grenoble, France
| | - Sónia R Q Serra
- Departamento de Ciência da Vida, Centro de Ciências do Mar e do Ambiente, MARE, Universidade de Coimbra, Coimbra, Portugal
| | - Pierre Taberlet
- Laboratoire d'Ecologie Alpine (LECA), CNRS, Université Grenoble Alpes, Grenoble, France.,Tromsø Museum, UiT - The Arctic University of Norway, Tromsø, Norway
| | - Pedro Beja
- CIBIO/InBio, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vila do Conde, Portugal.,CIBIO/InBio, Centro de Investigação em Biodiversidade e Recursos Genéticos, Instituto Superior de Agronomia, Universidade de Lisboa, Lisboa, Portugal
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49
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Antich A, Palacín C, Cebrian E, Golo R, Wangensteen OS, Turon X. Marine biomonitoring with eDNA: Can metabarcoding of water samples cut it as a tool for surveying benthic communities? Mol Ecol 2020; 30:3175-3188. [PMID: 32974967 DOI: 10.1111/mec.15641] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 08/06/2020] [Accepted: 09/07/2020] [Indexed: 12/21/2022]
Abstract
In the marine realm, biomonitoring using environmental DNA (eDNA) of benthic communities requires destructive direct sampling or the setting-up of settlement structures. Comparatively much less effort is required to sample the water column, which can be accessed remotely. In this study we assess the feasibility of obtaining information from the eukaryotic benthic communities by sampling the adjacent water layer. We studied two different rocky-substrate benthic communities with a technique based on quadrat sampling. We also took replicate water samples at four distances (0, 0.5, 1.5, and 20 m) from the benthic habitat. Using broad range primers to amplify a ca. 313 bp fragment of the cytochrome oxidase subunit I gene, we obtained a total of 3,543 molecular operational taxonomic units (MOTUs). The structure obtained in the two environments was markedly different, with Metazoa, Archaeplastida and Stramenopiles being the most diverse groups in benthic samples, and Hacrobia, Metazoa and Alveolata in the water. Only 265 MOTUs (7.5%) were shared between benthos and water samples and, of these, 180 (5.1%) were identified as benthic taxa that left their DNA in the water. Most of them were found immediately adjacent to the benthos, and their number decreased as we moved apart from the benthic habitat. It was concluded that water eDNA, even in the close vicinity of the benthos, was a poor proxy for the analysis of benthic structure, and that direct sampling methods are required for monitoring these complex communities via metabarcoding.
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Affiliation(s)
- Adrià Antich
- Department of Marine Ecology, Center for Advanced Studies of Blanes (CEAB-CSIC), Girona, Spain
| | - Cruz Palacín
- Department of Evolutionary Biology, Ecology and Environmental Sciences, University of Barcelona, and Research Institute of Biodiversity (IRBIO), Barcelona, Spain
| | - Emma Cebrian
- Institute of Aquatic Ecology, University of Girona, Girona, Spain
| | - Raül Golo
- Institute of Aquatic Ecology, University of Girona, Girona, Spain
| | - Owen S Wangensteen
- Norwegian College of Fishery Science, UiT The Arctic University of Norway, Tromsø, Norway
| | - Xavier Turon
- Department of Marine Ecology, Center for Advanced Studies of Blanes (CEAB-CSIC), Girona, Spain
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50
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Schenk J, Höss S, Brinke M, Kleinbölting N, Brüchner-Hüttemann H, Traunspurger W. Nematodes as bioindicators of polluted sediments using metabarcoding and microscopic taxonomy. ENVIRONMENT INTERNATIONAL 2020; 143:105922. [PMID: 32663713 DOI: 10.1016/j.envint.2020.105922] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 03/04/2020] [Accepted: 06/20/2020] [Indexed: 05/19/2023]
Abstract
The use of bioindicator species is a widely applied approach to evaluate ecological conditions, and several indices have been designed for this purpose. To assess the impact of pollution, especially in sediments, a pollution-sensitive index based on nematodes, one of the most abundant and species-rich groups of metazoa, was developed. The NemaSPEAR[%] index in its original form relies on the morphological inspection of nematode species. The application of a morphologically based NemaSPEAR[%] at the genus-level was previously validated. The present study evaluated a NemaSPEAR[%] index based on metabarcoding of nematode communities and tested the potential of fragments from the 28S rDNA, 18S rDNA and cytochrome c oxidase subunit I (COI) genes. In general, molecular-based results tended to show a poorer condition than morphology-based results for the investigated sites. At the genus level, NemaSPEAR[%] values based on morphological data strongly correlated with those based on molecular data for both the 28S rDNA and the 18S rDNA gene fragments (R2 = 0.86 and R2 = 0.74, respectively). Within the dominant genera (>3%) identified by morphology, 68% were detected by at least one of the two ribosomal markers. At the species level, however, concordance was less pronounced, as there were several deviations of the molecular from the morphological data. These differences could mostly be attributed to shortcomings in the reference database used in the molecular-based assignments. Our pilot study shows that a molecularly based, genus-level NemaSPEAR[%] can be successfully applied to evaluate polluted sediment. Future studies need to validate this approach further, e.g. with bulk extractions of whole meiofaunal communities in order to circumvent time-consuming nematode isolation. Further database curation with abundant NemaSPEAR[%] species will also increase the applicability of this approach.
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Affiliation(s)
- Janina Schenk
- Department of Animal Ecology, Bielefeld University, Konsequenz 45, 33615 Bielefeld, Germany.
| | - Sebastian Höss
- Department of Animal Ecology, Bielefeld University, Konsequenz 45, 33615 Bielefeld, Germany; Ecossa, Giselastrasse 6, 82319 Starnberg, Germany.
| | - Marvin Brinke
- Federal Institute of Hydrology (BfG), Mainzer Tor 1, 56068 Koblenz, Germany.
| | - Nils Kleinbölting
- Center for Biotechnology, Bielefeld University, Universitaetsstrasse 25, 33615 Bielefeld, Germany.
| | | | - Walter Traunspurger
- Department of Animal Ecology, Bielefeld University, Konsequenz 45, 33615 Bielefeld, Germany.
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