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Macé B, Mouillot D, Dalongeville A, Bruno M, Deter J, Varenne A, Gudefin A, Boissery P, Manel S. The Tree of Life eDNA metabarcoding reveals a similar taxonomic richness but dissimilar evolutionary lineages between seaports and marine reserves. Mol Ecol 2024; 33:e17373. [PMID: 38703047 DOI: 10.1111/mec.17373] [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: 12/27/2023] [Revised: 04/08/2024] [Accepted: 04/22/2024] [Indexed: 05/06/2024]
Abstract
Coastal areas host a major part of marine biodiversity but are seriously threatened by ever-increasing human pressures. Transforming natural coastlines into urban seascapes through habitat artificialization may result in loss of biodiversity and key ecosystem functions. Yet, the extent to which seaports differ from nearby natural habitats and marine reserves across the whole Tree of Life is still unknown. This study aimed to assess the level of α and β-diversity between seaports and reserves, and whether these biodiversity patterns are conserved across taxa and evolutionary lineages. For that, we used environmental DNA (eDNA) metabarcoding to survey six seaports on the French Mediterranean coast and four strictly no-take marine reserves nearby. By targeting four different groups-prokaryotes, eukaryotes, metazoans and fish-with appropriate markers, we provide a holistic view of biodiversity on contrasted habitats. In the absence of comprehensive reference databases, we used bioinformatic pipelines to gather similar sequences into molecular operational taxonomic units (MOTUs). In contrast to our expectations, we obtained no difference in MOTU richness (α-diversity) between habitats except for prokaryotes and threatened fishes with higher diversity in reserves than in seaports. However, we observed a marked dissimilarity (β-diversity) between seaports and reserves for all taxa. Surprisingly, this biodiversity signature of seaports was preserved across the Tree of Life, up to the order. This result reveals that seaports and nearby marine reserves share few taxa and evolutionary lineages along urbanized coasts and suggests major differences in terms of ecosystem functioning between both habitats.
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Affiliation(s)
- Bastien Macé
- CEFE, Univ Montpellier, CNRS, EPHE-PSL University, IRD, Montpellier, France
| | - David Mouillot
- MARBEC, Univ Montpellier, CNRS, Ifremer, IRD, Montpellier, France
- Institut Universitaire de France, Paris, France
| | | | - Morgane Bruno
- CEFE, Univ Montpellier, CNRS, EPHE-PSL University, IRD, Montpellier, France
| | - Julie Deter
- MARBEC, Univ Montpellier, CNRS, Ifremer, IRD, Montpellier, France
- Andromède Océanologie, Mauguio, France
| | - Alix Varenne
- Université Côte d'Azur, CNRS, ECOSEAS, Nice, France
- Ecocean, Montpellier, France
| | | | - Pierre Boissery
- Agence de l'eau Rhône-Méditerranée-Corse, Délégation de Marseille, Marseille, France
| | - Stéphanie Manel
- CEFE, Univ Montpellier, CNRS, EPHE-PSL University, IRD, Montpellier, France
- Institut Universitaire de France, Paris, France
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2
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Flo S, Vader A, Præbel K. Brute force prey metabarcoding to explore the diets of small invertebrates. Ecol Evol 2024; 14:e11369. [PMID: 38711484 PMCID: PMC11070772 DOI: 10.1002/ece3.11369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 04/16/2024] [Accepted: 04/17/2024] [Indexed: 05/08/2024] Open
Abstract
Prey metabarcoding has become a popular tool in molecular ecology for resolving trophic interactions at high resolution, from various sample types and animals. To date, most predator-prey studies of small-sized animals (<1 mm) have met the problem of overabundant predator DNA in dietary samples by adding blocking primers/peptide nucleic acids. These primers aim to limit the PCR amplification and detection of the predator DNA but may introduce bias to the prey composition identified by interacting with sequences that are similar to those of the predator. Here we demonstrate the use of an alternative method to explore the prey of small marine copepods using whole-body DNA extracts and deep, brute force metabarcoding of an 18S rDNA fragment. After processing and curating raw data from two sequencing runs of varying depths (0.4 and 5.4 billion raw reads), we isolated 1.3 and 52.2 million prey reads, with average depths of ~15,900 and ~120,000 prey reads per copepod individual, respectively. While data from both sequencing runs were sufficient to distinguish dietary compositions from disparate seasons, locations, and copepod species, greater sequencing depth led to better separation of clusters. As computation and sequencing are becoming ever more powerful and affordable, we expect the brute force approach to become a general standard for prey metabarcoding, as it offers a simple and affordable solution to consumers that is impractical to dissect or unknown to science.
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Affiliation(s)
- Snorre Flo
- Department of Arctic BiologyThe University Centre in SvalbardLongyearbyen, SvalbardNorway
- Faculty of Biosciences, Fisheries and EconomicsUiT The Arctic University of NorwayTromsøNorway
| | - Anna Vader
- Department of Arctic BiologyThe University Centre in SvalbardLongyearbyen, SvalbardNorway
| | - Kim Præbel
- The Norwegian College of Fishery Science (NFH)UiT The Arctic University of NorwayTromsøNorway
- Department of Forestry and Wildlife ManagementInland Norway University of Applied SciencesElverumNorway
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3
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Ficetola GF, Guerrieri A, Cantera I, Bonin A. In silico assessment of 18S rDNA metabarcoding markers for the characterization of nematode communities. PLoS One 2024; 19:e0298905. [PMID: 38578734 PMCID: PMC10997105 DOI: 10.1371/journal.pone.0298905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 01/31/2024] [Indexed: 04/07/2024] Open
Abstract
Nematodes are keystone actors of soil, freshwater and marine ecosystems, but the complexity of morphological identification has limited broad-scale monitoring of nematode biodiversity. DNA metabarcoding is increasingly used to assess nematode diversity but requires universal primers with high taxonomic coverage and high taxonomic resolution. Several primers have been proposed for the metabarcoding of nematode diversity, many of which target the 18S rRNA gene. In silico analyses have a great potential to assess key parameters of primers, including taxonomic coverage, resolution and specificity. Based on a recently-available reference database, we tested in silico the performance of fourteen commonly used and one newly optimized primer for nematode metabarcoding. Most primers showed very good coverage, amplifying most of the sequences in the reference database, while four markers showed limited coverage. All primers showed good taxonomic resolution. Resolution was particularly good if the aim was the identification of higher-level taxa, such as genera or families. Overall, species-level resolution was higher for primers amplifying long fragments. None of the primers was highly specific for nematodes as, despite some variation, they all amplified a large number of other eukaryotes. Differences in performance across primers highlight the complexity of the choice of markers appropriate for the metabarcoding of nematodes, which depends on a trade-off between taxonomic resolution and the length of amplified fragments. Our in silico analyses provide new insights for the identification of the most appropriate primers, depending on the study goals and the origin of DNA samples. This represents an essential step to design and optimize metabarcoding studies assessing nematode diversity.
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Affiliation(s)
- Gentile Francesco Ficetola
- Department of Environmental Science and Policy, University of Milan, Milan, Italy
- LECA, Laboratoire d’Ecologie Alpine, Univ. Grenoble Alpes, CNRS, Univ. Savoie Mont Blanc, Grenoble, France
| | | | - Isabel Cantera
- Department of Environmental Science and Policy, University of Milan, Milan, Italy
| | - Aurelie Bonin
- Argaly, Bâtiment Cleanspace, Sainte-Hélène-du-Lac, France
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4
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Neby M, Ims RA, Kamenova S, Devineau O, Soininen EM. Is the diet cyclic phase-dependent in boreal vole populations? Ecol Evol 2024; 14:e11227. [PMID: 38638368 PMCID: PMC11024456 DOI: 10.1002/ece3.11227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 03/13/2024] [Accepted: 03/21/2024] [Indexed: 04/20/2024] Open
Abstract
Herbivorous rodents in boreal, alpine and arctic ecosystems are renowned for their multi-annual population cycles. Researchers have hypothesised that these cycles may result from herbivore-plant interactions in various ways. For instance, if the biomass of preferred food plants is reduced after a peak phase of a cycle, rodent diets can be expected to become dominated by less preferred food plants, leading the population to a crash. It could also be expected that the taxonomic diversity of rodent diets increases from the peak to the crash phase of a cycle. The present study is the first to use DNA metabarcoding to quantify the diets of two functionally important boreal rodent species (bank vole and tundra vole) to assess whether their diet changed systematically in the expected cyclic phase-dependent manner. We found the taxonomic diet spectrum broad in both vole species but with little interspecific overlap. There was no evidence of systematic shifts in diet diversity metrics between the phases of the population cycle in either species. While both species' diet composition changed moderately between cycle phases and seasons, these changes were small compared to other sources of diet variation-especially differences between individuals. Thus, the variation in diet that could be attributed to cyclic phases is marginal relative to the overall diet flexibility. Based on general consumer-resource theory, we suggest that the broad diets with little interspecific overlap render it unlikely that herbivore-plant interactions generate their synchronous population cycles. We propose that determining dietary niche width should be the first step in scientific inquiries about the role of herbivore-plant interactions in cyclic vole populations.
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Affiliation(s)
- Magne Neby
- Department of Applied EcologyInland Norway University of Applied SciencesKoppangNorway
- Department of Agricultural SciencesInland Norway University of Applied SciencesHamarNorway
| | - Rolf A. Ims
- Department of Arctic and Marine BiologyUiT – The Arctic University of NorwayTromsøNorway
| | - Stefaniya Kamenova
- Department of Biosciences, Centre for Ecological and Evolutionary SynthesisUniversity of OsloOsloNorway
- Faculty of Environmental Sciences and Natural Resource ManagementNorwegian University of Life SciencesÅsNorway
- National Museum of Natural HistoryBulgarian Academy of SciencesSofiaBulgaria
| | - Olivier Devineau
- Department of Applied EcologyInland Norway University of Applied SciencesKoppangNorway
| | - Eeva M. Soininen
- Department of Arctic and Marine BiologyUiT – The Arctic University of NorwayTromsøNorway
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Zeng Y, Chen Z, Cao J, Li S, Xia Z, Sun Y, Zhang J, He P. Revolutionizing early-stage green tide monitoring: eDNA metabarcoding insights into Ulva prolifera and microecology in the South Yellow Sea. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:169022. [PMID: 38043827 DOI: 10.1016/j.scitotenv.2023.169022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 11/27/2023] [Accepted: 11/29/2023] [Indexed: 12/05/2023]
Abstract
Green tides, characterized by excessive Ulva prolifera blooms, pose significant ecological and economic challenges, especially in the South Yellow Sea. We successfully employed 18S environmental DNA (eDNA) metabarcoding to detect Ulva prolifera micropropagules, confirming the technique's reliability and introducing a rapid green tide monitoring method. Our investigation revealed notable disparities in the eukaryotic microbial community composition within Ulva prolifera habitats across different regions. Particularly, during the early stages of the South Yellow Sea green tide outbreak, potential interactions emerged between Ulva prolifera micropropagules and certain previously undocumented microorganisms from neighboring waters. These findings enhance our comprehension of early-stage green tide ecosystem dynamics, underscoring the value of merging advanced molecular techniques with conventional ecological methods to gain a comprehensive understanding of the impact of green tide on the local ecosystem. Overall, our study advances our understanding of green tide dynamics, offering novel avenues for control, ecological restoration, and essential scientific support for sustainable marine conservation and management.
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Affiliation(s)
- Yinqing Zeng
- College of Marine Ecology and Environment, Shanghai Ocean University, Shanghai 201306, China
| | - Zehua Chen
- College of Marine Ecology and Environment, Shanghai Ocean University, Shanghai 201306, China
| | - Jiaxing Cao
- College of Marine Ecology and Environment, Shanghai Ocean University, Shanghai 201306, China
| | - Shuang Li
- College of Marine Ecology and Environment, Shanghai Ocean University, Shanghai 201306, China
| | - Zhangyi Xia
- College of Marine Ecology and Environment, Shanghai Ocean University, Shanghai 201306, China
| | - Yuqing Sun
- College of Marine Ecology and Environment, Shanghai Ocean University, Shanghai 201306, China
| | - Jianheng Zhang
- College of Marine Ecology and Environment, Shanghai Ocean University, Shanghai 201306, China; Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai 201306, China; Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang 222005, China.
| | - Peimin He
- College of Marine Ecology and Environment, Shanghai Ocean University, Shanghai 201306, China; Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai 201306, China; Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang 222005, China.
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6
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Geraldi NR, Krause-Jensen D, Ørberg SB, Frühe L, Sejr MK, Hansen JLS, Lund-Hansen L, Duarte CM. Environmental drivers of Arctic communities based on metabarcoding of marine sediment eDNA. Proc Biol Sci 2024; 291:20231614. [PMID: 38264782 PMCID: PMC10806441 DOI: 10.1098/rspb.2023.1614] [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: 07/19/2023] [Accepted: 12/15/2023] [Indexed: 01/25/2024] Open
Abstract
Our ability to assess biodiversity at relevant spatial and temporal scales for informing management is of increasing importance given this is foundational to identify and mitigate the impacts of global change. Collecting baseline information and tracking ecological changes are particularly important for areas experiencing rapid changes and representing data gaps such as Arctic marine ecosystems. Environmental DNA has the potential to provide such data. We extracted environmental DNA from 90 surface sediment samples to assess eukaryote diversity around Greenland and Svalbard using two separate primer pairs amplifying different sections of the 18S rRNA gene. We detected 27 different phyla and 99 different orders and found that temperature and the change in temperature explained the most variation in the community in a single linear model, while latitude, sea ice cover and change in temperature explained the most variation in the community when assessed by individual non-linear models. We identified potential indicator taxa for Arctic climate change, including a terebellid annelid worm. In conclusion, our study demonstrates that environmental DNA offers a feasible method to assess biodiversity and identifies warming as a key driver of differences in biodiversity across these remote ecosystems.
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Affiliation(s)
- Nathan R. Geraldi
- Red Sea Research Center (RSRC) and Computational Biosciences Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Department of Ecoscience, Aarhus University, Aarhus, Denmark
| | - Dorte Krause-Jensen
- Department of Ecoscience, Aarhus University, Aarhus, Denmark
- Arctic Research Centre, Aarhus University, Aarhus, Denmark
| | - Sarah B. Ørberg
- Department of Ecoscience, Aarhus University, Aarhus, Denmark
- Arctic Research Centre, Aarhus University, Aarhus, Denmark
| | - Larissa Frühe
- Red Sea Research Center (RSRC) and Computational Biosciences Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Mikael K. Sejr
- Department of Ecoscience, Aarhus University, Aarhus, Denmark
- Arctic Research Centre, Aarhus University, Aarhus, Denmark
| | | | - Lars Lund-Hansen
- Arctic Research Centre, Aarhus University, Aarhus, Denmark
- Department of Biology, Aarhus University, Aarhus, Denmark
| | - Carlos M. Duarte
- Red Sea Research Center (RSRC) and Computational Biosciences Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Arctic Research Centre, Aarhus University, Aarhus, Denmark
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7
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Fracasso I, Zaccone C, Oskolkov N, Da Ros L, Dinella A, Belelli Marchesini L, Buzzini P, Sannino C, Turchetti B, Cesco S, Le Roux G, Tonon G, Vernesi C, Mimmo T, Ventura M, Borruso L. Exploring different methodological approaches to unlock paleobiodiversity in peat profiles using ancient DNA. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 908:168159. [PMID: 37923262 DOI: 10.1016/j.scitotenv.2023.168159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 09/28/2023] [Accepted: 10/25/2023] [Indexed: 11/07/2023]
Abstract
Natural and human-induced environmental changes deeply affected terrestrial ecosystems throughout the Holocene. Paleoenvironmental reconstructions provide information about the past and allow us to predict/model future scenarios. Among potential records, peat bogs are widely used because they present a precise stratigraphy and act as natural archives of highly diverse organic remains. Over the decades, several techniques have been developed to identify debris occurring in peat, including their morphological description. However, this is strongly constrained by the researcher's ability to distinguish residues at the species level, which typically requires many years of experience. In addition, potential contamination hampers using these techniques to obtain information from organisms such as fungi or bacteria. Environmental DNA metabarcoding and shotgun metagenome sequencing could represent a solution to detect specific groups of organisms without any a priori knowledge of their characteristics and/or to identify organisms that have rarely been considered in previous investigations. Moreover, shotgun metagenomics may allow the identification of bacteria and fungi (including both yeast and filamentous life forms), ensuring discrimination between ancient and modern organisms through the study of deamination/damage patterns. In the present review, we aim to i) present the state-of-the-art methodologies in paleoecological and paleoclimatic studies focusing on peat core analyses, proposing alternative approaches to the classical morphological identification of plant residues, and ii) suggest biomolecular approaches that will allow the use of proxies such as invertebrates, fungi, and bacteria, which are rarely employed in paleoenvironmental reconstructions.
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Affiliation(s)
- Ilaria Fracasso
- Faculty of Agricultural, Environmental and Food Sciences, Free University of Bozen-Bolzano, 39100 Bolzano, Italy.
| | - Claudio Zaccone
- Department of Biotechnology, University of Verona, 37134 Verona, Italy
| | - Nikolay Oskolkov
- Department of Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Lund University, 221 00 Lund, Sweden
| | - Luca Da Ros
- Faculty of Agricultural, Environmental and Food Sciences, Free University of Bozen-Bolzano, 39100 Bolzano, Italy
| | - Anna Dinella
- Faculty of Agricultural, Environmental and Food Sciences, Free University of Bozen-Bolzano, 39100 Bolzano, Italy
| | - Luca Belelli Marchesini
- Forest Ecology Unit, Research and Innovation Centre, Fondazione Edmund Mach, 38098 San Michele all'Adige, Italy
| | - Pietro Buzzini
- Department of Agricultural, Food and Environmental Science, University of Perugia, 06123 Perugia, Italy
| | - Ciro Sannino
- Department of Agricultural, Food and Environmental Science, University of Perugia, 06123 Perugia, Italy
| | - Benedetta Turchetti
- Department of Agricultural, Food and Environmental Science, University of Perugia, 06123 Perugia, Italy
| | - Stefano Cesco
- Faculty of Agricultural, Environmental and Food Sciences, Free University of Bozen-Bolzano, 39100 Bolzano, Italy
| | - Gael Le Roux
- Laboratoire Ecologie Fonctionnelle et Environnement (UMR5245 CNRS/UPS/INPT), Université de Toulouse, 31326 Castanet-Tolosan, France
| | - Giustino Tonon
- Faculty of Agricultural, Environmental and Food Sciences, Free University of Bozen-Bolzano, 39100 Bolzano, Italy
| | - Cristiano Vernesi
- Forest Ecology Unit, Research and Innovation Centre, Fondazione Edmund Mach, 38098 San Michele all'Adige, Italy
| | - Tanja Mimmo
- Faculty of Agricultural, Environmental and Food Sciences, Free University of Bozen-Bolzano, 39100 Bolzano, Italy
| | - Maurizio Ventura
- Faculty of Agricultural, Environmental and Food Sciences, Free University of Bozen-Bolzano, 39100 Bolzano, Italy
| | - Luigimaria Borruso
- Faculty of Agricultural, Environmental and Food Sciences, Free University of Bozen-Bolzano, 39100 Bolzano, Italy.
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8
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Guerrieri A, Cantera I, Marta S, Bonin A, Carteron A, Ambrosini R, Caccianiga M, Anthelme F, Azzoni RS, Almond P, Alviz Gazitúa P, Cauvy-Fraunié S, Ceballos Lievano JL, Chand P, Chand Sharma M, Clague J, Cochachín Rapre JA, Compostella C, Cruz Encarnación R, Dangles O, Deline P, Eger A, Erokhin S, Franzetti A, Gielly L, Gili F, Gobbi M, Hågvar S, Khedim N, Meneses RI, Peyre G, Pittino F, Proietto A, Rabatel A, Urseitova N, Yang Y, Zaginaev V, Zerboni A, Zimmer A, Taberlet P, Diolaiuti GA, Poulenard J, Fontaneto D, Thuiller W, Ficetola GF. Local climate modulates the development of soil nematode communities after glacier retreat. GLOBAL CHANGE BIOLOGY 2024; 30:e17057. [PMID: 38273541 DOI: 10.1111/gcb.17057] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 10/10/2023] [Indexed: 01/27/2024]
Abstract
The worldwide retreat of glaciers is causing a faster than ever increase in ice-free areas that are leading to the emergence of new ecosystems. Understanding the dynamics of these environments is critical to predicting the consequences of climate change on mountains and at high latitudes. Climatic differences between regions of the world could modulate the emergence of biodiversity and functionality after glacier retreat, yet global tests of this hypothesis are lacking. Nematodes are the most abundant soil animals, with keystone roles in ecosystem functioning, but the lack of global-scale studies limits our understanding of how the taxonomic and functional diversity of nematodes changes during the colonization of proglacial landscapes. We used environmental DNA metabarcoding to characterize nematode communities of 48 glacier forelands from five continents. We assessed how different facets of biodiversity change with the age of deglaciated terrains and tested the hypothesis that colonization patterns are different across forelands with different climatic conditions. Nematodes colonized ice-free areas almost immediately. Both taxonomic and functional richness quickly increased over time, but the increase in nematode diversity was modulated by climate, so that colonization started earlier in forelands with mild summer temperatures. Colder forelands initially hosted poor communities, but the colonization rate then accelerated, eventually leveling biodiversity differences between climatic regimes in the long term. Immediately after glacier retreat, communities were dominated by colonizer taxa with short generation time and r-ecological strategy but community composition shifted through time, with increased frequency of more persister taxa with K-ecological strategy. These changes mostly occurred through the addition of new traits instead of their replacement during succession. The effects of local climate on nematode colonization led to heterogeneous but predictable patterns around the world that likely affect soil communities and overall ecosystem development.
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Affiliation(s)
- Alessia Guerrieri
- Dipartimento di Scienze e Politiche Ambientali, Università degli Studi di Milano, Milano, Italy
- Argaly, Bâtiment CleanSpace, Sainte-Hélène-du-Lac, France
| | - Isabel Cantera
- Dipartimento di Scienze e Politiche Ambientali, Università degli Studi di Milano, Milano, Italy
| | - Silvio Marta
- Dipartimento di Scienze e Politiche Ambientali, Università degli Studi di Milano, Milano, Italy
- Institute of Geosciences and Earth Resources, CNR, Pisa, Italy
| | - Aurélie Bonin
- Argaly, Bâtiment CleanSpace, Sainte-Hélène-du-Lac, France
| | - Alexis Carteron
- Dipartimento di Scienze e Politiche Ambientali, Università degli Studi di Milano, Milano, Italy
| | - Roberto Ambrosini
- Dipartimento di Scienze e Politiche Ambientali, Università degli Studi di Milano, Milano, Italy
| | - Marco Caccianiga
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano, Italy
| | - Fabien Anthelme
- Laboratory AMAP, IRD, University of Montpellier, CIRAD, CNRS, INRA, Montpellier, France
| | - Roberto Sergio Azzoni
- Dipartimento di Scienze e Politiche Ambientali, Università degli Studi di Milano, Milano, Italy
- Dipartimento di Scienze della Terra "Ardito Desio", Università degli Studi di Milano, Milano, Italy
| | - Peter Almond
- Department of Soil and Physical Sciences, Lincoln University, Lincoln, New Zealand
| | - Pablo Alviz Gazitúa
- Departamento de Ciencias Biológicas y Biodiversidad, Universidad de Los Lagos, Osorno, Chile
| | | | | | - Pritam Chand
- Department of Geography, School of Environment and Earth Sciences, Central University of Punjab, Bathinda, Punjab, India
| | - Milap Chand Sharma
- Centre for the Study of Regional Development - School of Social Sciences, Jawaharlal Nehru University, New Delhi, India
| | - John Clague
- Department of Earth Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | | | - Chiara Compostella
- Dipartimento di Scienze della Terra "Ardito Desio", Università degli Studi di Milano, Milano, Italy
| | | | - Olivier Dangles
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Univ Paul Valéry Montpellier 3, Montpellier, France
| | - Philip Deline
- Univ. Savoie Mont Blanc, Univ. Grenoble Alpes, EDYTEM, Chambéry, France
| | - Andre Eger
- Mannaki Whenua - Landcare Research, Soils and Landscapes, Lincoln, New Zealand
| | - Sergey Erokhin
- Institute of Water Problems and Hydro-Energy, Kyrgyz National Academy of Sciences, Bishkek, Kyrgyzstan
| | - Andrea Franzetti
- Department of Earth and Environmental Sciences (DISAT), University of Milano-Bicocca, Milano, Italy
| | - Ludovic Gielly
- Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, Grenoble, France
| | - Fabrizio Gili
- Dipartimento di Scienze e Politiche Ambientali, Università degli Studi di Milano, Milano, Italy
- Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
| | - Mauro Gobbi
- Research and Museum Collections Office, Climate and Ecology Unit, MUSE-Science Museum, Corso del Lavoro e della Scienza, Trento, Italy
| | - Sigmund Hågvar
- Faculty of Environmental Sciences and Natural Resource Management (INA), Norwegian University of Life Sciences, Ås, Norway
- UiT - The Arctic University of Norway, Tromsø Museum, Tromsø, Norway
| | - Norine Khedim
- Univ. Savoie Mont Blanc, Univ. Grenoble Alpes, EDYTEM, Chambéry, France
| | - Rosa Isela Meneses
- Herbario Nacional de Bolivia: La Paz, La Paz, Bolivia
- Universidad Católica del Norte, Antofagasta, Chile
| | - Gwendolyn Peyre
- Department of Civil and Environmental Engineering, University of the Andes, Bogotá, Colombia
| | - Francesca Pittino
- Department of Earth and Environmental Sciences (DISAT), University of Milano-Bicocca, Milano, Italy
| | - Angela Proietto
- Dipartimento di Scienze della Terra "Ardito Desio", Università degli Studi di Milano, Milano, Italy
| | - Antoine Rabatel
- Univ. Grenoble Alpes, CNRS, IRD, Grenoble-INP, Institut des Géosciences de l'Environnement (IGE, UMR 5001), Grenoble, France
| | - Nurai Urseitova
- Institute of Water Problems and Hydro-Energy, Kyrgyz National Academy of Sciences, Bishkek, Kyrgyzstan
| | - Yan Yang
- Institute of Mountain Hazards and Environment, Chinese Academy of Sciences, Chengdu, China
| | - Vitalii Zaginaev
- Mountain Societies Research Institute, University of Central Asia, Bishkek, Kyrgyzstan
| | - Andrea Zerboni
- Dipartimento di Scienze della Terra "Ardito Desio", Università degli Studi di Milano, Milano, Italy
| | - Anaïs Zimmer
- Department of Geography and the Environment, University of Texas at Austin, Austin, Texas, USA
| | - Pierre Taberlet
- Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, Grenoble, France
- UiT - The Arctic University of Norway, Tromsø Museum, Tromsø, Norway
| | | | - Jerome Poulenard
- Univ. Savoie Mont Blanc, Univ. Grenoble Alpes, EDYTEM, Chambéry, France
| | - Diego Fontaneto
- CNR - Water Research Institute, Verbania, Italy
- NBFC - National Biodiversity Future Center, Palermo, Italy
| | - Wilfried Thuiller
- Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, Grenoble, France
| | - Gentile Francesco Ficetola
- Dipartimento di Scienze e Politiche Ambientali, Università degli Studi di Milano, Milano, Italy
- Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, Grenoble, France
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9
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Guerrieri A, Carteron A, Bonin A, Marta S, Ambrosini R, Caccianiga M, Cantera I, Compostella C, Diolaiuti G, Fontaneto D, Gielly L, Gili F, Gobbi M, Poulenard J, Taberlet P, Zerboni A, Thuiller W, Ficetola GF. Metabarcoding data reveal vertical multitaxa variation in topsoil communities during the colonization of deglaciated forelands. Mol Ecol 2023; 32:6304-6319. [PMID: 35997629 DOI: 10.1111/mec.16669] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 07/21/2022] [Accepted: 08/15/2022] [Indexed: 11/27/2022]
Abstract
Ice-free areas are expanding worldwide due to dramatic glacier shrinkage and are undergoing rapid colonization by multiple lifeforms, thus representing key environments to study ecosystem development. It has been proposed that the colonization dynamics of deglaciated terrains is different between surface and deep soils but that the heterogeneity between communities inhabiting surface and deep soils decreases through time. Nevertheless, tests of this hypothesis remain scarce, and it is unclear whether patterns are consistent among different taxonomic groups. Here, we used environmental DNA metabarcoding to test whether community diversity and composition of six groups (Eukaryota, Bacteria, Mycota, Collembola, Insecta, and Oligochaeta) differ between the surface (0-5 cm) and deeper (7.5-20 cm) soil at different stages of development and across five Alpine glaciers. Taxonomic diversity increased with time since glacier retreat and with soil evolution. The pattern was consistent across groups and soil depths. For Eukaryota and Mycota, alpha-diversity was highest at the surface. Time since glacier retreat explained more variation of community composition than depth. Beta-diversity between surface and deep layers decreased with time since glacier retreat, supporting the hypothesis that the first 20 cm of soil tends to homogenize through time. Several molecular operational taxonomic units of bacteria and fungi were significant indicators of specific depths and/or soil development stages, confirming the strong functional variation of microbial communities through time and depth. The complexity of community patterns highlights the importance of integrating information from multiple taxonomic groups to unravel community variation in response to ongoing global changes.
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Affiliation(s)
- Alessia Guerrieri
- Department of Environmental Science and Policy, Università degli Studi di Milano, Milan, Italy
| | - Alexis Carteron
- Department of Environmental Science and Policy, Università degli Studi di Milano, Milan, Italy
| | - Aurélie Bonin
- Department of Environmental Science and Policy, Università degli Studi di Milano, Milan, Italy
- Argaly, Bâtiment CleanSpace, Sainte-Hélène-du-Lac, France
| | - Silvio Marta
- Department of Environmental Science and Policy, Università degli Studi di Milano, Milan, Italy
| | - Roberto Ambrosini
- Department of Environmental Science and Policy, Università degli Studi di Milano, Milan, Italy
| | - Marco Caccianiga
- Department of Environmental Science and Policy, Università degli Studi di Milano, Milan, Italy
| | - Isabel Cantera
- Department of Environmental Science and Policy, Università degli Studi di Milano, Milan, Italy
| | - Chiara Compostella
- Department of Earth Sciences, "A. Desio," Università degli Studi di Milano, Milan, Italy
| | - Guglielmina Diolaiuti
- Department of Environmental Science and Policy, Università degli Studi di Milano, Milan, Italy
| | | | - Ludovic Gielly
- Univ. Grenoble Alpes, CNRS, Univ. Savoie Mont Blanc, LECA, Laboratoire d'Ecologie Alpine, Grenoble, France
| | - Fabrizio Gili
- Department of Environmental Science and Policy, Università degli Studi di Milano, Milan, Italy
| | - Mauro Gobbi
- Research & Museum Collections Office, Climate and Ecology Unit, MUSE-Science Museum, Trento, Italy
| | | | - Pierre Taberlet
- Univ. Grenoble Alpes, CNRS, Univ. Savoie Mont Blanc, LECA, Laboratoire d'Ecologie Alpine, Grenoble, France
- UiT - The Arctic University of Norway, Tromsø Museum, Tromsø, Norway
| | - Andrea Zerboni
- Department of Earth Sciences, "A. Desio," Università degli Studi di Milano, Milan, Italy
| | - Wilfried Thuiller
- Univ. Grenoble Alpes, CNRS, Univ. Savoie Mont Blanc, LECA, Laboratoire d'Ecologie Alpine, Grenoble, France
| | - Gentile Francesco Ficetola
- Department of Environmental Science and Policy, Università degli Studi di Milano, Milan, Italy
- Univ. Grenoble Alpes, CNRS, Univ. Savoie Mont Blanc, LECA, Laboratoire d'Ecologie Alpine, Grenoble, France
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10
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Ficetola GF, Taberlet P. Towards exhaustive community ecology via DNA metabarcoding. Mol Ecol 2023; 32:6320-6329. [PMID: 36762839 DOI: 10.1111/mec.16881] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 01/30/2023] [Accepted: 02/06/2023] [Indexed: 02/11/2023]
Abstract
Exhaustive biodiversity data, covering all the taxa in an environment, would be fundamental to understand how global changes influence organisms living at different trophic levels, and to evaluate impacts on interspecific interactions. Molecular approaches such as DNA metabarcoding are boosting our ability to perform biodiversity inventories. Nevertheless, even though a few studies have recently attempted exhaustive reconstructions of communities, holistic assessments remain rare. The majority of metabarcoding studies published in the last years used just one or two markers and analysed a limited number of taxonomic groups. Here, we provide an overview of emerging approaches that can allow all-taxa biological inventories. Exhaustive biodiversity assessments can be attempted by combining a large number of specific primers, by exploiting the power of universal primers, or by combining specific and universal primers to obtain good information on key taxa while limiting the overlooked biodiversity. Multiplexes of primers, shotgun sequencing and capture enrichment may provide a better coverage of biodiversity compared to standard metabarcoding, but still require major methodological advances. Here, we identify the strengths and limitations of different approaches, and suggest new development lines that might improve broad scale biodiversity analyses in the near future. More holistic reconstructions of ecological communities can greatly increase the value of metabarcoding studies, improving understanding of the consequences of ongoing environmental changes on the multiple components of biodiversity.
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Affiliation(s)
- Gentile Francesco Ficetola
- Department of Environmental Science and Policy, Università degli Studi di Milano, Milan, Italy
- University Grenoble Alpes, University Savoie Mont Blanc, CNRS, LECA, Laboratoire d'Écologie Alpine, Grenoble, France
| | - Pierre Taberlet
- University Grenoble Alpes, University Savoie Mont Blanc, CNRS, LECA, Laboratoire d'Écologie Alpine, Grenoble, France
- UiT - The Arctic University of Norway, Tromsø Museum, Tromsø, Norway
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11
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Qin S, Li F, Zou Y, Xue J, Zhang Y, Yang Z. eDNA-based diversity and multitrophic network reveal the effects of land use and pollutants on the subtropical Dongjiang River systems. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 334:122157. [PMID: 37454713 DOI: 10.1016/j.envpol.2023.122157] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 06/20/2023] [Accepted: 07/06/2023] [Indexed: 07/18/2023]
Abstract
Biodiversity and its constituted multitrophic network in rivers are accelerating change under human land use and pollutants. However, due to the lack of complete datasets across taxa limited by traditional morphological biomonitoring, the change patterns of biodiversity and multitrophic networks are still unclear. Here, we used the eDNA approach to capture multitrophic communities (including fish, aquatic insects, protozoa, diatom and bacteria) in the Dongjiang River, a typical subtropical river in southeast China, and analyzed the changing patterns of biodiversity and multitrophic networks in relation to land use and water pollution. First, our data showed that the eDNA approach provided a snapshot of the multitrophic communities in the Dongjiang River, and the monitored 5833 OTUs were annotated to 55 phyla, 144 classes, 329 orders, 521 families, 945 genera and 406 species. Second, the multitrophic diversity index had similar patterns on the longitudinal scale of rivers, with significant decreases from the upstream to the downstream, while individual taxonomic groups exhibited variable spatial patterns. While there were similar spatial patterns between network metrics and diversity index, the former had stronger relationships with the spatial distance. Third, the multitrophic diversity and networks were significantly negatively correlated with land use and water pollution (e.g., CODMn), and network structures often had stronger and non-linear responses. Overall, this study highlights that eDNA biomonitoring of multitrophic communities and networks can provide deeper insights into ecosystem changes and help develop more targeted management strategies.
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Affiliation(s)
- Shan Qin
- Guangdong Provincial Key Laboratory of Water Quality Improvement and Ecological Restoration for Watersheds, School of Ecology, Environment and Resources, Guangdong University of Technology, Guangzhou, 510006, China
| | - Feilong Li
- Guangdong Provincial Key Laboratory of Water Quality Improvement and Ecological Restoration for Watersheds, School of Ecology, Environment and Resources, Guangdong University of Technology, Guangzhou, 510006, China
| | - Yanting Zou
- Guangdong Provincial Key Laboratory of Water Quality Improvement and Ecological Restoration for Watersheds, School of Ecology, Environment and Resources, Guangdong University of Technology, Guangzhou, 510006, China
| | - Jingchuan Xue
- Guangdong Provincial Key Laboratory of Water Quality Improvement and Ecological Restoration for Watersheds, School of Ecology, Environment and Resources, Guangdong University of Technology, Guangzhou, 510006, China
| | - Yuan Zhang
- Guangdong Provincial Key Laboratory of Water Quality Improvement and Ecological Restoration for Watersheds, School of Ecology, Environment and Resources, Guangdong University of Technology, Guangzhou, 510006, China.
| | - Zhifeng Yang
- Guangdong Provincial Key Laboratory of Water Quality Improvement and Ecological Restoration for Watersheds, School of Ecology, Environment and Resources, Guangdong University of Technology, Guangzhou, 510006, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China
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12
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Liang A, Ma C, Xiao J, Hao Y, Li H, Guo Y, Cao Y, Jia W, Han L, Chen G, Tan Q, White JC, Xing B. Micro/nanoscale bone char alleviates cadmium toxicity and boosts rice growth via positively altering the rhizosphere and endophytic microbial community. JOURNAL OF HAZARDOUS MATERIALS 2023; 454:131491. [PMID: 37121038 DOI: 10.1016/j.jhazmat.2023.131491] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 04/10/2023] [Accepted: 04/23/2023] [Indexed: 05/19/2023]
Abstract
This present study investigated pork bone-derived biochar as a promising amendment to reduce Cd accumulation and alleviate Cd-induced oxidative stress in rice. Micro/nanoscale bone char (MNBC) pyrolyzed at 400 °C and 600 °C was synthesized and characterized before use. The application rates for MNBCs were set at 5 and 25 g·kg-1 and the Cd exposure concentration was 15 mg·kg-1. MNBCs increased rice biomass by 15.3-26.0% as compared to the Cd-alone treatment. Both types of MNBCs decreased the bioavailable Cd content by 27.4-54.8%; additionally, the acid-soluble Cd fraction decreased by 10.0-12.3% relative to the Cd alone treatment. MNBC significantly reduced the cell wall Cd content by 50.4-80.2% relative to the Cd-alone treatment. TEM images confirm the toxicity of Cd to rice cells and that MNBCs alleviated Cd-induced damage to the chloroplast ultrastructure. Importantly, the addition of MNBCs decreased the abundance of heavy metal tolerant bacteria, Acidobacteria and Chloroflexi, by 29.6-41.1% in the rhizosphere but had less impact on the endophytic microbial community. Overall, our findings demonstrate the significant potential of MNBC as both a soil amendment for heavy metal-contaminated soil remediation and for crop nutrition in sustainable agriculture.
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Affiliation(s)
- Anqi Liang
- Key Laboratory for City Cluster Environmental Safety and Green Development of the Ministry of Education, Institute of Environmental and Ecological Engineering, Guangdong University of Technology, Guangzhou 510006, China
| | - Chuanxin Ma
- Key Laboratory for City Cluster Environmental Safety and Green Development of the Ministry of Education, Institute of Environmental and Ecological Engineering, Guangdong University of Technology, Guangzhou 510006, China; Stockbridge School of Agriculture, University of Massachusetts, Amherst, MA 01003, United States; The Connecticut Agricultural Experiment Station, New Haven, CT 06504, United States.
| | - Jiang Xiao
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang 311400, China
| | - Yi Hao
- Key Laboratory for City Cluster Environmental Safety and Green Development of the Ministry of Education, Institute of Environmental and Ecological Engineering, Guangdong University of Technology, Guangzhou 510006, China; Stockbridge School of Agriculture, University of Massachusetts, Amherst, MA 01003, United States
| | - Hao Li
- Key Laboratory for City Cluster Environmental Safety and Green Development of the Ministry of Education, Institute of Environmental and Ecological Engineering, Guangdong University of Technology, Guangzhou 510006, China
| | - Yaozu Guo
- Key Laboratory for City Cluster Environmental Safety and Green Development of the Ministry of Education, Institute of Environmental and Ecological Engineering, Guangdong University of Technology, Guangzhou 510006, China
| | - Yini Cao
- Faculty of Life Science and Technology, Central South University of Forestry and Technology, Changsha, Hunan 410004, China
| | - Weili Jia
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, School of Environment, South China Normal University, Guangzhou 510006, China
| | - Lanfang Han
- Key Laboratory for City Cluster Environmental Safety and Green Development of the Ministry of Education, Institute of Environmental and Ecological Engineering, Guangdong University of Technology, Guangzhou 510006, China
| | - Guangcai Chen
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang 311400, China
| | - Qian Tan
- Key Laboratory for City Cluster Environmental Safety and Green Development of the Ministry of Education, Institute of Environmental and Ecological Engineering, Guangdong University of Technology, Guangzhou 510006, China
| | - Jason C White
- The Connecticut Agricultural Experiment Station, New Haven, CT 06504, United States
| | - Baoshan Xing
- Stockbridge School of Agriculture, University of Massachusetts, Amherst, MA 01003, United States
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13
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Merten Cruz M, Sauvage T, Chariton A, de Freitas TRO. The challenge of implementing environmental DNA metabarcoding to detect elasmobranchs in a resource-limited marine protected area. JOURNAL OF FISH BIOLOGY 2023. [PMID: 37060349 DOI: 10.1111/jfb.15406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 04/13/2023] [Indexed: 05/06/2023]
Abstract
Elasmobranchs are threatened and eDNA metabarcoding is a powerful tool that can help efforts to better understand and conserve them. Nevertheless, the inter-calibration between optimal methodological practices and its implementation in resource-limited situations is still an issue. Based on promising results from recent studies, the authors applied a cost-effective protocol with parameters that could be easily replicated by any conservationist. Nonetheless, the results with fewer elasmobranchs detected than expected reveal that endorsed primers and sampling strategies still require further optimization, especially for applications in resource-limited conservation programmes.
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Affiliation(s)
- Marcelo Merten Cruz
- Programa de Pós-graduação em Genética e Biologia Molecular, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Thomas Sauvage
- Programa de Pós-graduação em Ecologia, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Anthony Chariton
- School of Life Sciences, Macquarie University, Sydney, Australia
| | - Thales Renato Ochotorena de Freitas
- Programa de Pós-graduação em Genética e Biologia Molecular, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
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14
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Bonin A, Guerrieri A, Ficetola GF. Optimal sequence similarity thresholds for clustering of molecular operational taxonomic units in DNA metabarcoding studies. Mol Ecol Resour 2023; 23:368-381. [PMID: 36052659 DOI: 10.1111/1755-0998.13709] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Revised: 08/08/2022] [Accepted: 08/25/2022] [Indexed: 01/04/2023]
Abstract
Clustering approaches are pivotal to handle the many sequence variants obtained in DNA metabarcoding data sets, and therefore they have become a key step of metabarcoding analysis pipelines. Clustering often relies on a sequence similarity threshold to gather sequences into molecular operational taxonomic units (MOTUs), each of which ideally represents a homogeneous taxonomic entity (e.g., a species or a genus). However, the choice of the clustering threshold is rarely justified, and its impact on MOTU over-splitting or over-merging even less tested. Here, we evaluated clustering threshold values for several metabarcoding markers under different criteria: limitation of MOTU over-merging, limitation of MOTU over-splitting, and trade-off between over-merging and over-splitting. We extracted sequences from a public database for nine markers, ranging from generalist markers targeting Bacteria or Eukaryota, to more specific markers targeting a class or a subclass (e.g., Insecta, Oligochaeta). Based on the distributions of pairwise sequence similarities within species and within genera, and on the rates of over-splitting and over-merging across different clustering thresholds, we were able to propose threshold values minimizing the risk of over-splitting, that of over-merging, or offering a trade-off between the two risks. For generalist markers, high similarity thresholds (0.96-0.99) are generally appropriate, while more specific markers require lower values (0.85-0.96). These results do not support the use of a fixed clustering threshold. Instead, we advocate careful examination of the most appropriate threshold based on the research objectives, the potential costs of over-splitting and over-merging, and the features of the studied markers.
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Affiliation(s)
- Aurélie Bonin
- Department of Environmental Science and Policy, University of Milan, Milan, Italy.,Argaly, Bâtiment Clean space, Sainte-Hélène-du-Lac, France
| | - Alessia Guerrieri
- Department of Environmental Science and Policy, University of Milan, Milan, Italy
| | - Gentile Francesco Ficetola
- Department of Environmental Science and Policy, University of Milan, Milan, Italy.,LECA, Laboratoire d'Ecologie Alpine, Univ. Grenoble Alpes, CNRS, Univ. Savoie Mont Blanc, Grenoble, France
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15
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Li F, Qin S, Wang Z, Zhang Y, Yang Z. Environmental DNA metabarcoding reveals the impact of different land use on multitrophic biodiversity in riverine systems. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 855:158958. [PMID: 36152857 DOI: 10.1016/j.scitotenv.2022.158958] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 08/25/2022] [Accepted: 09/19/2022] [Indexed: 06/16/2023]
Abstract
Human-induced changes in land use drive an alarming decline in river biodiversity and related ecosystem services worldwide. However, how different land use shapes aquatic multitrophic communities is still not well understood. Here, we used the biodiversity dataset from bacteria to fish captured by the environmental DNA (eDNA) approach in the four riverine systems with spatially different land use (i.e., Slightly disturbed group, Upstream disturbed group, Downstream disturbed group, and Strongly disturbed group) to reveal the changes in multitrophic biodiversity in relation to human land use. Firstly, our data showed that spatially different land use determined the pollutant loads of the riverine systems, most pollutants (e.g., TN and NH3-N) had significant differences among the four riverine systems. Secondly, taxonomic α diversity across multitrophic levels did not necessarily change significantly, yet the change in community structure can be considered as a more sensitive indicator to reflect different land use, because different land use shaped the unique structure of multitrophic communities, and the dissimilarity of community structure was closely associated with land use gradient (e.g., positive relationships in the Slightly disturbed group, negative relationships in the Strongly disturbed group). Thirdly, different land use induced the shifts of key taxa, resulting in the variation of community structure and the change of co-occurrence network. Overall, these findings suggest that spatially different land use plays a critical role in shaping aquatic multitrophic communities, and an in-depth understanding of the interdependences between biodiversity and land use is a critical prerequisite for formulating river management strategies.
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Affiliation(s)
- Feilong Li
- Guangdong Provincial Key Laboratory of Water Quality Improvement and Ecological Restoration for Watersheds, School of Ecology, Environment and Resources, Guangdong University of Technology, Guangzhou 510006, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Shan Qin
- Guangdong Provincial Key Laboratory of Water Quality Improvement and Ecological Restoration for Watersheds, School of Ecology, Environment and Resources, Guangdong University of Technology, Guangzhou 510006, China
| | - Zongyang Wang
- Guangdong Provincial Key Laboratory of Water Quality Improvement and Ecological Restoration for Watersheds, School of Ecology, Environment and Resources, Guangdong University of Technology, Guangzhou 510006, China
| | - Yuan Zhang
- Guangdong Provincial Key Laboratory of Water Quality Improvement and Ecological Restoration for Watersheds, School of Ecology, Environment and Resources, Guangdong University of Technology, Guangzhou 510006, China.
| | - Zhifeng Yang
- Guangdong Provincial Key Laboratory of Water Quality Improvement and Ecological Restoration for Watersheds, School of Ecology, Environment and Resources, Guangdong University of Technology, Guangzhou 510006, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
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16
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Li F, Guo F, Gao W, Cai Y, Zhang Y, Yang Z. Environmental DNA Biomonitoring Reveals the Interactive Effects of Dams and Nutrient Enrichment on Aquatic Multitrophic Communities. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:16952-16963. [PMID: 36383447 DOI: 10.1021/acs.est.2c06919] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Dam construction and nutrient enrichment are two pervasive stressors in rivers worldwide, which trigger a sharp decline in biodiversity and ecosystem services. However, the interactive effects of both stressors on multitrophic taxonomic groups remain largely unclear. Here, we used the multitrophic datasets captured by the environmental DNA (eDNA) approach to reveal the interactions between dams and nutrient enrichment on aquatic communities from the aspects of taxonomic α diversity, β diversity, and food webs. First, our data showed that dams and nutrient enrichment jointly shaped a unique spatial pattern of aquatic communities across the four river systems, and the dissimilarity of community structure significantly declined (i.e., structural homogenization) under both stressors. Second, dams and nutrients together explained 40-50% of the variations in aquatic communities, and dams had a stronger impact on fish, aquatic insects, and bacteria, yet nutrients had a stronger power to drive protozoa, fungi, and eukaryotic algae. Finally, we found that additive, synergistic, and antagonistic interactions of dams and nutrient enrichment were common and coexisted in river systems and led to significantly simplified aquatic food webs, with decreases in modularity (synergistic) and robustness (additive) and an increase in coherence (synergistic). Overall, our study highlights that eDNA-based datasets can provide multitrophic perspectives for fostering the understanding of the interactive effects of multiple stressors on rivers.
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Affiliation(s)
- Feilong Li
- Guangdong Provincial Key Laboratory of Water Quality Improvement and Ecological Restoration for Watersheds, School of Ecology, Environment and Resources, Guangdong University of Technology, Guangzhou510006, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou511458, China
| | - Fen Guo
- Guangdong Provincial Key Laboratory of Water Quality Improvement and Ecological Restoration for Watersheds, School of Ecology, Environment and Resources, Guangdong University of Technology, Guangzhou510006, China
| | - Wei Gao
- Guangdong Provincial Key Laboratory of Water Quality Improvement and Ecological Restoration for Watersheds, School of Ecology, Environment and Resources, Guangdong University of Technology, Guangzhou510006, China
| | - Yanpeng Cai
- Guangdong Provincial Key Laboratory of Water Quality Improvement and Ecological Restoration for Watersheds, School of Ecology, Environment and Resources, Guangdong University of Technology, Guangzhou510006, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou511458, China
| | - Yuan Zhang
- Guangdong Provincial Key Laboratory of Water Quality Improvement and Ecological Restoration for Watersheds, School of Ecology, Environment and Resources, Guangdong University of Technology, Guangzhou510006, China
| | - Zhifeng Yang
- Guangdong Provincial Key Laboratory of Water Quality Improvement and Ecological Restoration for Watersheds, School of Ecology, Environment and Resources, Guangdong University of Technology, Guangzhou510006, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou511458, China
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17
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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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18
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Good E, Holman LE, Pusceddu A, Russo T, Rius M, Iacono CL. Detection of community-wide impacts of bottom trawl fishing on deep-sea assemblages using environmental DNA metabarcoding. MARINE POLLUTION BULLETIN 2022; 183:114062. [PMID: 36075115 DOI: 10.1016/j.marpolbul.2022.114062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 08/15/2022] [Accepted: 08/17/2022] [Indexed: 06/15/2023]
Abstract
Although considerable research progress on the effects of anthropogenic disturbance in the deep sea has been made in recent years, our understanding of these impacts at community level remains limited. Here, we studied deep-sea assemblages of Sicily (Mediterranean Sea) subject to different intensities of benthic trawling using environmental DNA (eDNA) metabarcoding and taxonomic identification of meiofauna communities. Firstly, eDNA metabarcoding data did not detect trawling impacts using alpha diversity whereas meiofauna data detected a significant effect of trawling. Secondly, both eDNA and meiofauna data detected significantly different communities across distinct levels of trawling intensity when we examined beta diversity. Taxonomic assignment of the eDNA data revealed that Bryozoa was present only at untrawled sites, highlighting their vulnerability to trawling. Our results provide evidence for community-wide impacts of trawling, with different trawling intensities leading to distinct deep-sea communities. Finally, we highlight the need for further studies to unravel understudied deep-sea biodiversity.
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Affiliation(s)
- Edward Good
- School of Ocean and Earth Science, University of Southampton, Waterfront Campus, Southampton, United Kingdom.
| | - Luke E Holman
- School of Ocean and Earth Science, University of Southampton, Waterfront Campus, Southampton, United Kingdom; Section for Molecular Ecology and Evolution, Faculty of Health and Medical Sciences, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Antonio Pusceddu
- Department of Life and Environmental Sciences, University of Cagliari, Via T. Fiorelli, 1, 09126 Cagliari, Italy
| | - Tommaso Russo
- Laboratory of Experimental Ecology and Aquaculture, Department of Biology, University of Rome Tor Vergata, Rome 00133, Italy
| | - Marc Rius
- School of Ocean and Earth Science, University of Southampton, Waterfront Campus, Southampton, United Kingdom; Centre for Advanced Studies of Blanes - Spanish National Research Council (CEAB-CSIC), Accés a la Cala Sant Francesc 14, 17300 Blanes (Girona), Spain; Centre for Ecological Genomics and Wildlife Conservation, Department of Zoology, University of Johannesburg, South Africa
| | - Claudio Lo Iacono
- Marine Sciences Institute - Spanish National Research Council (ICM-CSIC), Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Spain
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19
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Ye M, Zhang Z, Sun M, Shi Y. Dynamics, gene transfer, and ecological function of intracellular and extracellular DNA in environmental microbiome. IMETA 2022; 1:e34. [PMID: 38868707 PMCID: PMC10989830 DOI: 10.1002/imt2.34] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 05/16/2022] [Accepted: 05/25/2022] [Indexed: 06/14/2024]
Abstract
Extracellular DNA (eDNA) and intracellular DNA (iDNA) extensively exist in both terrestrial and aquatic environment systems and have been found to play a significant role in the nutrient cycling and genetic information transmission between the environment and microorganisms. As inert DNA sequences, eDNA is able to present stability in the environment from the ribosome enzyme lysis, therein acting as the historical genetic information archive of the microbiome. As a consequence, both eDNA and iDNA can shed light on the functional gene variety and the corresponding microbial activity. In addition, eDNA is a ubiquitous composition of the cell membrane, which exerts a great impact on the resistance of outer stress from environmental pollutants, such as heavy metals, antibiotics, pesticides, and so on. This study focuses on the environmental dynamics and the ecological functions of the eDNA and iDNA from the perspectives of environmental behavior, genetic information transmission, resistance to the environmental contaminants, and so on. By reviewing the status quo and the future vista of the e/iDNAs research, this article sheds light on exploring the ecological functioning of the e/iDNAs in the environmental microbiome.
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Affiliation(s)
- Mao Ye
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil ScienceChinese Academy of SciencesNanjingChina
| | - Zhongyun Zhang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil ScienceChinese Academy of SciencesNanjingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Mingming Sun
- Soil Ecology Lab, College of Resources and Environmental SciencesNanjing Agricultural UniversityNanjingChina
| | - Yu Shi
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life SciencesHenan UniversityKaifengChina
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20
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Harbuzov Z, Farberova V, Tom M, Pallavicini A, Stanković D, Lotan T, Lubinevsky H. Amplicon sequence variant-based meiofaunal community composition revealed by DADA2 tool is compatible with species composition. Mar Genomics 2022; 65:100980. [PMID: 35963148 DOI: 10.1016/j.margen.2022.100980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Revised: 07/15/2022] [Accepted: 07/15/2022] [Indexed: 11/16/2022]
Abstract
The present study is aimed at implementing the morphological identification-free amplicon sequence variant (ASV) concept for describing meiofaunal species composition, while strongly indicating reasonable compatibility with the underlying species. A primer pair was constructed and demonstrated to PCR amplify a 470-490 bp 18S barcode from a variety of meiofaunal taxa, high throughput sequenced using the Illumina 300 × 2 bps platform. Sixteen 18S multi-species HTS assemblies were created from meiofaunal samples and merged to one assembly of ~2,150,000 reads. Five quality scores (q = 35, 30, 25, 20, 15) were implemented to filter five 18S barcode assemblies, which served as inputs for the DADA2 software, ending with five reference ASV libraries. Each of these libraries was clustered, applying 3% dissimilarity threshold, revealed an average number of 1.38 ± 0.078 ASVs / cluster. Hence, demonstrating high level of ASV uniqueness. The libraries which were based on q ≤ 25 reached a near-asymptote number of ASVs which together with the low average number of ASVs / cluster, strongly indicated fair representation of the actual number of the underlying species. Hence, the q = 25 library was selected to be used as metabarcoding reference library. It contained 461 ASVs and 342-3% clusters with average number of 1.34 ± 1.036 ASV / cluster and their BLASTN annotation elucidated a variety of expected meiofaunal taxa. The sixteen assemblies of sample-specific paired reads were mapped to this reference library and sample ASV profiles, namely the list of ASVs and their proportional copy numbers were created and clustered.
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Affiliation(s)
- Zoya Harbuzov
- National Institute of Oceanography, Department of Biology and Biotechnology, Israel Oceanographic & Limnological Research, P.O.B 9753, Haifa 3109701, Israel; Leon H. Charney School of Marine Sciences, Department of Marine Biology, University of Haifa, 199 Aba Koushy Ave., Mount Carmel, Haifa 3498838, Israel.
| | - Valeria Farberova
- National Institute of Oceanography, Department of Biology and Biotechnology, Israel Oceanographic & Limnological Research, P.O.B 9753, Haifa 3109701, Israel; Leon H. Charney School of Marine Sciences, Department of Marine Biology, University of Haifa, 199 Aba Koushy Ave., Mount Carmel, Haifa 3498838, Israel
| | - Moshe Tom
- National Institute of Oceanography, Department of Biology and Biotechnology, Israel Oceanographic & Limnological Research, P.O.B 9753, Haifa 3109701, Israel
| | - Alberto Pallavicini
- Department of Life Sciences, University of Trieste, Via Licio Giorgieri 5, 34127 Trieste, Italy
| | - David Stanković
- National institute of Biology, Department of Organisms and Ecosystems Research, Večna pot 111, 1000 Ljubljana, Slovenia
| | - Tamar Lotan
- Leon H. Charney School of Marine Sciences, Department of Marine Biology, University of Haifa, 199 Aba Koushy Ave., Mount Carmel, Haifa 3498838, Israel
| | - Hadas Lubinevsky
- National Institute of Oceanography, Department of Biology and Biotechnology, Israel Oceanographic & Limnological Research, P.O.B 9753, Haifa 3109701, Israel
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21
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A Critical Assessment of the Congruency between Environmental DNA and Palaeoecology for the Biodiversity Monitoring and Palaeoenvironmental Reconstruction. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19159445. [PMID: 35954801 PMCID: PMC9368151 DOI: 10.3390/ijerph19159445] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 07/25/2022] [Accepted: 07/27/2022] [Indexed: 02/01/2023]
Abstract
The present study suggests that standardized methodology, careful site selection, and stratigraphy are essential for investigating ancient ecosystems in order to evaluate biodiversity and DNA-based time series. Based on specific keywords, this investigation reviewed 146 publications using the SCOPUS, Web of Science (WoS), PUBMED, and Google Scholar databases. Results indicate that environmental deoxyribose nucleic acid (eDNA) can be pivotal for assessing and conserving ecosystems. Our review revealed that in the last 12 years (January 2008–July 2021), 63% of the studies based on eDNA have been reported from aquatic ecosystems, 25% from marine habitats, and 12% from terrestrial environments. Out of studies conducted in aquatic systems using the environmental DNA (eDNA) technique, 63% of the investigations have been reported from freshwater ecosystems, with an utmost focus on fish diversity (40%). Further analysis of the literature reveals that during the same period, 24% of the investigations using the environmental DNA technique were carried out on invertebrates, 8% on mammals, 7% on plants, 6% on reptiles, and 5% on birds. The results obtained clearly indicate that the environmental DNA technique has a clear-cut edge over other biodiversity monitoring methods. Furthermore, we also found that eDNA, in conjunction with different dating techniques, can provide better insight into deciphering eco-evolutionary feedback. Therefore, an attempt has been made to offer extensive information on the application of dating methods for different taxa present in diverse ecosystems. Last, we provide suggestions and elucidations on how to overcome the caveats and delineate some of the research avenues that will likely shape this field in the near future. This paper aims to identify the gaps in environmental DNA (eDNA) investigations to help researchers, ecologists, and decision-makers to develop a holistic understanding of environmental DNA (eDNA) and its utility as a palaeoenvironmental contrivance.
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22
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Sarkis CM, Hoenig BD, Seney EE, Gaspar SA, Forsman AM. Sea Snacks from DNA Tracks: Using DNA Metabarcoding to Characterize The Diet of Green Turtles (Chelonia Mydas). Integr Comp Biol 2022; 62:223-236. [PMID: 35679089 DOI: 10.1093/icb/icac080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 05/20/2022] [Accepted: 05/23/2022] [Indexed: 11/12/2022] Open
Abstract
The green turtle (Chelonia mydas) is a circumglobal species with a wide dietary breadth that varies among regions and life history stages. Comprehensive understanding of foraging ecology over space and time is critical to inform conservation and management of this species and its habitats. Here, we used DNA metabarcoding to test candidate primer sets with 39 gut content homogenates from stranded green turtles (FL, USA) to identify primer sets that maximize detection of food items and specificity of taxonomic classifications. We tested six existing universal primer sets to detect plants, animals, and eukaryotes more broadly (CO1, 18SV1-V3, 18SV4, rbcL, UPA, ITS). The CO1 and 18SV4 primer sets produced the greatest number of dietary amplicon sequence variants (ASVs) and unique taxonomic classifications, and they were the only primer sets to amplify taxa from all three kingdoms relevant to green turtle diet (Animalia, Chromista, and Plantae). Even though the majority of CO1-derived reads were of host origin (>90%), this primer set still produced the largest number of dietary ASVs classified to species among the six primer sets. However, because the CO1 primer set failed to detect both vascular plants and green algae, we do not recommend the use of this primer set on its own to characterize green turtle diet. Instead, our findings support previous research highlighting the utility of using multiple primer sets, specifically targeting CO1 and the V4 region of the 18S gene, as doing so will provide the most comprehensive understanding of green turtle diet. More generally, our results highlight the importance of primer and loci selection and the need to validate primer sets against the study system of interest. The addition of DNA metabarcoding with optimized primer sets to the sea turtle researcher's toolbox will both increase our understanding of foraging ecology and better inform science-based conservation and ecosystem management.
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Affiliation(s)
- Christine M Sarkis
- Department of Biology, University of Central Florida, Orlando, Florida, USA
| | - Brandon D Hoenig
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Erin E Seney
- Department of Biology, University of Central Florida, Orlando, Florida, USA.,Marine Turtle Research Group, Department of Biology, University of Central Florida, Orlando, Florida, USA
| | - Stephanie A Gaspar
- Department of Biology, University of Central Florida, Orlando, Florida, USA
| | - Anna M Forsman
- Department of Biology, University of Central Florida, Orlando, Florida, USA.,Genomics & Bioinformatics Cluster, University of Central Florida, Orlando, Florida, USA
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23
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Pawlowski J, Bruce K, Panksep K, Aguirre FI, Amalfitano S, Apothéloz-Perret-Gentil L, Baussant T, Bouchez A, Carugati L, Cermakova K, Cordier T, Corinaldesi C, Costa FO, Danovaro R, Dell'Anno A, Duarte S, Eisendle U, Ferrari BJD, Frontalini F, Frühe L, Haegerbaeumer A, Kisand V, Krolicka A, Lanzén A, Leese F, Lejzerowicz F, Lyautey E, Maček I, Sagova-Marečková M, Pearman JK, Pochon X, Stoeck T, Vivien R, Weigand A, Fazi S. Environmental DNA metabarcoding for benthic monitoring: A review of sediment sampling and DNA extraction methods. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 818:151783. [PMID: 34801504 DOI: 10.1016/j.scitotenv.2021.151783] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 11/06/2021] [Accepted: 11/14/2021] [Indexed: 06/13/2023]
Abstract
Environmental DNA (eDNA) metabarcoding (parallel sequencing of DNA/RNA for identification of whole communities within a targeted group) is revolutionizing the field of aquatic biomonitoring. To date, most metabarcoding studies aiming to assess the ecological status of aquatic ecosystems have focused on water eDNA and macroinvertebrate bulk samples. However, the eDNA metabarcoding has also been applied to soft sediment samples, mainly for assessing microbial or meiofaunal biota. Compared to classical methodologies based on manual sorting and morphological identification of benthic taxa, eDNA metabarcoding offers potentially important advantages for assessing the environmental quality of sediments. The methods and protocols utilized for sediment eDNA metabarcoding can vary considerably among studies, and standardization efforts are needed to improve their robustness, comparability and use within regulatory frameworks. Here, we review the available information on eDNA metabarcoding applied to sediment samples, with a focus on sampling, preservation, and DNA extraction steps. We discuss challenges specific to sediment eDNA analysis, including the variety of different sources and states of eDNA and its persistence in the sediment. This paper aims to identify good-practice strategies and facilitate method harmonization for routine use of sediment eDNA in future benthic monitoring.
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Affiliation(s)
- J Pawlowski
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland; Institute of Oceanology, Polish Academy of Sciences, 81-712 Sopot, Poland; ID-Gene Ecodiagnostics, 1202 Geneva, Switzerland
| | - K Bruce
- NatureMetrics Ltd, CABI Site, Bakeham Lane, Egham TW20 9TY, UK
| | - K Panksep
- Institute of Technology, University of Tartu, Tartu 50411, Estonia; Chair of Hydrobiology and Fishery, Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Tartu, Estonia; Chair of Aquaculture, Institute of Veterinary Medicine and Animal Sciences, Estonian University of Life Sciences, Estonia
| | - F I Aguirre
- Water Research Institute, National Research Council of Italy (IRSA-CNR), Monterotondo, Rome, Italy
| | - S Amalfitano
- Water Research Institute, National Research Council of Italy (IRSA-CNR), Monterotondo, Rome, Italy
| | - L Apothéloz-Perret-Gentil
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland; ID-Gene Ecodiagnostics, 1202 Geneva, Switzerland
| | - T Baussant
- Norwegian Research Center AS, NORCE Environment, Marine Ecology Group, Mekjarvik 12, 4070 Randaberg, Norway
| | - A Bouchez
- INRAE, CARRTEL, 74200 Thonon-les-Bains, France
| | - L Carugati
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, Ancona 60131, Italy
| | - K Cermakova
- ID-Gene Ecodiagnostics, 1202 Geneva, Switzerland
| | - T Cordier
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland; NORCE Climate, NORCE Norwegian Research Centre AS, Bjerknes Centre for Climate Research, Jahnebakken 5, 5007 Bergen, Norway
| | - C Corinaldesi
- Department of Materials, Environmental Sciences and Urban Planning, Polytechnic University of Marche, Via Brecce Bianche, Ancona 60131, Italy
| | - F O Costa
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal; Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - R Danovaro
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, Ancona 60131, Italy
| | - A Dell'Anno
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, Ancona 60131, Italy
| | - S Duarte
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal; Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - U Eisendle
- University of Salzburg, Dept. of Biosciences, 5020 Salzburg, Austria
| | - B J D Ferrari
- Swiss Centre for Applied Ecotoxicology (Ecotox Centre), EPFL ENAC IIE-GE, 1015 Lausanne, Switzerland
| | - F Frontalini
- Department of Pure and Applied Sciences, Urbino University, Urbino, Italy
| | - L Frühe
- Technische Universität Kaiserslautern, Ecology Group, D-67663 Kaiserslautern, Germany
| | - A Haegerbaeumer
- Bielefeld University, Animal Ecology, 33615 Bielefeld, Germany
| | - V Kisand
- Institute of Technology, University of Tartu, Tartu 50411, Estonia
| | - A Krolicka
- Norwegian Research Center AS, NORCE Environment, Marine Ecology Group, Mekjarvik 12, 4070 Randaberg, Norway
| | - A Lanzén
- AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), Pasaia, Gipuzkoa, Spain; IKERBASQUE, Basque Foundation for Science, Bilbao, Bizkaia, Spain
| | - F Leese
- University of Duisburg-Essen, Faculty of Biology, Aquatic Ecosystem Research, Germany
| | - F Lejzerowicz
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA
| | - E Lyautey
- Univ. Savoie Mont Blanc, INRAE, CARRTEL, 74200 Thonon-les-Bains, France
| | - I Maček
- Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000 Ljubljana, Slovenia; Faculty of Mathematics, Natural Sciences and Information Technologies (FAMNIT), University of Primorska, Glagoljaška 8, 6000 Koper, Slovenia
| | - M Sagova-Marečková
- Czech University of Life Sciences, Dept. of Microbiology, Nutrition and Dietetics, Prague, Czech Republic
| | - J K Pearman
- Coastal and Freshwater Group, Cawthron Institute, Private Bag 2, Nelson 7042, New Zealand
| | - X Pochon
- Coastal and Freshwater Group, Cawthron Institute, Private Bag 2, Nelson 7042, New Zealand; Institute of Marine Science, University of Auckland, Warkworth 0941, New Zealand
| | - T Stoeck
- Technische Universität Kaiserslautern, Ecology Group, D-67663 Kaiserslautern, Germany
| | - R Vivien
- Swiss Centre for Applied Ecotoxicology (Ecotox Centre), EPFL ENAC IIE-GE, 1015 Lausanne, Switzerland
| | - A Weigand
- National Museum of Natural History Luxembourg, 25 Rue Münster, L-2160 Luxembourg, Luxembourg
| | - S Fazi
- Water Research Institute, National Research Council of Italy (IRSA-CNR), Monterotondo, Rome, Italy.
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24
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Development of Quantitative Real-Time PCR for Detecting Environmental DNA Derived from Marine Macrophytes and Its Application to a Field Survey in Hiroshima Bay, Japan. WATER 2022. [DOI: 10.3390/w14050827] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The sequestration and storage of carbon dioxide by marine macrophytes is called blue carbon; this ecosystem function of coastal marine ecosystems constitutes an important countermeasure to global climate change. The contribution of marine macrophytes to blue carbon requires a detailed examination of the organic carbon stock released by these macrophytes. Here, we introduce a quantitative real-time polymerase chain reaction (qPCR)-based environmental DNA (eDNA) system for the species-specific detection of marine macrophytes. and report its application in a field survey in Hiroshima Bay, Japan. A method of qPCR-based quantification was developed for mangrove, seagrass, Phaeophyceae, Rhodophyta and Chlorophyta species, or species-complex, collected from the Japanese coast to investigate their dynamics after they wither and die in the marine environment. A trial of the designed qPCR system was conducted using sediment samples from Hiroshima Bay. Ulva spp. were abundant in coastal areas of the bay, yet their eDNA in the sediments was scarce. In contrast, Zostera marina and the Sargassum subgenus Bactrophycus spp. were found at various sites in the bay, and high amounts of their eDNA were detected in the sediments. These results suggest that the fate of macrophyte-derived organic carbon after death varies among species.
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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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Ritter CD, Forster D, Azevedo JAR, Antonelli A, Nilsson RH, Trujillo ME, Dunthorn M. Assessing Biotic and Abiotic Interactions of Microorganisms in Amazonia through Co-Occurrence Networks and DNA Metabarcoding. MICROBIAL ECOLOGY 2021; 82:746-760. [PMID: 33604703 PMCID: PMC8463405 DOI: 10.1007/s00248-021-01719-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 02/08/2021] [Indexed: 06/12/2023]
Abstract
Species may co-occur due to responses to similar environmental conditions, biological associations, or simply because of coincident geographical distributions. Disentangling patterns of co-occurrence and potential biotic and abiotic interactions is crucial to understand ecosystem function. Here, we used DNA metabarcoding data from litter and mineral soils collected from a longitudinal transect in Amazonia to explore patterns of co-occurrence. We compared data from different Amazonian habitat types, each with a characteristic biota and environmental conditions. These included non-flooded rainforests (terra-firme), forests seasonally flooded by fertile white waters (várzeas) or by unfertile black waters (igapós), and open areas associated with white sand soil (campinas). We ran co-occurrence network analyses based on null models and Spearman correlation for all samples and for each habitat separately. We found that one third of all operational taxonomic units (OTUs) were bacteria and two thirds were eukaryotes. The resulting networks were nevertheless mostly composed of bacteria, with fewer fungi, protists, and metazoans. Considering the functional traits of the OTUs, there is a combination of metabolism modes including respiration and fermentation for bacteria, and a high frequency of saprotrophic fungi (those that feed on dead organic matter), indicating a high turnover of organic material. The organic carbon and base saturation indices were important in the co-occurrences in Amazonian networks, whereas several other soil properties were important for the co-exclusion. Different habitats had similar network properties with some variation in terms of modularity, probably associated with flooding pulse. We show that Amazonian microorganism communities form highly interconnected co-occurrence and co-exclusion networks, which highlights the importance of complex biotic and abiotic interactions in explaining the outstanding biodiversity of the region.
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Affiliation(s)
- Camila Duarte Ritter
- Eukaryotic Microbiology, University of Duisburg-Essen, Universitätsstrasse 5 S05 R04 H83, D-45141, Essen, Germany.
| | - Dominik Forster
- Department of Ecology, University of Kaiserslautern, D-67663, Kaiserslautern, Germany
| | - Josue A R Azevedo
- Programa de Coleções Científicas Biológicas, Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Manaus, 69060-000, Brazil
- Gothenburg Global Biodiversity Centre, Box 461, SE-405 30, Göteborg, Sweden
| | - Alexandre Antonelli
- Gothenburg Global Biodiversity Centre, Box 461, SE-405 30, Göteborg, Sweden
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 463, SE-405 30, Göteborg, Sweden
- Royal Botanic Gardens, Kew, TW9 3AE, Richmond, Surrey, UK
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| | - R Henrik Nilsson
- Gothenburg Global Biodiversity Centre, Box 461, SE-405 30, Göteborg, Sweden
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 463, SE-405 30, Göteborg, Sweden
| | - Martha E Trujillo
- Departamento de Microbiología y Genética, Campus Miguel de Unamuno, 37007, Salamanca, Spain
| | - Micah Dunthorn
- Eukaryotic Microbiology, University of Duisburg-Essen, Universitätsstrasse 5 S05 R04 H83, D-45141, Essen, Germany
- Centre for Water and Environmental Research (ZWU), University of Duisburg-Essen, Essen, Germany
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27
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Hestetun JT, Lanzén A, Dahlgren TG. Grab what you can-an evaluation of spatial replication to decrease heterogeneity in sediment eDNA metabarcoding. PeerJ 2021; 9:e11619. [PMID: 34221724 PMCID: PMC8223902 DOI: 10.7717/peerj.11619] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 05/25/2021] [Indexed: 11/20/2022] Open
Abstract
Environmental DNA methods such as metabarcoding have been suggested as possible alternatives or complements to the current practice of morphology-based diversity assessment for characterizing benthic communities in marine sediment. However, the source volume used in sediment eDNA studies is several magnitudes lower than that used in morphological identification. Here, we used data from a North Sea benthic sampling station to investigate to what extent metabarcoding data is affected by sampling bias and spatial heterogeneity. Using three grab parallels, we sampled five separate sediment samples from each grab. We then made five DNA extraction replicates from each sediment sample. Each extract was amplified targeting both the 18S SSU rRNA V1–V2 region for total eukaryotic composition, and the cytochrome c oxidase subunit I (COI) gene for metazoans only. In both datasets, extract replicates from the same sediment sample were significantly more similar than different samples from the same grab. Further, samples from different grabs were less similar than those from the same grab for 18S. Interestingly, this was not true for COI metabarcoding, where the differences within the same grab were similar to the differences between grabs. We also investigated how much of the total identified richness could be covered by extract replicates, individual sediment samples and all sediment samples from a single grab, as well as the variability of Shannon diversity and, for COI, macrofaunal biotic indices indicating environmental status. These results were largely consistent with the beta diversity findings, and show that total eukaryotic diversity can be well represented using 18S metabarcoding with a manageable number of biological replicates. Based on these results, we strongly recommend the combination of different parts of the surface of single grabs for eDNA extraction as well as several grab replicates, or alternatively box cores or similar. This will dilute the effects of dominating species and increase the coverage of alpha diversity. COI-based metabarcoding consistency was found to be lower compared to 18S, but COI macrofauna-based indices were more consistent than direct COI alpha diversity measures.
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Affiliation(s)
| | - Anders Lanzén
- Marine Ecosystems Functioning, AZTI, Pasaia, Basque Country, Spain.,IKERBASQUE, Basque Foundation of Science, Bilbao, Basque Country, Spain
| | - Thomas G Dahlgren
- NORCE Environment, Bergen, Vestland, Norway.,Department of Marine Sciences, University of Gothenburg, Gothenburg, Sweden
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28
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Lake Sedimentary DNA Research on Past Terrestrial and Aquatic Biodiversity: Overview and Recommendations. QUATERNARY 2021. [DOI: 10.3390/quat4010006] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The use of lake sedimentary DNA to track the long-term changes in both terrestrial and aquatic biota is a rapidly advancing field in paleoecological research. Although largely applied nowadays, knowledge gaps remain in this field and there is therefore still research to be conducted to ensure the reliability of the sedimentary DNA signal. Building on the most recent literature and seven original case studies, we synthesize the state-of-the-art analytical procedures for effective sampling, extraction, amplification, quantification and/or generation of DNA inventories from sedimentary ancient DNA (sedaDNA) via high-throughput sequencing technologies. We provide recommendations based on current knowledge and best practises.
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29
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Francioli D, Lentendu G, Lewin S, Kolb S. DNA Metabarcoding for the Characterization of Terrestrial Microbiota-Pitfalls and Solutions. Microorganisms 2021; 9:361. [PMID: 33673098 PMCID: PMC7918050 DOI: 10.3390/microorganisms9020361] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 02/04/2021] [Accepted: 02/09/2021] [Indexed: 02/06/2023] Open
Abstract
Soil-borne microbes are major ecological players in terrestrial environments since they cycle organic matter, channel nutrients across trophic levels and influence plant growth and health. Therefore, the identification, taxonomic characterization and determination of the ecological role of members of soil microbial communities have become major topics of interest. The development and continuous improvement of high-throughput sequencing platforms have further stimulated the study of complex microbiota in soils and plants. The most frequently used approach to study microbiota composition, diversity and dynamics is polymerase chain reaction (PCR), amplifying specific taxonomically informative gene markers with the subsequent sequencing of the amplicons. This methodological approach is called DNA metabarcoding. Over the last decade, DNA metabarcoding has rapidly emerged as a powerful and cost-effective method for the description of microbiota in environmental samples. However, this approach involves several processing steps, each of which might introduce significant biases that can considerably compromise the reliability of the metabarcoding output. The aim of this review is to provide state-of-the-art background knowledge needed to make appropriate decisions at each step of a DNA metabarcoding workflow, highlighting crucial steps that, if considered, ensures an accurate and standardized characterization of microbiota in environmental studies.
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Affiliation(s)
- Davide Francioli
- Microbial Biogeochemistry, Research Area Landscape Functioning, Leibniz Centre for Agricultural Landscape Research (ZALF), Eberswalder Str. 84, 15374 Müncheberg, Germany; (S.L.); (S.K.)
| | - Guillaume Lentendu
- Laboratory of Soil Biodiversity, University of Neuchâtel, Rue Emile-Argand 11, 2000 Neuchâtel, Switzerland;
| | - Simon Lewin
- Microbial Biogeochemistry, Research Area Landscape Functioning, Leibniz Centre for Agricultural Landscape Research (ZALF), Eberswalder Str. 84, 15374 Müncheberg, Germany; (S.L.); (S.K.)
| | - Steffen Kolb
- Microbial Biogeochemistry, Research Area Landscape Functioning, Leibniz Centre for Agricultural Landscape Research (ZALF), Eberswalder Str. 84, 15374 Müncheberg, Germany; (S.L.); (S.K.)
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30
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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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31
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Laroche O, Kersten O, Smith CR, Goetze E. Environmental DNA surveys detect distinct metazoan communities across abyssal plains and seamounts in the western Clarion Clipperton Zone. Mol Ecol 2020; 29:4588-4604. [PMID: 32452072 PMCID: PMC7754508 DOI: 10.1111/mec.15484] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 05/08/2020] [Accepted: 05/18/2020] [Indexed: 01/13/2023]
Abstract
The deep seafloor serves as a reservoir of biodiversity in the global ocean, with >80% of invertebrates at abyssal depths still undescribed. These diverse and remote deep-sea communities are critically under-sampled and increasingly threatened by anthropogenic impacts, including future polymetallic nodule mining. Using a multigene environmental DNA (eDNA) metabarcoding approach, we characterized metazoan communities sampled from sediments, polymetallic nodules and seawater in the western Clarion Clipperton Zone (CCZ) to test the hypotheses that deep seamounts (a) are species richness hotspots in the abyss, (b) have structurally distinct communities in comparison to other deep-sea habitats, and (c) that seafloor particulate organic carbon (POC) flux and polymetallic nodule density are positively correlated with metazoan diversity. eDNA metabarcoding was effective at characterizing distinct biotas known to occur in association with different abyssal substrate types (e.g., nodule- and sediment-specific fauna), with distinct community composition and few taxa shared across substrates. Seamount faunas had higher overall taxonomic richness, and different community composition and biogeography than adjacent abyssal plains, with seamount communities displaying less connectivity between regions than comparable assemblages on the abyssal plains. Across an estimated gradient of low to moderate POC flux, we find lowest taxon richness at the lowest POC flux, as well as an effect of nodule size on community composition. Our results suggest that while abyssal seamounts are important reservoirs of metazoan diversity in the CCZ, given limited taxonomic overlap between seamount and plains fauna, conservation of seamount assemblages will be insufficient to protect biodiversity and ecosystem function in regions targeted for mining.
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Affiliation(s)
- Olivier Laroche
- Department of OceanographySchool of Ocean and Earth Science and TechnologyUniversity of Hawaii at MānoaHonoluluHIUSA
| | - Oliver Kersten
- Centre for Ecological and Evolutionary SynthesisUniversity of OsloOsloNorway
| | - Craig R. Smith
- Department of OceanographySchool of Ocean and Earth Science and TechnologyUniversity of Hawaii at MānoaHonoluluHIUSA
| | - Erica Goetze
- Department of OceanographySchool of Ocean and Earth Science and TechnologyUniversity of Hawaii at MānoaHonoluluHIUSA
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32
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Meyer A, Boyer F, Valentini A, Bonin A, Ficetola GF, Beisel JN, Bouquerel J, Wagner P, Gaboriaud C, Leese F, Dejean T, Taberlet P, Usseglio-Polatera P. Morphological vs. DNA metabarcoding approaches for the evaluation of stream ecological status with benthic invertebrates: Testing different combinations of markers and strategies of data filtering. Mol Ecol 2020; 30:3203-3220. [PMID: 33150613 DOI: 10.1111/mec.15723] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 09/15/2020] [Accepted: 10/09/2020] [Indexed: 12/16/2022]
Abstract
Macroinvertebrate assemblages are the most common bioindicators used for stream biomonitoring, yet the standard approach exhibits several time-consuming steps, including the sorting and identification of organisms based on morphological criteria. In this study, we examined if DNA metabarcoding could be used as an efficient molecular-based alternative to the morphology-based monitoring of streams using macroinvertebrates. We compared results achieved with the standard morphological identification of organisms sampled in 18 sites located on 15 French wadeable streams to results obtained with the DNA metabarcoding identification of sorted bulk material of the same macroinvertebrate samples, using read numbers (expressed as relative frequencies) as a proxy for abundances. In particular, we evaluated how combining and filtering metabarcoding data obtained from three different markers (COI: BF1-BR2, 18S: Euka02 and 16S: Inse01) could improve the efficiency of bioassessment. In total, 140 taxa were identified based on morphological criteria, and 127 were identified based on DNA metabarcoding using the three markers, with an overlap of 99 taxa. The threshold values used for sequence filtering based on the "best identity" criterion and the number of reads had an effect on the assessment efficiency of data obtained with each marker. Compared to single marker results, combining data from different markers allowed us to improve the match between biotic index values obtained with the bulk DNA versus morphology-based approaches. Both approaches assigned the same ecological quality class to a majority (86%) of the site sampling events, highlighting both the efficiency of metabarcoding as a biomonitoring tool but also the need for further research to improve this efficiency.
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Affiliation(s)
- Albin Meyer
- Université de Lorraine, CNRS, LIEC, Metz, France
| | - Frédéric Boyer
- Université Grenoble Alpes, CNRS, LECA, Laboratoire d'Ecologie Alpine, Grenoble, France
| | | | - Aurélie Bonin
- Université Grenoble Alpes, CNRS, LECA, Laboratoire d'Ecologie Alpine, Grenoble, France.,SPYGEN, Le Bourget du Lac, France.,Department of Environmental Science and Policy, Università degli Studi di Milano, Milano, Italy
| | - Gentile Francesco Ficetola
- Université Grenoble Alpes, CNRS, LECA, Laboratoire d'Ecologie Alpine, Grenoble, France.,Department of Environmental Science and Policy, Università degli Studi di Milano, Milano, Italy
| | | | | | | | | | - Florian Leese
- University of Duisburg-Essen, Aquatic Ecosystem Research, Essen, Germany
| | | | - Pierre Taberlet
- Université Grenoble Alpes, CNRS, LECA, Laboratoire d'Ecologie Alpine, Grenoble, France.,UiT - The Arctic University of Norway, Tromsø Museum, Tromsø, Norway
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33
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Harnessing the power of eDNA metabarcoding for the detection of deep-sea fishes. PLoS One 2020; 15:e0236540. [PMID: 33147221 PMCID: PMC7641347 DOI: 10.1371/journal.pone.0236540] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 09/25/2020] [Indexed: 01/04/2023] Open
Abstract
The deep ocean is the largest biome on Earth and faces increasing anthropogenic pressures from climate change and commercial fisheries. Our ability to sustainably manage this expansive habitat is impeded by our poor understanding of its inhabitants and by the difficulties in surveying and monitoring these areas. Environmental DNA (eDNA) metabarcoding has great potential to improve our understanding of this region and to facilitate monitoring across a broad range of taxa. Here, we evaluate two eDNA sampling protocols and seven primer sets for elucidating fish diversity from deep sea water samples. We found that deep sea water samples (> 1400 m depth) had significantly lower DNA concentrations than surface or mid-depth samples necessitating a refined protocol with a larger sampling volume. We recovered significantly more DNA in large volume water samples (1.5 L) filtered at sea compared to small volume samples (250 mL) held for lab filtration. Furthermore, the number of unique sequences (exact sequence variants; ESVs) recovered per sample was higher in large volume samples. Since the number of ESVs recovered from large volume samples was less variable and consistently high, we recommend the larger volumes when sampling water from the deep ocean. We also identified three primer sets which detected the most fish taxa but recommend using multiple markers due the variability in detection probabilities and taxonomic resolution among fishes for each primer set. Overall, fish diversity results obtained from metabarcoding were comparable to conventional survey methods. While eDNA sampling and processing need be optimized for this unique environment, the results of this study demonstrate that eDNA metabarcoding can facilitate biodiversity surveys in the deep ocean, require less dedicated survey effort per unit identification, and are capable of simultaneously providing valuable information on other taxonomic groups.
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34
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Guerrieri A, Bonin A, Münkemüller T, Gielly L, Thuiller W, Francesco Ficetola G. Effects of soil preservation for biodiversity monitoring using environmental DNA. Mol Ecol 2020; 30:3313-3325. [PMID: 33034070 DOI: 10.1111/mec.15674] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 09/10/2020] [Accepted: 09/23/2020] [Indexed: 12/13/2022]
Abstract
Environmental DNA (eDNA) metabarcoding is becoming a key tool for biodiversity monitoring over large geographical or taxonomic scales and for elusive taxa such as soil organisms. Increasing sample sizes and interest in remote or extreme areas often require the preservation of soil samples and thus deviations from optimal standardized protocols. However, we still ignore the impact of different methods of soil sample preservation on the results of metabarcoding studies and there is no guideline for best practices so far. Here, we assessed the impact of four methods of soil sample preservation that can be conveniently used also in metabarcoding studies targeting remote or difficult to access areas. Tested methods include: preservation at room temperature for 6 hr, preservation at 4°C for 3 days, desiccation immediately after sampling and preservation for 21 days, and desiccation after 6 hr at room temperature and preservation for 21 days. For each preservation method, we benchmarked resulting estimates of taxon diversity and community composition of three different taxonomic groups (bacteria, fungi and eukaryotes) in three different habitats (forest, river bank and grassland) against results obtained under ideal conditions (i.e., extraction of eDNA immediately after sampling). Overall, the different preservation methods only marginally impaired results and only under certain conditions. When rare taxa were considered, we detected small but significant changes in molecular operational taxonomic units (MOTU) richness of bacteria, fungi and eukaryotes across treatments, but MOTU richness was similar across preservation methods if rare taxa were not considered. All the approaches were able to identify differences in community structure among habitats, and the communities retrieved using the different preservation conditions were extremely similar. We propose guidelines on the selection of the optimal soil sample preservation conditions for metabarcoding studies, depending on the practical constraints, costs and ultimate research goals.
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Affiliation(s)
- Alessia Guerrieri
- Department of Environmental Science and Policy, Università degli Studi di Milano, Milano, Italy
| | - Aurélie Bonin
- Department of Environmental Science and Policy, Università degli Studi di Milano, Milano, Italy
| | - Tamara Münkemüller
- Laboratoire d'Ecologie Alpine, Univ. Grenoble Alpes, CNRS, Univ. Savoie Mont Blanc, LECA, Grenoble, France
| | - Ludovic Gielly
- Laboratoire d'Ecologie Alpine, Univ. Grenoble Alpes, CNRS, Univ. Savoie Mont Blanc, LECA, Grenoble, France
| | - Wilfried Thuiller
- Laboratoire d'Ecologie Alpine, Univ. Grenoble Alpes, CNRS, Univ. Savoie Mont Blanc, LECA, Grenoble, France
| | - Gentile Francesco Ficetola
- Department of Environmental Science and Policy, Università degli Studi di Milano, Milano, Italy.,Laboratoire d'Ecologie Alpine, Univ. Grenoble Alpes, CNRS, Univ. Savoie Mont Blanc, LECA, Grenoble, France
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35
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Pawlowski J, Apothéloz‐Perret‐Gentil L, Altermatt F. Environmental DNA: What's behind the term? Clarifying the terminology and recommendations for its future use in biomonitoring. Mol Ecol 2020; 29:4258-4264. [DOI: 10.1111/mec.15643] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 08/20/2020] [Accepted: 09/07/2020] [Indexed: 02/06/2023]
Affiliation(s)
- Jan Pawlowski
- Department of Genetics and Evolution University of Geneva Geneva Switzerland
- ID‐Gene ecodiagnostics, Campus Biotech Innovation Park Geneva Switzerland
- Institute of Oceanology Polish Academy of Sciences Sopot Poland
| | - Laure Apothéloz‐Perret‐Gentil
- Department of Genetics and Evolution University of Geneva Geneva Switzerland
- ID‐Gene ecodiagnostics, Campus Biotech Innovation Park Geneva Switzerland
| | - Florian Altermatt
- 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 Zürich Switzerland
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36
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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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37
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Ficetola GF, Boyer F, Valentini A, Bonin A, Meyer A, Dejean T, Gaboriaud C, Usseglio-Polatera P, Taberlet P. Comparison of markers for the monitoring of freshwater benthic biodiversity through DNA metabarcoding. Mol Ecol 2020; 30:3189-3202. [PMID: 32920861 DOI: 10.1111/mec.15632] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 08/16/2020] [Accepted: 08/27/2020] [Indexed: 12/22/2022]
Abstract
Metabarcoding of bulk or environmental DNA has great potential for biomonitoring of freshwater environments. However, successful application of metabarcoding to biodiversity monitoring requires universal primers with high taxonomic coverage that amplify highly variable, short metabarcodes with high taxonomic resolution. Moreover, reliable and extensive reference databases are essential to match the outcome of metabarcoding analyses with available taxonomy and biomonitoring indices. Benthic invertebrates, particularly insects, are key taxa for freshwater bioassessment. Nevertheless, few studies have so far assessed markers for metabarcoding of freshwater macrobenthos. Here we combined in silico and laboratory analyses to test the performance of different markers amplifying regions in the 18S rDNA (Euka02), 16S rDNA (Inse01) and COI (BF1_BR2-COI) genes, and developed an extensive database of benthic macroinvertebrates of France and Europe, with a particular focus on key insect orders (Ephemeroptera, Plecoptera and Trichoptera). Analyses on 1,514 individuals representing different taxa of benthic macroinvertebrates showed very different amplification success across primer combinations. The Euka02 marker showed the highest universality, while the Inse01 marker showed excellent performance for the amplification of insects. BF1_BR2-COI showed the highest resolution, while the resolution of Euka02 was often limited. By combining our data with GenBank information, we developed a curated database including sequences representing 822 genera. The heterogeneous performance of the different primers highlights the complexity in identifying the best markers, and advocates for the integration of multiple metabarcodes for a more comprehensive and accurate understanding of ecological impacts on freshwater biodiversity.
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Affiliation(s)
- Gentile Francesco Ficetola
- LECA, Laboratoire d'Ecologie Alpine, Univ. Grenoble Alpes, CNRS, Univ. Savoie Mont Blanc, Grenoble, France.,Department of Environmental Sciences and Policy, University of Milano, Milano, Italy
| | - Frédéric Boyer
- LECA, Laboratoire d'Ecologie Alpine, Univ. Grenoble Alpes, CNRS, Univ. Savoie Mont Blanc, Grenoble, France
| | | | - Aurélie Bonin
- LECA, Laboratoire d'Ecologie Alpine, Univ. Grenoble Alpes, CNRS, Univ. Savoie Mont Blanc, Grenoble, France.,Department of Environmental Sciences and Policy, University of Milano, Milano, Italy
| | - Albin Meyer
- Université de Lorraine, CNRS, LIEC, Metz, France
| | | | | | | | - Pierre Taberlet
- LECA, Laboratoire d'Ecologie Alpine, Univ. Grenoble Alpes, CNRS, Univ. Savoie Mont Blanc, Grenoble, France.,UiT - The Arctic University of Norway, Tromsø Museum, Tromsø, Norway
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38
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Zawierucha K, Porazinska DL, Ficetola GF, Ambrosini R, Baccolo G, Buda J, Ceballos JL, Devetter M, Dial R, Franzetti A, Fuglewicz U, Gielly L, Łokas E, Janko K, Novotna Jaromerska T, Kościński A, Kozłowska A, Ono M, Parnikoza I, Pittino F, Poniecka E, Sommers P, Schmidt SK, Shain D, Sikorska S, Uetake J, Takeuchi N. A hole in the nematosphere: tardigrades and rotifers dominate the cryoconite hole environment, whereas nematodes are missing. J Zool (1987) 2020. [DOI: 10.1111/jzo.12832] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- K. Zawierucha
- Department of Animal Taxonomy and Ecology Adam Mickiewicz University Poznań Poland
| | - D. L. Porazinska
- Department of Entomology and Nematology University of Florida Gainesville FL USA
| | - G. F. Ficetola
- Department of Environmental Science and Policy University of Milan Milan Italy
- Laboratoire d'Ecologie Alpine University Grenoble Alpes Univ. Savoie Mont Blanc CNRS LECA Grenoble France
| | - R. Ambrosini
- Department of Environmental Science and Policy University of Milan Milan Italy
| | - G. Baccolo
- Earth and Environmental Sciences Department University of Milano‐Bicocca Milan Italy
| | - J. Buda
- Department of Animal Taxonomy and Ecology Adam Mickiewicz University Poznań Poland
| | - J. L. Ceballos
- Institute of Hydrology, Meteorology and Environmental Studies IDEAM Bogota' Colombia
| | - M. Devetter
- Institute of soil Biology Biology Centre CAS České Budějovice Czech Republic
- Centre for Polar Ecology Faculty of Science University of South Bohemia České Budějovice Czech Republic
| | - R. Dial
- Institute of Culture and the Environment Alaska Pacific University Anchorage AK USA
| | - A. Franzetti
- Earth and Environmental Sciences Department University of Milano‐Bicocca Milan Italy
| | | | - L. Gielly
- Laboratoire d'Ecologie Alpine University Grenoble Alpes Univ. Savoie Mont Blanc CNRS LECA Grenoble France
| | - E. Łokas
- Department of Mass Spectroscopy Institute of Nuclear Physics Polish Academy of Sciences Kraków Poland
| | - K. Janko
- Laboratory of Fish Genetics Institute of Animal Physiology and Genetics Academy of Sciences of the Czech Republic Libechov Czech Republic
- Department of Biology and Ecology Faculty of Science University of Ostrava Ostrava Czech Republic
| | | | | | - A. Kozłowska
- Department of Animal Taxonomy and Ecology Adam Mickiewicz University Poznań Poland
| | - M. Ono
- Graduate School of Science and Engineering Chiba University Chiba Japan
| | - I. Parnikoza
- State Institution National Antarctic Center of Ministry of Education and Science of Ukraine Kyiv Ukraine
- Institute of Molecular Biology and Genetics National Academy of Sciences of Ukraine Kyiv Ukraine
| | - F. Pittino
- Earth and Environmental Sciences Department University of Milano‐Bicocca Milan Italy
| | - E. Poniecka
- School of Earth and Ocean Sciences Cardiff University Cardiff UK
| | - P. Sommers
- Ecology and Evolutionary Biology Department University of Colorado Boulder CO USA
| | - S. K. Schmidt
- Ecology and Evolutionary Biology Department University of Colorado Boulder CO USA
| | - D. Shain
- Biology Department Rutgers, The State University of New Jersey Camden NJ USA
| | - S. Sikorska
- Department of Animal Taxonomy and Ecology Adam Mickiewicz University Poznań Poland
| | - J. Uetake
- The Arctic Environment Research Center National Institute of Polar Research Tachikawa Japan
| | - N. Takeuchi
- Department of Earth Sciences Graduate School of Science Chiba University Chiba Japan
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39
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Roy L, Taudière A, Papaïx J, Blatrix R, Chiron G, Zriki G, Bonato O, Barnagaud JY. Evaluating the link between predation and pest control services in the mite world. Ecol Evol 2020; 10:9968-9980. [PMID: 33005357 PMCID: PMC7520221 DOI: 10.1002/ece3.6655] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Accepted: 07/20/2020] [Indexed: 01/21/2023] Open
Abstract
Pest regulation by natural enemies has a strong potential to reduce the use of synthetic pesticides in agroecosystems. However, the effective role of predation as an ecosystem service remains largely speculative, especially with minute organisms such as mites.Predatory mites are natural enemies for ectoparasites in livestock farms. We tested for an ecosystem level control of the poultry pest Dermanyssus gallinae by other mites naturally present in manure in poultry farms and investigated differences among farming practices (conventional, free-range, and organic).We used a multiscale approach involving (a) in vitro behavioral predation experiments, (b) arthropod inventories in henhouses with airborne DNA, and (c) a statistical model of covariations in mite abundances comparing farming practices.Behavioral experiments revealed that three mites are prone to feed on D. gallinae. Accordingly, we observed covariations between the pest and these three taxa only, in airborne DNA at the henhouse level, and in mites sampled from manure. In most situations, covariations in abundances were high in magnitude and their sign was positive.Predation on a pest happens naturally in livestock farms due to predatory mites. However, the complex dynamics of mite trophic network prevents the emergence of a consistent assemblage-level signal of predation. Based on these results, we suggest perspectives for mite-based pest control and warn against any possible disruption of ignored services through the application of veterinary drugs or pesticides.
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Affiliation(s)
- Lise Roy
- CEFE University of Montpellier CNRS EPHE, IRD Université Paul-Valéry Montpellier 3 Montpellier France
| | - Adrien Taudière
- CEFE University of Montpellier CNRS EPHE, IRD Université Paul-Valéry Montpellier 3 Montpellier France
| | | | - Rumsais Blatrix
- CEFE University of Montpellier CNRS EPHE, IRD Université Paul-Valéry Montpellier 3 Montpellier France
| | - Geoffrey Chiron
- Institut Technique de l'AVIculture (ITAVI) Lyon Lyon Cedex 07 France
| | - Ghais Zriki
- CEFE University of Montpellier CNRS EPHE, IRD Université Paul-Valéry Montpellier 3 Montpellier France
| | - Olivier Bonato
- Interactions Plantes Microorganismes Environnement (IPME) IRD Cirad, UM Montpellier France
| | - Jean-Yves Barnagaud
- CEFE University of Montpellier CNRS EPHE-PSL University IRD Université Paul-Valéry Montpellier 3 Montpellier France
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40
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McElroy ME, Dressler TL, Titcomb GC, Wilson EA, Deiner K, Dudley TL, Eliason EJ, Evans NT, Gaines SD, Lafferty KD, Lamberti GA, Li Y, Lodge DM, Love MS, Mahon AR, Pfrender ME, Renshaw MA, Selkoe KA, Jerde CL. Calibrating Environmental DNA Metabarcoding to Conventional Surveys for Measuring Fish Species Richness. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.00276] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
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41
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Ortega A, Geraldi NR, Díaz-Rúa R, Ørberg SB, Wesselmann M, Krause-Jensen D, Duarte CM. A DNA mini-barcode for marine macrophytes. Mol Ecol Resour 2020; 20:920-935. [PMID: 32279439 DOI: 10.1111/1755-0998.13164] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 03/13/2020] [Accepted: 03/27/2020] [Indexed: 11/26/2022]
Abstract
Studies focusing on marine macrophyte metabarcoding from environmental samples are scarce, due to the lack of a universal barcode for these taxa, and to their poor representation in DNA databases. Here, we searched for a short barcode able to identify marine macrophytes from tissue samples; then, we created a DNA reference library which was used to identify macrophytes in eDNA from coastal sediments. Barcoding of seagrasses, mangroves and marine macroalgae (Chlorophyta, Rhodophyta and Phaeophyceae) was tested using 18 primer pairs from six barcoding genes: the plant barcodes rbcL, matK and trnL, plus the genes ITS2, COI and 18S. The 18S gene showed the highest universality among marine macrophytes, amplifying 95%-100% of samples; amplification performance of the other barcodes was limited. Taxonomy was assigned using a phylogeny-based approach to create an 18S DNA reference library. Macrophyte tissue sequences were accurately identified within their phyla (88%), order (76%), genus (71%) and species (23%). Nevertheless, out of 86 macrophytes tested, only 48% and 15% had a reference sequence at genus and at species level, respectively. Identification at these levels can be improved by more inclusive reference libraries. Using the 18S mini-barcode and the reference library, we recovered eDNA from 21 marine macrophytes in sediments, demonstrating the barcode's ability to trace primary producers that contribute to blue carbon. We expect this barcode to also be useful for other ecological questions, such as tracing macro primary producers in marine food webs.
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Affiliation(s)
- Alejandra Ortega
- Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Nathan R Geraldi
- Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Rubén Díaz-Rúa
- Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Sarah B Ørberg
- Department of Bioscience, and Arctic Research Centre, Aarhus University, Aarhus, Denmark
| | - Marlene Wesselmann
- Global Change Research Group, Institut Mediterrani d'Estudis Avançats IMEDEA (CSIC-UIB), Esporles, Spain
| | - Dorte Krause-Jensen
- Department of Bioscience, and Arctic Research Centre, Aarhus University, Aarhus, Denmark
| | - Carlos M Duarte
- Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
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42
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Laroche O, Kersten O, Smith CR, Goetze E. Environmental DNA surveys detect distinct metazoan communities across abyssal plains and seamounts in the western Clarion Clipperton Zone. Mol Ecol 2020. [PMID: 32452072 DOI: 10.1111/mec.15484[epub] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The deep seafloor serves as a reservoir of biodiversity in the global ocean, with >80% of invertebrates at abyssal depths still undescribed. These diverse and remote deep-sea communities are critically under-sampled and increasingly threatened by anthropogenic impacts, including future polymetallic nodule mining. Using a multigene environmental DNA (eDNA) metabarcoding approach, we characterized metazoan communities sampled from sediments, polymetallic nodules and seawater in the western Clarion Clipperton Zone (CCZ) to test the hypotheses that deep seamounts (a) are species richness hotspots in the abyss, (b) have structurally distinct communities in comparison to other deep-sea habitats, and (c) that seafloor particulate organic carbon (POC) flux and polymetallic nodule density are positively correlated with metazoan diversity. eDNA metabarcoding was effective at characterizing distinct biotas known to occur in association with different abyssal substrate types (e.g., nodule- and sediment-specific fauna), with distinct community composition and few taxa shared across substrates. Seamount faunas had higher overall taxonomic richness, and different community composition and biogeography than adjacent abyssal plains, with seamount communities displaying less connectivity between regions than comparable assemblages on the abyssal plains. Across an estimated gradient of low to moderate POC flux, we find lowest taxon richness at the lowest POC flux, as well as an effect of nodule size on community composition. Our results suggest that while abyssal seamounts are important reservoirs of metazoan diversity in the CCZ, given limited taxonomic overlap between seamount and plains fauna, conservation of seamount assemblages will be insufficient to protect biodiversity and ecosystem function in regions targeted for mining.
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Affiliation(s)
- Olivier Laroche
- Department of Oceanography, School of Ocean and Earth Science and Technology, University of Hawaii at Mānoa, Honolulu, HI, USA
| | - Oliver Kersten
- Centre for Ecological and Evolutionary Synthesis, University of Oslo, Oslo, Norway
| | - Craig R Smith
- Department of Oceanography, School of Ocean and Earth Science and Technology, University of Hawaii at Mānoa, Honolulu, HI, USA
| | - Erica Goetze
- Department of Oceanography, School of Ocean and Earth Science and Technology, University of Hawaii at Mānoa, Honolulu, HI, USA
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43
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DNA Metabarcoding of Deep-Sea Sediment Communities Using COI: Community Assessment, Spatio-Temporal Patterns and Comparison with 18S rDNA. DIVERSITY-BASEL 2020. [DOI: 10.3390/d12040123] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Among the complex ecosystems and habitats that form the deep sea, submarine canyons and open slope systems are regarded as potential hotspots of biodiversity. We assessed the spatial and temporal patterns of biodiversity in sediment communities of a NW Mediterranean Canyon and its adjacent open slope (Blanes Canyon) with DNA metabarcoding. We sampled three layers of sediment and four different depths (900–1750 m) at two seasons, and used a fragment of the mitochondrial gene cytochrome c oxidase subunit I (COI) as a metabarcoding marker. The final dataset contained a total of 15,318 molecular operational taxonomic units (MOTUs). Metazoa, Stramenopiles and Archaeplastida were the dominant taxa and, within metazoans, Arthropoda, Nematoda and Cnidaria were the most diverse. There was a trend towards decreasing MOTU richness and diversity in the first few cm (1 to 5) of the sediment, with only 26.3% of the MOTUs shared across sediment layers. Our results show the presence of heterogeneous communities in the studied area, which was significantly different between zones, depths and seasons. We compared our results with the ones presented in a previous study, obtained using the v7 region of the 18S rRNA gene in the same samples. There were remarkable differences in the total number of MOTUs and in the most diverse taxa. COI recovered a higher number of MOTUs, but more remained unassigned taxonomically. However, the broad spatio-temporal patterns elucidated from both datasets coincided, with both markers retrieving the same ecological information. Our results showed that COI can be used to accurately characterize the studied communities and constitute a high-resolution method to detect ecological shifts. We also highlight that COI reference databases for deep-sea organisms have important gaps, and their completeness is essential in order to successfully apply metabarcoding techniques.
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44
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Ritter CD, Faurby S, Bennett DJ, Naka LN, Ter Steege H, Zizka A, Haenel Q, Nilsson RH, Antonelli A. The pitfalls of biodiversity proxies: Differences in richness patterns of birds, trees and understudied diversity across Amazonia. Sci Rep 2019; 9:19205. [PMID: 31844092 PMCID: PMC6915760 DOI: 10.1038/s41598-019-55490-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 11/25/2019] [Indexed: 01/09/2023] Open
Abstract
Most knowledge on biodiversity derives from the study of charismatic macro-organisms, such as birds and trees. However, the diversity of micro-organisms constitutes the majority of all life forms on Earth. Here, we ask if the patterns of richness inferred for macro-organisms are similar for micro-organisms. For this, we barcoded samples of soil, litter and insects from four localities on a west-to-east transect across Amazonia. We quantified richness as Operational Taxonomic Units (OTUs) in those samples using three molecular markers. We then compared OTU richness with species richness of two relatively well-studied organism groups in Amazonia: trees and birds. We find that OTU richness shows a declining west-to-east diversity gradient that is in agreement with the species richness patterns documented here and previously for birds and trees. These results suggest that most taxonomic groups respond to the same overall diversity gradients at large spatial scales. However, our results show a different pattern of richness in relation to habitat types, suggesting that the idiosyncrasies of each taxonomic group and peculiarities of the local environment frequently override large-scale diversity gradients. Our findings caution against using the diversity distribution of one taxonomic group as an indication of patterns of richness across all groups.
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Affiliation(s)
- Camila D Ritter
- Department of Eukaryotic Microbiology, University of Duisburg-Essen, Universitätsstrasse 5 S05 R04 H83, D-45141, Essen, Germany. .,Gothenburg Global Biodiversity Centre, Box 461, SE-405 30, Göteborg, Sweden. .,Department of Biological and Environmental Sciences, University of Gothenburg, Box 463, SE-405 30, Göteborg, Sweden.
| | - Søren Faurby
- Gothenburg Global Biodiversity Centre, Box 461, SE-405 30, Göteborg, Sweden.,Department of Biological and Environmental Sciences, University of Gothenburg, Box 463, SE-405 30, Göteborg, Sweden
| | - Dominic J Bennett
- Gothenburg Global Biodiversity Centre, Box 461, SE-405 30, Göteborg, Sweden.,Department of Biological and Environmental Sciences, University of Gothenburg, Box 463, SE-405 30, Göteborg, Sweden
| | - Luciano N Naka
- Laboratório de Ornitologia, Departamento de Zoologia, Universidade Federal de Pernambuco, Recife, PE, Brazil
| | - Hans Ter Steege
- Naturalis Biodiversity Center, Leiden, Netherlands.,Systems Ecology, Free University, Amsterdam, Netherlands
| | - Alexander Zizka
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103, Leipzig, Germany
| | - Quiterie Haenel
- Zoological Institute, University of Basel, Vesalgasse 1, CH-4051, Basel, Switzerland
| | - R Henrik Nilsson
- Gothenburg Global Biodiversity Centre, Box 461, SE-405 30, Göteborg, Sweden.,Department of Biological and Environmental Sciences, University of Gothenburg, Box 463, SE-405 30, Göteborg, Sweden
| | - Alexandre Antonelli
- Gothenburg Global Biodiversity Centre, Box 461, SE-405 30, Göteborg, Sweden.,Department of Biological and Environmental Sciences, University of Gothenburg, Box 463, SE-405 30, Göteborg, Sweden.,Royal Botanic Gardens, Kew, TW9 3AE, Richmond, Surrey, UK
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45
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Bakker J, Wangensteen OS, Baillie C, Buddo D, Chapman DD, Gallagher AJ, Guttridge TL, Hertler H, Mariani S. Biodiversity assessment of tropical shelf eukaryotic communities via pelagic eDNA metabarcoding. Ecol Evol 2019; 9:14341-14355. [PMID: 31938523 PMCID: PMC6953649 DOI: 10.1002/ece3.5871] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 10/31/2019] [Accepted: 11/03/2019] [Indexed: 01/12/2023] Open
Abstract
Our understanding of marine communities and their functions in an ecosystem relies on the ability to detect and monitor species distributions and abundances. Currently, the use of environmental DNA (eDNA) metabarcoding is increasingly being applied for the rapid assessment and monitoring of aquatic species. Most eDNA metabarcoding studies have either focussed on the simultaneous identification of a few specific taxa/groups or have been limited in geographical scope. Here, we employed eDNA metabarcoding to compare beta diversity patterns of complex pelagic marine communities in tropical coastal shelf habitats spanning the whole Caribbean Sea. We screened 68 water samples using a universal eukaryotic COI barcode region and detected highly diverse communities, which varied significantly among locations, and proved good descriptors of habitat type and environmental conditions. Less than 15% of eukaryotic taxa were assigned to metazoans, most DNA sequences belonged to a variety of planktonic "protists," with over 50% of taxa unassigned at the phylum level, suggesting that the sampled communities host an astonishing amount of micro-eukaryotic diversity yet undescribed or absent from COI reference databases. Although such a predominance of micro-eukaryotes severely reduces the efficiency of universal COI markers to investigate vertebrate and other metazoans from aqueous eDNA, the study contributes to the advancement of rapid biomonitoring methods and brings us closer to a full inventory of extant marine biodiversity.
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Affiliation(s)
- Judith Bakker
- Department of Biological Sciences Florida International University Miami FL USA
- School of Engineering & Environment University of Salford Salford UK
| | - Owen S Wangensteen
- Norwegian College of Fishery Science UiT The Arctic University of Norway Tromsø Norway
| | - Charles Baillie
- School of Engineering & Environment University of Salford Salford UK
| | - Dayne Buddo
- Discovery Bay Marine Laboratory and Field Station University of the West Indies St. Ann Jamaica
| | - Demian D Chapman
- Department of Biological Sciences Florida International University Miami FL USA
| | | | | | - Heidi Hertler
- The School for Field Studies Centre for Marine Resource Studies South Caicos Turks and Caicos Islands
| | - Stefano Mariani
- School of Engineering & Environment University of Salford Salford UK
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46
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Mitsi K, Arroyo AS, Ruiz-Trillo I. A global metabarcoding analysis expands molecular diversity of Platyhelminthes and reveals novel early-branching clades. Biol Lett 2019; 15:20190182. [PMID: 31506037 PMCID: PMC6769146 DOI: 10.1098/rsbl.2019.0182] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 08/14/2019] [Indexed: 01/29/2023] Open
Abstract
Understanding biological diversity is crucial for ecological and evolutionary studies. Even though a great part of animal diversity has already been documented, both morphological surveys and metabarcoding analyses have previously shown that some animal groups, such as Platyhelminthes, may harbour hidden diversity. To better understand the molecular diversity of Platyhelminthes, one of the most diverse and biomedically important animal phyla, we here combined data from six marine and two freshwater metabarcoding expeditions that cover a broad variety of aquatic habitats and analysed the data by phylogenetic placement. Our results show that a great part of the hidden diversity is located in early-branching clades such as Catenulida and Macrostomorpha, as well as in late-diverging clades such as Proseriata and Rhabdocoela. We also report the first freshwater record of Gnosonesimida, a group previously thought to be exclusively marine. Finally, we identified two putative novel freshwater Platyhelminthes clades that branch between well-defined orders of the phylum. Thus, our analyses of several environmental datasets confirm that a large part of the diversity of Platyhelminthes remains undiscovered, point to groups with more potential novel species and identify freshwater environments as potential reservoirs for novel species of flatworms.
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Affiliation(s)
- Konstantina Mitsi
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta 37-49, Barcelona 08003, Catalonia, Spain
| | - Alicia S. Arroyo
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta 37-49, Barcelona 08003, Catalonia, Spain
| | - Iñaki Ruiz-Trillo
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta 37-49, Barcelona 08003, Catalonia, Spain
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona (UB), Barcelona 08028, Catalonia, Spain
- ICREA, Pg. Lluís Companys 23, Barcelona 08010, Catalonia, Spain
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47
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Collins RA, Bakker J, Wangensteen OS, Soto AZ, Corrigan L, Sims DW, Genner MJ, Mariani S. Non‐specific amplification compromises environmental DNA metabarcoding with COI. Methods Ecol Evol 2019. [DOI: 10.1111/2041-210x.13276] [Citation(s) in RCA: 132] [Impact Index Per Article: 26.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
| | - Judith Bakker
- Department of Biological Sciences Florida International University Miami FL USA
- Ecosystems & Environment Research Centre, School of Environment & Life Sciences University of Salford Salford UK
| | - Owen S. Wangensteen
- Ecosystems & Environment Research Centre, School of Environment & Life Sciences University of Salford Salford UK
- Norwegian College of Fishery Science, UiT The Arctic University of Norway Tromsø Norway
| | - Ana Z. Soto
- Ecosystems & Environment Research Centre, School of Environment & Life Sciences University of Salford Salford UK
| | - Laura Corrigan
- Environment Agency Tyneside House Newcastle upon Tyne UK
| | - David W. Sims
- The Laboratory Marine Biological Association of the United Kingdom Plymouth UK
- Ocean and Earth Science, National Oceanography Centre Southampton University of Southampton Southampton UK
| | | | - Stefano Mariani
- Ecosystems & Environment Research Centre, School of Environment & Life Sciences University of Salford Salford UK
- School of Natural Sciences & Psychology Liverpool John Moores University Liverpool UK
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48
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Sow A, Brévault T, Benoit L, Chapuis MP, Galan M, Coeur d'acier A, Delvare G, Sembène M, Haran J. Deciphering host-parasitoid interactions and parasitism rates of crop pests using DNA metabarcoding. Sci Rep 2019; 9:3646. [PMID: 30842584 PMCID: PMC6403368 DOI: 10.1038/s41598-019-40243-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 02/12/2019] [Indexed: 12/26/2022] Open
Abstract
An accurate estimation of parasitism rates and diversity of parasitoids of crop insect pests is a prerequisite for exploring processes leading to efficient natural biocontrol. Traditional methods such as rearing have been often limited by taxonomic identification, insect mortality and intensive work, but the advent of high-throughput sequencing (HTS) techniques, such as DNA metabarcoding, is increasingly seen as a reliable and powerful alternative approach. Little has been done to explore the benefits of such an approach for estimating parasitism rates and parasitoid diversity in an agricultural context. In this study, we compared the composition of parasitoid species and parasitism rates between rearing and DNA metabarcoding of host eggs and larvae of the millet head miner, Heliocheilus albipunctella De Joannis (Lepidoptera, Noctuidae), collected from millet fields in Senegal. We first assessed the detection threshold for the main ten endoparasitoids, by sequencing PCR products obtained from artificial dilution gradients of the parasitoid DNAs in the host moth. We then assessed the potential of DNA metabarcoding for diagnosing parasitism rates in samples collected from the field. Under controlled conditions, our results showed that relatively small quantities of parasitoid DNA (0.07 ng) were successfully detected within an eight-fold larger quantity of host DNA. Parasitoid diversity and parasitism rate estimates were always higher for DNA metabarcoding than for host rearing. Furthermore, metabarcoding detected multi-parasitism, cryptic parasitoid species and differences in parasitism rates between two different sampling sites. Metabarcoding shows promise for gaining a clearer understanding of the importance and complexity of host-parasitoid interactions in agro-ecosystems, with a view to improving pest biocontrol strategies.
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Affiliation(s)
- Ahmadou Sow
- Département de Biologie Animale, FST-UCAD, Dakar, Senegal. .,BIOPASS, CIRAD-IRD-ISRA-UCAD, Dakar, Senegal.
| | - Thierry Brévault
- BIOPASS, CIRAD-IRD-ISRA-UCAD, Dakar, Senegal.,CIRAD, UPR AIDA, F-34398, Montpellier, France.,AIDA, University Montpellier, CIRAD, Montpellier, France
| | - Laure Benoit
- CIRAD, CBGP, Montpellier, France.,CBGP, CIRAD, INRA, IRD, Montpellier SupAgro, University Montpellier, Montpellier, France
| | - Marie-Pierre Chapuis
- CIRAD, CBGP, Montpellier, France.,CBGP, CIRAD, INRA, IRD, Montpellier SupAgro, University Montpellier, Montpellier, France
| | - Maxime Galan
- CBGP, INRA, CIRAD, IRD, Montpellier SupAgro, University Montpellier, Montpellier, France
| | - Armelle Coeur d'acier
- CBGP, INRA, CIRAD, IRD, Montpellier SupAgro, University Montpellier, Montpellier, France
| | - Gérard Delvare
- CIRAD, CBGP, Montpellier, France.,CBGP, CIRAD, INRA, IRD, Montpellier SupAgro, University Montpellier, Montpellier, France
| | - Mbacké Sembène
- Département de Biologie Animale, FST-UCAD, Dakar, Senegal.,BIOPASS, CIRAD-IRD-ISRA-UCAD, Dakar, Senegal
| | - Julien Haran
- CIRAD, CBGP, Montpellier, France.,CBGP, CIRAD, INRA, IRD, Montpellier SupAgro, University Montpellier, Montpellier, France
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49
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Ritter CD, Häggqvist S, Karlsson D, Sääksjärvi IE, Muasya AM, Nilsson RH, Antonelli A. Biodiversity assessments in the 21st century: the potential of insect traps to complement environmental samples for estimating eukaryotic and prokaryotic diversity using high-throughput DNA metabarcoding. Genome 2019; 62:147-159. [DOI: 10.1139/gen-2018-0096] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The rapid loss of biodiversity, coupled with difficulties in species identification, call for innovative approaches to assess biodiversity. Insects make up a substantial proportion of extant diversity and play fundamental roles in any given ecosystem. To complement morphological species identification, new techniques such as metabarcoding make it possible to quantify insect diversity and insect–ecosystem interactions through DNA sequencing. Here we examine the potential of bulk insect samples (i.e., containing many non-sorted specimens) to assess prokaryote and eukaryote biodiversity and to complement the taxonomic coverage of soil samples. We sampled 25 sites on three continents and in various ecosystems, collecting insects with SLAM traps (Brazil) and Malaise traps (South Africa and Sweden). We then compared our diversity estimates with the results obtained with biodiversity data from soil samples from the same localities. We found a largely different taxonomic composition between the soil and insect samples, testifying to the potential of bulk insect samples to complement soil samples. Finally, we found that non-destructive DNA extraction protocols, which preserve insect specimens for morphological studies, constitute a promising choice for cost-effective biodiversity assessments. We propose that the sampling and sequencing of insect samples should become a standard complement for biodiversity studies based on environmental DNA.
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Affiliation(s)
- Camila D. Ritter
- Department of Eukaryotic Microbiology, University of Duisburg-Essen, Universitätsstrasse 5 S05 R04 H83 D-45141 Essen, Germany
| | - Sibylle Häggqvist
- Swedish Museum of Natural History, Department of Zoology, Box 50007, 104 05 Stockholm, Sweden
| | - Dave Karlsson
- Station Linné, Skogsby 161, 386 94 Färjestaden, Sweden
| | | | - A. Muthama Muasya
- Department of Biological Sciences, University of Cape Town, Rondebosch 7701, RSA
| | - R. Henrik Nilsson
- Gothenburg Global Biodiversity Centre, Box 461, SE-405 30 Göteborg, Sweden
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 463, 405 30 Göteborg, Sweden
| | - Alexandre Antonelli
- Gothenburg Global Biodiversity Centre, Box 461, SE-405 30 Göteborg, Sweden
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 463, 405 30 Göteborg, Sweden
- Gothenburg Botanical Garden, Carl Skottsbergs gata 22A, SE-41319 Göteborg, Sweden
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50
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DiBattista JD, Reimer JD, Stat M, Masucci GD, Biondi P, De Brauwer M, Bunce M. Digging for DNA at depth: rapid universal metabarcoding surveys (RUMS) as a tool to detect coral reef biodiversity across a depth gradient. PeerJ 2019; 7:e6379. [PMID: 30755831 PMCID: PMC6368839 DOI: 10.7717/peerj.6379] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 12/24/2018] [Indexed: 11/20/2022] Open
Abstract
Background Effective biodiversity monitoring is fundamental in tracking changes in ecosystems as it relates to commercial, recreational, and conservation interests. Current approaches to survey coral reef ecosystems center on the use of indicator species and repeat surveying at specific sites. However, such approaches are often limited by the narrow snapshot of total marine biodiversity that they describe and are thus hindered in their ability to contribute to holistic ecosystem-based monitoring. In tandem, environmental DNA (eDNA) and next-generation sequencing metabarcoding methods provide a new opportunity to rapidly assess the presence of a broad spectrum of eukaryotic organisms within our oceans, ranging from microbes to macrofauna. Methods We here investigate the potential for rapid universal metabarcoding surveys (RUMS) of eDNA in sediment samples to provide snapshots of eukaryotic subtropical biodiversity along a depth gradient at two coral reefs in Okinawa, Japan based on 18S rRNA. Results Using 18S rRNA metabarcoding, we found that there were significant separations in eukaryotic community assemblages (at the family level) detected in sediments when compared across different depths ranging from 10 to 40 m (p = 0.001). Significant depth zonation was observed across operational taxonomic units assigned to the class Demospongiae (sponges), the most diverse class (contributing 81% of species) within the phylum Porifera; the oldest metazoan phylum on the planet. However, zonation was not observed across the class Anthozoa (i.e., anemones, stony corals, soft corals, and octocorals), suggesting that the former may serve as a better source of indicator species based on sampling over fine spatial scales and using this universal assay. Furthermore, despite their abundance on the examined coral reefs, we did not detect any octocoral DNA, which may be due to low cellular shedding rates, assay sensitivities, or primer biases. Discussion Overall, our pilot study demonstrates the importance of exploring depth effects in eDNA and suggest that RUMS may be applied to provide a baseline of information on eukaryotic marine taxa at coastal sites of economic and conservation importance.
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Affiliation(s)
- Joseph D DiBattista
- Trace and Environmental DNA (TrEnD) laboratory, School of Molecular and Life Sciences, Curtin University of Technology, Perth, WA, Australia.,Australian Museum Research Institute, Australian Museum, Sydney, NSW, Australia
| | - James D Reimer
- Graduate School of Engineering and Science, University of the Ryukyus, Okinawa, Japan.,Tropical Biosphere Research Center, University of the Ryukyus, Okinawa, Japan
| | - Michael Stat
- Trace and Environmental DNA (TrEnD) laboratory, School of Molecular and Life Sciences, Curtin University of Technology, Perth, WA, Australia.,Department of Biological Sciences, Macquarie University, North Ryde, NSW, Australia
| | - Giovanni D Masucci
- Graduate School of Engineering and Science, University of the Ryukyus, Okinawa, Japan
| | - Piera Biondi
- Graduate School of Engineering and Science, University of the Ryukyus, Okinawa, Japan
| | - Maarten De Brauwer
- Trace and Environmental DNA (TrEnD) laboratory, School of Molecular and Life Sciences, Curtin University of Technology, Perth, WA, Australia
| | - Michael Bunce
- Trace and Environmental DNA (TrEnD) laboratory, School of Molecular and Life Sciences, Curtin University of Technology, Perth, WA, Australia
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