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Mazurkiewicz M, Pawłowska J, Barrenechea Angeles I, Grzelak K, Deja K, Zaborska A, Pawłowski J, Włodarska-Kowalczuk M. Sediment DNA metabarcoding and morphology provide complementary insight into macrofauna and meiobenthos response to environmental gradients in an Arctic glacial fjord. MARINE ENVIRONMENTAL RESEARCH 2024; 198:106552. [PMID: 38788477 DOI: 10.1016/j.marenvres.2024.106552] [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: 01/29/2024] [Revised: 05/09/2024] [Accepted: 05/10/2024] [Indexed: 05/26/2024]
Abstract
Arctic fjords ecosystems are highly dynamic, with organisms exposed to various natural stressors along with productivity clines driven by advection of water masses from shelves. The benthic response to these environmental clines has been extensively studied using traditional, morphology-based approaches mostly focusing on macroinvertebrates. In this study we analyse the effects of glacially mediated disturbance on the biodiversity of benthic macrofauna and meiobenthos (meiofauna and Foraminifera) in a Svalbard fjord by comparing morphology and eDNA metabarcoding. Three genetic markers targeting metazoans (COI), meiofauna (18S V1V2) and Foraminifera (18S 37f) were analyzed. Univariate measures of alpha diversity and multivariate compositional dissimilarities were calculated and tested for similarities in response to environmental gradients using correlation analysis. Our study showed different taxonomic composition of morphological and molecular datasets for both macrofauna and meiobenthos. Some taxonomic groups while abundant in metabarcoding data were almost absent in morphology-based inventory and vice versa. In general, species richness and diversity measures in macrofauna morphological data were higher than in metabarcoding, and similar for the meiofauna. Both methodological approaches showed different patterns of response to the glacially mediated disturbance for the macrofauna and the meiobenthos. Macrofauna showed an evident distinction in taxonomic composition and a dramatic cline in alpha diversity indices between the outer and inner parts of fjord, while the meiobenthos showed a gradual change and more subtle responses to environmental changes along the fjord axis. The two methods can be seen as complementing rather than replacing each other. Morphological approach provides more accurate inventory of larger size species and more reliable quantitative data, while metabarcoding allows identification of inconspicuous taxa that are overlooked in morphology-based studies. As different taxa may show different sensitivities to environmental changes, both methods shall be used to monitor marine biodiversity in Arctic ecosystems and its response to dramatically changing environmental conditions.
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Affiliation(s)
- Mikołaj Mazurkiewicz
- Institute of Oceanology Polish Academy of Sciences, Powstańców Warszawy 55, 81-712, Sopot, Poland.
| | - Joanna Pawłowska
- Institute of Oceanology Polish Academy of Sciences, Powstańców Warszawy 55, 81-712, Sopot, Poland
| | - Inés Barrenechea Angeles
- Department of Geosciences, The Arctic University of Norway, Dramsvegen 201, 9010, Tromsø, Norway
| | - Katarzyna Grzelak
- Institute of Oceanology Polish Academy of Sciences, Powstańców Warszawy 55, 81-712, Sopot, Poland
| | - Kajetan Deja
- Institute of Oceanology Polish Academy of Sciences, Powstańców Warszawy 55, 81-712, Sopot, Poland
| | - Agata Zaborska
- Institute of Oceanology Polish Academy of Sciences, Powstańców Warszawy 55, 81-712, Sopot, Poland
| | - Jan Pawłowski
- Institute of Oceanology Polish Academy of Sciences, Powstańców Warszawy 55, 81-712, Sopot, Poland; ID-Gene Ecodiagnostics, Chemin du Pont-du-Centenaire 109, 1228, Plan-les-Ouates, Switzerland
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Qiao L, Chen Y, Ren C, Li T, Zhao A, Fan S, Bao J. Benthic foraminiferal community structure and its response to environmental factors revealed using high-throughput sequencing in the Zhoushan Fishing Ground, East China Sea. MARINE POLLUTION BULLETIN 2024; 202:116385. [PMID: 38669854 DOI: 10.1016/j.marpolbul.2024.116385] [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: 09/11/2023] [Revised: 01/31/2024] [Accepted: 04/14/2024] [Indexed: 04/28/2024]
Abstract
Benthic foraminifera are excellent tools for monitoring marine environments and reconstructing paleoenvironments. This study investigated the structure and diversity of benthic foraminiferal communities in 20 superficial sediment samples obtained from the Zhoushan Fishing Ground (ZFG) using high-throughput sequencing based on small subunit ribosomal DNA and RNA amplification. The results revealed Rotaliida as the most dominant group, with spatial heterogeneity in foraminiferal distribution. Total benthic foraminiferal communities exhibited higher species richness and diversity compared to active communities. While heavy metal pollution in the ZFG was moderate, areas with elevated concentrations of heavy metals exhibited low diversity and richness in foraminiferal communities. Total foraminiferal community structure was primarily influenced by factors such as water depth and Hg, Pb, Cd, and Zn levels. Notably, Hg levels emerged as a critical factor impacting the structure and diversity of the active foraminiferal community. The dominant species, Operculina, exhibited tolerance toward heavy metal pollution.
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Affiliation(s)
- Ling Qiao
- Key Laboratory of Sustainable Utilization of Technology Research for Fishery Resource of Zhejiang Province, Zhejiang Marine Fisheries Research Institute, Zhoushan 316021, China
| | - Ye Chen
- Key Laboratory of Sustainable Utilization of Technology Research for Fishery Resource of Zhejiang Province, Zhejiang Marine Fisheries Research Institute, Zhoushan 316021, China
| | - Chengzhe Ren
- College of Marine Science & Technology, Zhejiang Ocean University, Zhoushan 316004, China.
| | - Tiejun Li
- Key Laboratory of Sustainable Utilization of Technology Research for Fishery Resource of Zhejiang Province, Zhejiang Marine Fisheries Research Institute, Zhoushan 316021, China
| | - Anran Zhao
- School of Fishery, Zhejiang Ocean University, Zhoushan 316004, China
| | - Songyao Fan
- College of Marine Science & Technology, Zhejiang Ocean University, Zhoushan 316004, China
| | - Jingjiao Bao
- Key Laboratory of Sustainable Utilization of Technology Research for Fishery Resource of Zhejiang Province, Zhejiang Marine Fisheries Research Institute, Zhoushan 316021, China
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Useros F, García-Cunchillos I, Henry N, Berney C, Lara E. How good are global DNA-based environmental surveys for detecting all protist diversity? Arcellinida as an example of biased representation. Environ Microbiol 2024; 26:e16606. [PMID: 38509748 DOI: 10.1111/1462-2920.16606] [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: 10/19/2023] [Accepted: 02/28/2024] [Indexed: 03/22/2024]
Abstract
Metabarcoding approaches targeting microeukaryotes have deeply changed our vision of protist environmental diversity. The public repository EukBank consists of 18S v4 metabarcodes from 12,672 samples worldwide. To estimate how far this database provides a reasonable overview of all eukaryotic diversity, we used Arcellinida (lobose testate amoebae) as a case study. We hypothesised that (1) this approach would allow the discovery of unexpected diversity, but also that (2) some groups would be underrepresented because of primer/sequencing biases. Most of the Arcellinida sequences appeared in freshwater and soil, but their abundance and diversity appeared underrepresented. Moreover, 84% of ASVs belonged to the suborder Phryganellina, a supposedly species-poor clade, whereas the best-documented suborder (Glutinoconcha, 600 described species) was only marginally represented. We explored some possible causes of these biases. Mismatches in the primer-binding site seem to play a minor role. Excessive length of the target region could explain some of these biases, but not all. There must be some other unknown factors involved. Altogether, while metabarcoding based on ribosomal genes remains a good first approach to document microbial eukaryotic clades, alternative approaches based on other genes or sequencing techniques must be considered for an unbiased picture of the diversity of some groups.
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Affiliation(s)
| | - Iván García-Cunchillos
- Institute of Evolutionary Biology, Biological and Chemical Research Centre, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Nicolas Henry
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, Paris, France
- CNRS, FR2424, ABiMS, Station Biologique de Roscoff, Sorbonne Université, Roscoff, France
| | - Cédric Berney
- CNRS, FR2424, ABiMS, Station Biologique de Roscoff, Sorbonne Université, Roscoff, France
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Barrenechea Angeles I, Nguyen NL, Greco M, Tan KS, Pawlowski J. Assigning the unassigned: A signature-based classification of rDNA metabarcodes reveals new deep-sea diversity. PLoS One 2024; 19:e0298440. [PMID: 38422100 PMCID: PMC10903905 DOI: 10.1371/journal.pone.0298440] [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: 08/02/2023] [Accepted: 01/23/2024] [Indexed: 03/02/2024] Open
Abstract
Environmental DNA metabarcoding reveals a vast genetic diversity of marine eukaryotes. Yet, most of the metabarcoding data remain unassigned due to the paucity of reference databases. This is particularly true for the deep-sea meiofauna and eukaryotic microbiota, whose hidden diversity is largely unexplored. Here, we tackle this issue by using unique DNA signatures to classify unknown metabarcodes assigned to deep-sea foraminifera. We analyzed metabarcoding data obtained from 311 deep-sea sediment samples collected in the Clarion-Clipperton Fracture Zone, an area of potential polymetallic nodule exploitation in the Eastern Pacific Ocean. Using the signatures designed in the 37F hypervariable region of the 18S rRNA gene, we were able to classify 802 unassigned metabarcodes into 61 novel lineages, which have been placed in 27 phylogenetic clades. The comparison of new lineages with other foraminiferal datasets shows that most novel lineages are widely distributed in the deep sea. Five lineages are also present in the shallow-water datasets; however, phylogenetic analysis of these lineages separates deep-sea and shallow-water metabarcodes except in one case. While the signature-based classification does not solve the problem of gaps in reference databases, this taxonomy-free approach provides insight into the distribution and ecology of deep-sea species represented by unassigned metabarcodes, which could be useful in future applications of metabarcoding for environmental monitoring.
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Affiliation(s)
- Inès Barrenechea Angeles
- Department of Earth Sciences, University of Geneva, Geneva, Switzerland
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
- Department of Geosciences, UiT-The Arctic University of Norway, Tromsø, Norway
| | - Ngoc-Loi Nguyen
- Institute of Oceanology, Polish Academy of Sciences, Sopot, Poland
| | - Mattia Greco
- Institute of Oceanology, Polish Academy of Sciences, Sopot, Poland
- Institute of Marine Sciences, Spanish National Research Council, Barcelona, Spain
| | - Koh Siang Tan
- Tropical Marine Science Institute, National University of Singapore, Singapore, Singapore
| | - Jan Pawlowski
- Institute of Oceanology, Polish Academy of Sciences, Sopot, Poland
- ID-Gene Ecodiagnostics Ltd., Plan-les-Ouates, Switzerland
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5
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Abraham JS, Somasundaram S, Maurya S, Sood U, Lal R, Toteja R, Makhija S. Insights into freshwater ciliate diversity through high throughput DNA metabarcoding. FEMS MICROBES 2024; 5:xtae003. [PMID: 38450097 PMCID: PMC10917447 DOI: 10.1093/femsmc/xtae003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 01/03/2024] [Accepted: 02/21/2024] [Indexed: 03/08/2024] Open
Abstract
The freshwater bodies of India are highly biodiverse but still understudied, especially concerning ciliates. Ciliates constitute a significant portion of eukaryotic diversity and play crucial roles in microbial loops, nutrient recycling, and ecosystem maintenance. The present study aimed to elucidate ciliate diversity in three freshwater sites in the Delhi region of India: Okhla Bird Sanctuary (OBS), Sanjay Lake (SL), and Raj Ghat pond (RJ). This study represents the first investigation into the taxonomic diversity and richness of freshwater ciliates in India using a high-throughput DNA metabarcoding approach. For the analysis, total environmental DNA was extracted from the three freshwater samples, followed by sequencing of the 18S V4 barcode region and subsequent phylogenetic analyses. Operational taxonomic units (OTU) analyses revealed maximum species diversity in OBS (106), followed by SL (104) and RJ (99) sites. Ciliates from the classes Oligohymenophorea, Prostomatea, and Spirotrichea were dominant in the three sites. The study discusses the ability of the metabarcoding approach to uncover unknown and rare species. The study highlights the need for refined reference databases and cautious interpretation of the high-throughput sequencing-generated data while emphasizing the complementary nature of molecular and morphological approaches in studying ciliate diversity.
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Affiliation(s)
- Jeeva Susan Abraham
- Ciliate Biology Laboratory, Department of Zoology, Acharya Narendra Dev College, University of Delhi, Govindpuri, Kalkaji, New Delhi 110019, India
| | - Sripoorna Somasundaram
- Ciliate Biology Laboratory, Department of Zoology, Acharya Narendra Dev College, University of Delhi, Govindpuri, Kalkaji, New Delhi 110019, India
| | - Swati Maurya
- Ciliate Biology Laboratory, Department of Zoology, Acharya Narendra Dev College, University of Delhi, Govindpuri, Kalkaji, New Delhi 110019, India
| | - Utkarsh Sood
- Department of Zoology, Kirori Mal College, University of Delhi, Delhi 110007, India
| | - Rup Lal
- Ciliate Biology Laboratory, Department of Zoology, Acharya Narendra Dev College, University of Delhi, Govindpuri, Kalkaji, New Delhi 110019, India
| | - Ravi Toteja
- Ciliate Biology Laboratory, Department of Zoology, Acharya Narendra Dev College, University of Delhi, Govindpuri, Kalkaji, New Delhi 110019, India
| | - Seema Makhija
- Ciliate Biology Laboratory, Department of Zoology, Acharya Narendra Dev College, University of Delhi, Govindpuri, Kalkaji, New Delhi 110019, India
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6
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Abd Malek MN, Frontalini F. Benthic foraminifera as bioindicators of marine pollution: A bibliometric approach to unravel trends, patterns and perspectives. MARINE POLLUTION BULLETIN 2024; 199:115941. [PMID: 38134870 DOI: 10.1016/j.marpolbul.2023.115941] [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: 11/04/2023] [Revised: 12/12/2023] [Accepted: 12/13/2023] [Indexed: 12/24/2023]
Abstract
Benthic foraminifera, single-celled marine organisms, are known for their wide distribution, high abundance and species diversity, test (i.e., shell) preservation in the sedimentary (e.g., historical) record, and sensitivity to environmental changes. Because of these characteristics, they have been widely used as bioindicators in environmental monitoring and, more recently, as Biological Quality Elements (BQEs) in the Ecological Quality Status (EcoQS) evaluation. The global scientific literature on benthic foraminifera as bioindicators was gathered from the Scopus database (overall 966 papers from 1973 to 2022) and explored with scientometric software. The outcomes highlight that the investigation of benthic foraminiferal response to pollutants started over 50 years ago. Indeed, not only the number of published documents has recently peaked (i.e., 2021 and 2022) but there has been also a growth in the percentages of papers falling within the Decision Sciences category that deals with the application of foraminiferal indices for the EcoQS assessment.
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Affiliation(s)
| | - Fabrizio Frontalini
- Department of Pure and Applied Science, Urbino University, 61029 Urbino, Italy
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Fan S, Yan Z, Qiao L, Gui F, Li T, Yang Q, Zhang X, Ren C. Biological effects on the migration and transformation of microplastics in the marine environment. MARINE ENVIRONMENTAL RESEARCH 2023; 185:105875. [PMID: 36652887 DOI: 10.1016/j.marenvres.2023.105875] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 12/28/2022] [Accepted: 01/06/2023] [Indexed: 06/17/2023]
Abstract
Microplastics(MPs) are ubiquitous, difficult to degrade, and potentially threatening to organisms in marine environment, so it is important to clarify the factors that affect their biogeochemical processes. The impact of biological activities on the MPs in marine environment is ubiquitous and complex, and there is currently a lack of systematic summaries. This paper reviews the effects of biological actions on the migration, distribution and degradation of MPs in marine environment from four aspects: biological ingestion and digestion, biological movement, biological colonization and biological adhesion. MPs in seawater and sediments can be closely combined with organisms through three pathways: biological ingestion, biofilm formation or adhesion to organisms, and are passed between species at different trophic levels through the food chain. The generation and degradation of faecal pellets and biofilms can alter the density of "environmental MPs", thereby affecting their vertical migration and deposition in water bodies. The movement of swimming organisms and the disturbance by benthic organisms can promote the migration of MPs in water and vertical migration and resuspension in sediments, thereby changing the distribution of MPs in local sea areas. The grinding effect of the digestive tract and the secretion of chemicals from the biofilm (such as enzymes and acids) can reduce the particle size and increase surface roughness of MPs, or even degrade them completely. Besides, biological adhesion may be an important mechanism affecting the distribution, migration and preservation of MPs. There may be complex interactions and linkages among marine dynamical processes, photochemical degradation and biological processes that collectively affect the biogeochemical processes of MPs, but their relative contributions remain to be more studied.
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Affiliation(s)
- Songyao Fan
- College of Marine Science & Technology, Zhejiang Ocean University, Zhoushan, 316004, China
| | - Zezheng Yan
- College of Marine Science & Technology, Zhejiang Ocean University, Zhoushan, 316004, China
| | - Ling Qiao
- Key Laboratory of Sustainable Utilization of Technology Research for Fishery Resource of Zhejiang Province, Zhejiang Marine Fisheries Research Institute, Zhoushan, 316012, China
| | - Feng Gui
- College of Marine Science & Technology, Zhejiang Ocean University, Zhoushan, 316004, China
| | - Tiejun Li
- Key Laboratory of Sustainable Utilization of Technology Research for Fishery Resource of Zhejiang Province, Zhejiang Marine Fisheries Research Institute, Zhoushan, 316012, China
| | - Qiao Yang
- ABI Group, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Xiaoling Zhang
- College of Marine Science & Technology, Zhejiang Ocean University, Zhoushan, 316004, China
| | - Chengzhe Ren
- College of Marine Science & Technology, Zhejiang Ocean University, Zhoushan, 316004, China.
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8
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Qiao L, Fan S, Ren C, Gui F, Li T, Zhao A, Yan Z. Total and active benthic foraminiferal community and their response to heavy metals revealed by high throughput DNA and RNA sequencing in the Zhejiang coastal waters, East China Sea. MARINE POLLUTION BULLETIN 2022; 184:114225. [PMID: 36307953 DOI: 10.1016/j.marpolbul.2022.114225] [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: 03/06/2022] [Revised: 09/12/2022] [Accepted: 10/04/2022] [Indexed: 06/16/2023]
Abstract
Benthic foraminifera, large protists abundant in marine environments, have been widely used as bioindicators of environmental conditions. In this study, high-throughput sequencing based on small subunit rDNA and rRNA amplifications was used to investigate total and active benthic foraminifera community composition and diversity from nineteen and twelve superficial marine sediment samples in the Zhejiang coastal waters, respectively. The results showed that the dominant taxa of total foraminifera changed from Buliminellidae (hyaline) to Saccamminidae (agglutinated) from north to south along the coastal waters of Zhejiang Province. According to our survey, heavy metal contamination was moderate in Zhejiang coastal waters, and the potential ecological risks posed by Cd and Hg were higher. The contamination level of heavy metals at Yueqing Bay was the highest, followed by those at Sanmen Bay and Hangzhou Bay. Cd, Cu and grain size may be key factors affecting the distribution and composition of active foraminiferal communities.
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Affiliation(s)
- Ling Qiao
- Key Laboratory of Sustainable Utilization of Technology Research for Fishery Resource of Zhejiang Province, Zhejiang Marine Fisheries Research Institute, Zhoushan 316021, China
| | - Songyao Fan
- Marine Science and Technology College, Zhejiang Ocean University, Zhoushan 316004, China
| | - Chengzhe Ren
- Marine Science and Technology College, Zhejiang Ocean University, Zhoushan 316004, China.
| | - Feng Gui
- Marine Science and Technology College, Zhejiang Ocean University, Zhoushan 316004, China
| | - Tiejun Li
- Key Laboratory of Sustainable Utilization of Technology Research for Fishery Resource of Zhejiang Province, Zhejiang Marine Fisheries Research Institute, Zhoushan 316021, China
| | - Anran Zhao
- Key Laboratory of Sustainable Utilization of Technology Research for Fishery Resource of Zhejiang Province, Zhejiang Marine Fisheries Research Institute, Zhoushan 316021, China; School of Fishery, Zhejiang Ocean University, Zhoushan 316004, China
| | - Zezheng Yan
- Marine Science and Technology College, Zhejiang Ocean University, Zhoushan 316004, China
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Macher JN, Bloska DM, Holzmann M, Girard EB, Pawlowski J, Renema W. Mitochondrial cytochrome c oxidase subunit I (COI) metabarcoding of Foraminifera communities using taxon-specific primers. PeerJ 2022; 10:e13952. [PMID: 36093332 PMCID: PMC9454970 DOI: 10.7717/peerj.13952] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 08/05/2022] [Indexed: 01/19/2023] Open
Abstract
Foraminifera are a species-rich phylum of rhizarian protists that are highly abundant in most marine environments. Molecular methods such as metabarcoding have revealed a high, yet undescribed diversity of Foraminifera. However, so far only one molecular marker, the 18S ribosomal RNA, was available for metabarcoding studies on Foraminifera. Primers that allow amplification of foraminiferal mitochondrial cytochrome oxidase I (COI) and identification of Foraminifera species were recently published. Here we test the performance of these primers for the amplification of whole foraminiferal communities, and compare their performance to that of the highly degenerate LerayXT primers, which amplify the same COI region in a wide range of eukaryotes. We applied metabarcoding to 48 samples taken along three transects spanning a North Sea beach in the Netherlands from dunes to the low tide level, and analysed both sediment samples and meiofauna samples, which contained taxa between 42 µm and 1 mm in body size obtained by decantation from sand samples. We used single-cell metabarcoding (Girard et al., 2022) to generate a COI reference library containing 32 species of Foraminifera, and used this to taxonomically annotate our community metabarcoding data. Our analyses show that the highly degenerate LerayXT primers do not amplify Foraminifera, while the Foraminifera primers are highly Foraminifera- specific, with about 90% of reads assigned to Foraminifera and amplifying taxa from all major groups, i.e., monothalamids, Globothalamea, and Tubothalamea. We identified 176 Foraminifera ASVs and found a change in Foraminifera community composition along the beach transects from high tide to low tide level, and a dominance of single-chambered monothalamid Foraminifera. Our results highlight that COI metabarcoding can be a powerful tool for assessing Foraminiferal communities.
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Affiliation(s)
- Jan-Niklas Macher
- Marine Biodiversity, Naturalis Biodiversity Center, Leiden, The Netherlands
| | | | - Maria Holzmann
- Department of Genetics & Evolution, University of Geneva, Geneva, Switzerland
| | - Elsa B. Girard
- Marine Biodiversity, Naturalis Biodiversity Center, Leiden, The Netherlands,Department of Ecosystem & Landscape Dynamics, University of Amsterdam, Amsterdam, Netherlands
| | - Jan Pawlowski
- Laboratory of Paleoceanography, Institute of Oceanology Polish Academy of Sciences, Sopot, Poland
| | - Willem Renema
- Marine Biodiversity, Naturalis Biodiversity Center, Leiden, The Netherlands,Department of Ecosystem & Landscape Dynamics, University of Amsterdam, Amsterdam, Netherlands
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10
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Al-Enezi E, Francescangeli F, Balassi E, Borderie S, Al-Hazeem S, Al-Salameen F, Boota Anwar A, Pawlowski J, Frontalini F. Benthic foraminifera as proxies for the environmental quality assessment of the Kuwait Bay (Kuwait, Arabian Gulf): Morphological and metabarcoding approaches. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 833:155093. [PMID: 35421459 DOI: 10.1016/j.scitotenv.2022.155093] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 01/26/2022] [Accepted: 04/03/2022] [Indexed: 06/14/2023]
Abstract
The rapid urbanization and industrialization of Kuwait and the consequent effluent discharges into marine environments have resulted in a degradation of water and sediment quality in the coastal marine ecosystems such as in the Kuwait Bay. This study investigates the ecological response of benthic foraminifera (protists) to environmental stress in the Kuwait Bay. The traditional morphological approach was compared to the innovative environmental DNA (eDNA) metabarcoding to evaluate the ecological quality status (EcoQS). Forty-six surface sediment samples were collected from selected stations in the Kuwait Bay. To detect the pollution gradient, environmental parameters from water (e.g., salinity, pH, dissolved oxygen) and sediment (e.g., grain-size, trace metals, total organic carbon, total petroleum hydrocarbons) were measured at each station. Although the foraminiferal assemblages were different in the morphological and molecular datasets, the species turnover was congruent and statistically significant. Diversity-based biotic indices derived from both morphological and metabarcoding approaches, reflect the environmental stress gradient (i.e., organic and metal contaminations) in the Kuwait Bay. The lowest values of EcoQS (i.e., bad to poor) are found in the innermost part (i.e., Sulaibikhat Bay and Ras Kazmah), while higher EcoQS values occur in the outer part of the bay. This study constitutes the first attempt to apply the foraminiferal metabarcoding to assess the EcoQS within the Arabian Gulf and presents its advantages compared to the conventional morphological approach.
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Affiliation(s)
- Eqbal Al-Enezi
- Environment & Life Sciences Research Center, Kuwait Institute for Scientific Research, Safat 13109, Kuwait
| | - Fabio Francescangeli
- Centre for Earth System Research and Sustainability, Institute for Geology, University of Hamburg, 20146 Hamburg, Germany; Department of Geosciences, University of Fribourg, Chemin du Musée 6, 1700 Fribourg/Freiburg, Switzerland.
| | - Eszter Balassi
- Department of Pure and Applied Sciences, Urbino University, 61029 Urbino, Italy
| | - Sandra Borderie
- Department of Geosciences, University of Fribourg, Chemin du Musée 6, 1700 Fribourg/Freiburg, Switzerland
| | - Shaker Al-Hazeem
- Environment & Life Sciences Research Center, Kuwait Institute for Scientific Research, Safat 13109, Kuwait
| | - Fadila Al-Salameen
- Environment & Life Sciences Research Center, Kuwait Institute for Scientific Research, Safat 13109, Kuwait
| | - Ahmad Boota Anwar
- Environment & Life Sciences Research Center, Kuwait Institute for Scientific Research, Safat 13109, Kuwait
| | - Jan Pawlowski
- ID-Gene ecodiagnostics Ltd, 1228 Plan-les-Ouates, Switzerland; Institute of Oceanology, Polish Academy of Sciences, 81-712 Sopot, Poland
| | - Fabrizio Frontalini
- Department of Pure and Applied Sciences, Urbino University, 61029 Urbino, Italy
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11
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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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12
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Frantal D, Agatha S, Beisser D, Boenigk J, Darienko T, Dirren-Pitsch G, Filker S, Gruber M, Kammerlander B, Nachbaur L, Scheffel U, Stoeck T, Qian K, Weißenbacher B, Pröschold T, Sonntag B. Molecular Data Reveal a Cryptic Diversity in the Genus Urotricha (Alveolata, Ciliophora, Prostomatida), a Key Player in Freshwater Lakes, With Remarks on Morphology, Food Preferences, and Distribution. Front Microbiol 2022; 12:787290. [PMID: 35185817 PMCID: PMC8854374 DOI: 10.3389/fmicb.2021.787290] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 12/07/2021] [Indexed: 11/13/2022] Open
Abstract
Species of the ciliate genus Urotricha are key players in freshwater plankton communities. In the pelagial of lakes, about 20 urotrich species occur throughout an annual cycle, some of which play a pivotal role in aquatic food webs. For example, during the phytoplankton spring bloom, they consume a remarkable proportion of the algal production. In ecological studies, urotrich ciliates are usually merely identified to genus rank and grouped into size classes. This is unsatisfying considering the distinct autecological properties of individual species and their specific spatial and temporal distribution patterns. As a basis for future research, we characterized in detail four common urotrich morphotypes, i.e., specimens identified as U. furcata and tentatively as U. agilis, U. pseudofurcata, and U. castalia, using state-of-the-art methods. We used an integrative polyphasic approach, in which morphological studies (in vivo observation, silver staining methods, scanning electron microscopy) were linked with a molecular approach exploiting four different gene fragments as taxonomic DNA barcodes with different resolution potential (SSU rDNA, ITS-1, ITS-2, hypervariable V4 and V9 regions of the SSU rDNA). We shed light on the diversity of urotrich ciliates as well as on their global distribution patterns, and annual cycles. Additionally, we coupled individual species occurrences and environmental parameters, and subsequently modeled the distribution and occurrence, using logistic regressions. Furthermore, for one strain putatively identified as U. castalia, we ascertained the optimal cultivation media and food preferences. Thereby, our comprehensive view on these important freshwater ciliates that frequently occur in environmental high throughput sequencing datasets worldwide will allow future studies to better exploit protistan plankton data from lakes.
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Affiliation(s)
- Daniela Frantal
- Research Department for Limnology, Mondsee, University of Innsbruck, Mondsee, Austria
| | - Sabine Agatha
- Department of Biosciences, Paris Lodron University of Salzburg, Salzburg, Austria
| | - Daniela Beisser
- Department of Biodiversity, University of Duisburg-Essen, Essen, Germany
| | - Jens Boenigk
- Department of Biodiversity, University of Duisburg-Essen, Essen, Germany
| | - Tatyana Darienko
- Research Department for Limnology, Mondsee, University of Innsbruck, Mondsee, Austria
- Experimental Phycology and Culture Collection of Algae, University of Göttingen, Göttingen, Germany
| | - Gianna Dirren-Pitsch
- Limnological Station, Department of Plant and Microbial Biology, University of Zurich, Kilchberg, Switzerland
| | - Sabine Filker
- Molecular Ecology Group, Technische Universität Kaiserslautern, Kaiserslautern, Germany
| | | | - Barbara Kammerlander
- Research Department for Limnology, Mondsee, University of Innsbruck, Mondsee, Austria
- Federal Agency for Water Management, Institute for Aquatic Ecology and Fisheries Management, Mondsee, Austria
| | - Laura Nachbaur
- Research Department for Limnology, Mondsee, University of Innsbruck, Mondsee, Austria
| | - Ulrike Scheffel
- Research Department for Limnology, Mondsee, University of Innsbruck, Mondsee, Austria
| | - Thorsten Stoeck
- Ecology Group, Technische Universität Kaiserslautern, Kaiserslautern, Germany
| | - Kuimei Qian
- Research Department for Limnology, Mondsee, University of Innsbruck, Mondsee, Austria
- College of Environmental Engineering, Xuzhou University of Technology, Xuzhou, China
| | - Birgit Weißenbacher
- Department of Biosciences, Paris Lodron University of Salzburg, Salzburg, Austria
| | - Thomas Pröschold
- Research Department for Limnology, Mondsee, University of Innsbruck, Mondsee, Austria
| | - Bettina Sonntag
- Research Department for Limnology, Mondsee, University of Innsbruck, Mondsee, Austria
- *Correspondence: Bettina Sonntag,
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13
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Brasell KA, Pochon X, Howarth J, Pearman JK, Zaiko A, Thompson L, Vandergoes MJ, Simon KS, Wood SA. Shifts in DNA yield and biological community composition in stored sediment: implications for paleogenomic studies. METABARCODING AND METAGENOMICS 2022. [DOI: 10.3897/mbmg.6.78128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Lake sediments hold a wealth of information from past environments that is highly valuable for paleolimnological reconstructions. These studies increasingly apply modern molecular tools targeting sedimentary DNA (sedDNA). However, sediment core sampling can be logistically difficult, making immediate subsampling for sedDNA challenging. Sediment cores are often refrigerated (4 °C) for weeks or months before subsampling. We investigated the impact of storage time on changes in DNA (purified or as cell lysate) concentrations and shifts in biological communities following storage of lake surface sediment at 4 °C for up to 24 weeks. Sediment samples (~ 0.22 g, in triplicate per time point) were spiked with purified DNA (100 or 200 ng) or lysate from a brackish water cyanobacterium that produces the cyanotoxin nodularin or non-spiked. Samples were analysed every 1–4 weeks over a 24-week period. Droplet digital PCR showed no significant decrease in the target gene (nodularin synthetase – subunit F; ndaF) over the 24-week period for samples spiked with purified DNA, while copy number decreased by more than half in cell lysate-spiked samples. There was significant change over time in bacteria and eukaryotic community composition assessed using metabarcoding. Amongst bacteria, the cyanobacterial signal became negligible after 5 weeks while Proteobacteria increased. In the eukaryotic community, Cercozoa became dominant after 6 weeks. These data demonstrate that DNA yields and community composition data shift significantly when sediments are stored chilled for more than 5 weeks. This highlights the need for rapid subsampling and appropriate storage of sediment core samples for paleogenomic studies.
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14
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Calculating dissolved marine oxygen values based on an enhanced Benthic Foraminifera Oxygen Index. Sci Rep 2022; 12:1376. [PMID: 35082337 PMCID: PMC8791969 DOI: 10.1038/s41598-022-05295-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 01/10/2022] [Indexed: 11/29/2022] Open
Abstract
Marine oxygen minimum zones (OMZs) trap greenhouse gases, reduce livable habitats, a critical factor for these changes is the amount of dissolved oxygen (DO). The frequently used tool to reconstruct DO values, the Benthic Foraminifera Oxygen Index (BFOI), showed major shortcomings and lacks effectiveness. Therefore, we enhanced the BFOI and introduce enhanced BFOI (EBFOI) formulas by using all available data benthic foraminifers provide, calculating the whole livable habitat of benthic foraminifers, including bottom water oxygenation (BWO) and pore water oxygenation (PWO). Further, we introduce for the first time a transfer function to convert EBFOI vales directly into DO values, increasing efficiency by up to 38%. All formulas are calibrated on modern samples and applied to fossil datasets. Our new approach provides a major improvement in defining and reconstructing marine oxygen levels and eutrophication, by, providing a new toolset for understanding past changes and tracking actual and predicted future expanding OMZs.
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15
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Macher JN, Wideman JG, Girard EB, Langerak A, Duijm E, Jompa J, Sadekov A, Vos R, Wissels R, Renema W. First report of mitochondrial COI in foraminifera and implications for DNA barcoding. Sci Rep 2021; 11:22165. [PMID: 34772985 PMCID: PMC8589990 DOI: 10.1038/s41598-021-01589-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 10/28/2021] [Indexed: 01/04/2023] Open
Abstract
Foraminifera are a species-rich phylum of rhizarian protists that are highly abundant in many marine environments and play a major role in global carbon cycling. Species recognition in Foraminifera is mainly based on morphological characters and nuclear 18S ribosomal RNA barcoding. The 18S rRNA contains variable sequence regions that allow for the identification of most foraminiferal species. Still, some species show limited variability, while others contain high levels of intragenomic polymorphisms, thereby complicating species identification. The use of additional, easily obtainable molecular markers other than 18S rRNA will enable more detailed investigation of evolutionary history, population genetics and speciation in Foraminifera. Here we present the first mitochondrial cytochrome c oxidase subunit 1 (COI) gene sequences ("barcodes") of Foraminifera. We applied shotgun sequencing to single foraminiferal specimens, assembled COI, and developed primers that allow amplification of COI in a wide range of foraminiferal species. We obtained COI sequences of 49 specimens from 17 species from the orders Rotaliida and Miliolida. Phylogenetic analysis showed that the COI tree is largely congruent with previously published 18S rRNA phylogenies. Furthermore, species delimitation with ASAP and ABGD algorithms showed that foraminiferal species can be identified based on COI barcodes.
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Affiliation(s)
- Jan-Niklas Macher
- Naturalis Biodiversity Center, Marine Biodiversity, Leiden, The Netherlands.
| | - Jeremy G Wideman
- Biodesign Center for Mechanisms of Evolution, School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Elsa B Girard
- Naturalis Biodiversity Center, Marine Biodiversity, Leiden, The Netherlands
- Department of Ecosystem and Landscape Dynamics, Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands
| | - Anouk Langerak
- Naturalis Biodiversity Center, Marine Biodiversity, Leiden, The Netherlands
| | - Elza Duijm
- Naturalis Biodiversity Center, Marine Biodiversity, Leiden, The Netherlands
| | | | - Aleksey Sadekov
- ARC Centre of Excellence for Coral Reef Studies, Ocean Graduate School, The University of Western Australia, Crawley, Australia
| | - Rutger Vos
- Naturalis Biodiversity Center, Marine Biodiversity, Leiden, The Netherlands
- Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Richard Wissels
- Naturalis Biodiversity Center, Marine Biodiversity, Leiden, The Netherlands
| | - Willem Renema
- Naturalis Biodiversity Center, Marine Biodiversity, Leiden, The Netherlands
- Department of Ecosystem and Landscape Dynamics, Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands
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16
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Cavaliere M, Barrenechea Angeles I, Montresor M, Bucci C, Brocani L, Balassi E, Margiotta F, Francescangeli F, Bouchet VMP, Pawlowski J, Frontalini F. Assessing the ecological quality status of the highly polluted Bagnoli area (Tyrrhenian Sea, Italy) using foraminiferal eDNA metabarcoding. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 790:147871. [PMID: 34098278 DOI: 10.1016/j.scitotenv.2021.147871] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Revised: 05/14/2021] [Accepted: 05/14/2021] [Indexed: 06/12/2023]
Abstract
Morphology-based benthic foraminifera indices are increasingly used worldwide for biomonitoring the ecological quality of marine sediments. The recent development of foraminiferal eDNA metabarcoding offers a reliable, time-, and cost-effective alternative to morphology-based foraminiferal biomonitoring. However, the practical applications of these new tools are still highly limited. In the present study, we evaluate the response of benthic foraminifera and define the ecological quality status (EcoQS) in the Bagnoli area (Tyrrhenian Sea, Italy) based on a traditional morphology-based approach and eDNA metabarcoding. The geochemical data show that several sites in front of the former industrial plant contain higher concentrations of potentially toxic elements than the effect range median and are characterized by the highest total organic carbon (TOC) content, whereas the distantly located sites can be considered relatively low- to unpolluted. Significant differences (i.e., diversity and assemblage composition) in both morphological and molecular datasets were found between the relatively low- to unpolluted and the most polluted areas. Similarly, the selected ecological indices of both morphological and molecular datasets strikingly and congruently resulted in a clear separation following the environmental stress gradient. The molecular indices (i.e., g-exp(H'bc), g-Foram AMBI, and g-Foram AMBI-MOTUs) reliably identified poor-to-bad EcoQS in the polluted area in front of the former industrial plant. On the other hand, the Foram-AMBI based on morphology well identified an overall trend but seemed to overestimate the EcoQS if the traditional class boundaries were considered. The congruent and complementary trends between morphological and metabarcoding data observed in the case of the Bagnoli site further support the application of foraminiferal metabarcoding in routine biomonitoring to assess the environmental impacts of heavily polluted marine areas.
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Affiliation(s)
- M Cavaliere
- Dipartimento di Scienze Pure e Applicate, Università degli Studi di Urbino "Carlo Bo", 61029 Urbino, Italy.
| | - I Barrenechea Angeles
- Department of Genetics and Evolution, University of Geneva, 1205 Geneva, Switzerland; Department of Earth Sciences, University of Geneva, 1205 Geneva, Switzerland
| | - M Montresor
- Stazione Zoologica Anton Dohrn, 80122 Naples, Italy
| | - C Bucci
- Dipartimento di Scienze Pure e Applicate, Università degli Studi di Urbino "Carlo Bo", 61029 Urbino, Italy
| | - L Brocani
- Dipartimento di Scienze Pure e Applicate, Università degli Studi di Urbino "Carlo Bo", 61029 Urbino, Italy
| | - E Balassi
- Dipartimento di Scienze Pure e Applicate, Università degli Studi di Urbino "Carlo Bo", 61029 Urbino, Italy
| | - F Margiotta
- Stazione Zoologica Anton Dohrn, 80122 Naples, Italy
| | - F Francescangeli
- University of Hamburg, Institute for Geology, Centre for Earth System Research and Sustainability, 20146 Hamburg, Germany
| | - V M P Bouchet
- University of Lille, CNRS, Univ. Littoral Côte d'Opale, UMR 8187, LOG, Laboratoire d'Océanologie et de Géosciences, Station Marine de Wimereux, F 59000 Lille, France
| | - J Pawlowski
- Department of Genetics and Evolution, University of Geneva, 1205 Geneva, Switzerland; ID-Gene ecodiagnostics, Campus Biotech Innovation Park, 1202 Geneva, Switzerland; Institute of Oceanology, Polish Academy of Sciences, 81-712 Sopot, Poland
| | - F Frontalini
- Dipartimento di Scienze Pure e Applicate, Università degli Studi di Urbino "Carlo Bo", 61029 Urbino, Italy
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17
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Rimet F, Aylagas E, Borja Á, Bouchez A, Canino A, Chauvin C, Chonova T, Ciampor Jr F, Costa FO, Ferrari BJD, Gastineau R, Goulon C, Gugger M, Holzmann M, Jahn R, Kahlert M, Kusber WH, Laplace-Treyture C, Leese F, Leliaert F, Mann DG, Marchand F, Méléder V, Pawlowski J, Rasconi S, Rivera S, Rougerie R, Schweizer M, Trobajo R, Vasselon V, Vivien R, Weigand A, Witkowski A, Zimmermann J, Ekrem T. Metadata standards and practical guidelines for specimen and DNA curation when building barcode reference libraries for aquatic life. METABARCODING AND METAGENOMICS 2021. [DOI: 10.3897/mbmg.5.58056] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
DNA barcoding and metabarcoding is increasingly used to effectively and precisely assess and monitor biodiversity in aquatic ecosystems. As these methods rely on data availability and quality of barcode reference libraries, it is important to develop and follow best practices to ensure optimal quality and traceability of the metadata associated with the reference barcodes used for identification. Sufficient metadata, as well as vouchers, corresponding to each reference barcode must be available to ensure reliable barcode library curation and, thereby, provide trustworthy baselines for downstream molecular species identification. This document (1) specifies the data and metadata required to ensure the relevance, the accessibility and traceability of DNA barcodes and (2) specifies the recommendations for DNA harvesting and for the storage of both voucher specimens/samples and barcode data.
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18
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Integrating morphology and metagenomics to understand taxonomic variability of Amphisorus (Foraminifera, Miliolida) from Western Australia and Indonesia. PLoS One 2021; 16:e0244616. [PMID: 33395419 PMCID: PMC7781389 DOI: 10.1371/journal.pone.0244616] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 12/11/2020] [Indexed: 12/13/2022] Open
Abstract
Foraminifera are a group of mostly marine protists with high taxonomic diversity. Species identification is often complex, as both morphological and molecular approaches can be challenging due to a lack of unique characters and reference sequences. An integrative approach combining state of the art morphological and molecular tools is therefore promising. In this study, we analysed large benthic Foraminifera of the genus Amphisorus from Western Australia and Indonesia. Based on previous findings on high morphological variability observed in the Soritidae and the discontinuous distribution of Amphisorus along the coast of western Australia, we expected to find multiple morphologically and genetically unique Amphisorus types. In order to gain detailed insights into the diversity of Amphisorus, we applied micro CT scanning and shotgun metagenomic sequencing. We identified four distinct morphotypes of Amphisorus, two each in Australia and Indonesia, and showed that each morphotype is a distinct genotype. Furthermore, metagenomics revealed the presence of three dinoflagellate symbiont clades. The most common symbiont was Fugacium Fr5, and we could show that its genotypes were mostly specific to Amphisorus morphotypes. Finally, we assembled the microbial taxa associated with the two Western Australian morphotypes, and analysed their microbial community composition. Even though each Amphisorus morphotype harboured distinct bacterial communities, sampling location had a stronger influence on bacterial community composition, and we infer that the prokaryotic community is primarily shaped by the microhabitat rather than host identity. The integrated approach combining analyses of host morphology and genetics, dinoflagellate symbionts, and associated microbes leads to the conclusion that we identified distinct, yet undescribed taxa of Amphisorus. We argue that the combination of morphological and molecular methods provides unprecedented insights into the diversity of foraminifera, which paves the way for a deeper understanding of their biodiversity, and facilitates future taxonomic and ecological work.
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19
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Soil bacterial community composition and diversity respond to soil environment in the Ebinur Lake Wetland. Arch Microbiol 2020; 203:1175-1182. [PMID: 33226465 DOI: 10.1007/s00203-020-02112-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Revised: 10/19/2020] [Accepted: 11/01/2020] [Indexed: 10/22/2022]
Abstract
To understand the relationship between the community structure of bacteria and soil environment, the diversity and composition of soil bacterial communities were investigated, based on 16S rRNA gene clone library, in three different sampling sites (SP1, SP2 and SP3) in the Bortala and Jinghe River basins of Ebinur Lake Wetland. The results showed that the diversity of bacteria among plots was SP2 > SP3 > SP1, and the richness was SP3 > SP2 > SP1. Community composition analysis of bacteria showed that Proteobacteria and Bacteroides accounted for 49.7% and 53.7%, respectively, making them the most dominant phyla observed. In SP1, Proteobacteria was the most dominant phylum, followed by Bacteroides. In SP2 and SP3, Bacteroides was the most dominant phylum, followed by Proteobacteria. At subphyla level, Gammaproteobacteria, Alphaproteobacteria and Deltaproteobacteria accounted for 50%, 51.0%, and 42.2% of the Proteobacteria of SP1, SP2, and SP3, respectively. Betaproteobacteria and Epsilonproteobacteria were found only in SP3. RDA results showed that SOM, SM and EC were the main soil environmental factors affecting bacterial community structure.
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20
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Frontalini F, Cordier T, Balassi E, Armynot du Chatelet E, Cermakova K, Apothéloz-Perret-Gentil L, Martins MVA, Bucci C, Scantamburlo E, Treglia M, Bonamin V, Pawlowski J. Benthic foraminiferal metabarcoding and morphology-based assessment around three offshore gas platforms: Congruence and complementarity. ENVIRONMENT INTERNATIONAL 2020; 144:106049. [PMID: 32835923 DOI: 10.1016/j.envint.2020.106049] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 08/07/2020] [Accepted: 08/07/2020] [Indexed: 06/11/2023]
Abstract
Since the 1960 s, there has been a rapid expansion of drilling activities in the central and northern Adriatic Sea to meet the increasing global energy demand. The discharges of organic and inorganic pollutants, as well as the alteration of the sediment substrate, are among the main impacts associated with these activities. In the present study, we evaluate the response of benthic foraminifera to the activities of three gas platforms in the northwestern Adriatic Sea, with a special focus on the Armida A platform for which extensive geochemical data (organic matter, trace elements, polycyclic aromatic hydrocarbons, other hydrocarbons, and volatile organic compounds) are available. The response to disturbance is assessed by analyzing the foraminiferal diversity using the traditional morphology-based approach and by 18S rDNA-based metabarcoding. The two methods give congruent results, showing relatively lower foraminiferal diversity and higher dominance values at stations closer to the platforms (<50 m). The taxonomic compositions of the morphological and metabarcoding datasets are very different, the latter being dominated by monothalamous, mainly soft-walled species. However, compositional changes consistently occur at 50 m from the platform and can be related to variations in sediment grain-size variation and higher concentrations of Ni, Zn, Ba, hydrocarbons and total organic carbon. Additionally, several morphospecies and Molecular Operational Taxonomic Units (MOTUs) show strong correlations with distance from the platform and with environmental parameters extracted from BIOENV analysis. Some of these MOTUs have the potential to become new bioindicators, complementing the assemblage of hard-shelled foraminiferal species detected through microscopic analyses. The congruence and complementarity between metabarcoding and morphological approaches support the application of foraminiferal metabarcoding in routine biomonitoring surveys as a reliable, time- and cost-effective methodology to assess the environmental impacts of marine industries.
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Affiliation(s)
- Fabrizio Frontalini
- Dipartimento di Scienze Pure e Applicate, Università degli Studi di Urbino "Carlo Bo", Urbino, Italy
| | - Tristan Cordier
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
| | - Eszter Balassi
- Dipartimento di Scienze Pure e Applicate, Università degli Studi di Urbino "Carlo Bo", Urbino, Italy
| | - Eric Armynot du Chatelet
- Laboratoire d'Océanologie et de Géosciences UMR 8187 LOG CNRS/Lille/ULCO, Université de Lille, Bât SN5, Cité Scientifique, 59655 Villeneuve d'Ascq, France
| | - Kristina Cermakova
- ID-Gene ecodiagnostics, Campus Biotech Innovation Park, 1202 Geneva, Switzerland
| | - Laure Apothéloz-Perret-Gentil
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland; ID-Gene ecodiagnostics, Campus Biotech Innovation Park, 1202 Geneva, Switzerland
| | - Maria Virginia Alves Martins
- Laboratory of Micropaleontology, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Brazil; Universidade de Aveiro, GeoBioTec, Departamento de Geociências, Aveiro, Portugal
| | - Carla Bucci
- Dipartimento di Scienze Pure e Applicate, Università degli Studi di Urbino "Carlo Bo", Urbino, Italy
| | | | | | | | - Jan Pawlowski
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland; ID-Gene ecodiagnostics, Campus Biotech Innovation Park, 1202 Geneva, Switzerland; Institute of Oceanology, Polish Academy of Sciences, 81-712 Sopot, Poland
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21
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Siemensma F, Holzmann M, Apothéloz-Perret-Gentil L, Clauß S, Voelcker E, Bettighofer W, Roshan SK, Walden S, Dumack K, Pawlowski J. Broad sampling of monothalamids (Rhizaria, Foraminifera) gives further insight into diversity of non-marine Foraminifera. Eur J Protistol 2020; 77:125744. [PMID: 33191053 DOI: 10.1016/j.ejop.2020.125744] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 09/08/2020] [Accepted: 10/07/2020] [Indexed: 11/17/2022]
Abstract
Non-marine foraminifera are among the least known groups of protists and only a handful of species have been described since the 19th century. We collected one naked and five morphologically almost identical organic-walled monothalamid species from freshwater and terrestrial environments from Germany and Austria. One of the species was identified as Lieberkuehnia wageneriClaparède and Lachmann, 1859. As its original description is ambiguous and its type specimen has been lost, a neotype is proposed. We describe four new organic-walled monothalamous foraminifera and a novel Reticulomyxa species both morphologically and genetically. Analyses of molecular data of the different isolates revealed that they are distributed across six different clades. Two new genera, Claparedellus gen. nov. and Velamentofex gen. nov., and five new monothalamous families, Lacogromiidae fam. nov., Limnogromiidae fam. nov., Lieberkuehniidae fam. nov., Edaphoallogromiidae fam. nov. and Velamentofexidae fam. nov., are established.
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Affiliation(s)
| | - Maria Holzmann
- Dept. of Genetics and Evolution, University of Geneva, Quai Ernest Ansermet 30, CH-1211 Geneva 4, Switzerland
| | | | - Steffen Clauß
- Penard Laboratory, 18 Stellenberg Avenue, Cape Town 7708, South Africa
| | - Eckhard Voelcker
- Penard Laboratory, 18 Stellenberg Avenue, Cape Town 7708, South Africa
| | | | - Samira Khanipour Roshan
- Institute for Biological Sciences, Applied Ecology and Phycology, Albert-Einstein-Str. 21, 18059 Rostock, Germany
| | - Susanne Walden
- Terrestrial Ecology, Institute of Zoology, University of Cologne, Zülpicher Str. 47b, 50674 Cologne, Germany
| | - Kenneth Dumack
- Terrestrial Ecology, Institute of Zoology, University of Cologne, Zülpicher Str. 47b, 50674 Cologne, Germany
| | - Jan Pawlowski
- Dept. of Genetics and Evolution, University of Geneva, Quai Ernest Ansermet 30, CH-1211 Geneva 4, Switzerland; Institute of Oceanology, Polish Academy of Sciences, Powstancow, Warszawy 55, PL 81-712, Sopot, Poland
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22
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Li Q, Lei Y, Morard R, Li T, Wang B. Diversity hotspot and unique community structure of foraminifera in the world's deepest marine blue hole - Sansha Yongle Blue Hole. Sci Rep 2020; 10:10257. [PMID: 32581270 PMCID: PMC7314809 DOI: 10.1038/s41598-020-67221-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 06/01/2020] [Indexed: 11/09/2022] Open
Abstract
Marine blue holes are precious geological heritages with high scientific research values. Their physical and chemical characteristics are unique because of the steep-walled structure and isolated water column which create isolated ecosystems in geographically restricted areas. The Sansha Yongle Blue Hole (SYBH) is the world's deepest marine blue hole. Here, we generated the first DNA metabarcoding dataset from SYBH sediment focusing on foraminifera, a group of protists that have colonized various marine environments. We collected sediment samples from SYBH along a depth gradient to characterize the foraminiferal diversity and compared them with the foraminiferal diversity of the costal Jiaozhou Bay (JZB) and the abyssal Northwest Pacific Ocean (NWP). We amplified the SSU rDNA of foraminifera and sequenced them with high-throughput sequencing. The results showed that the foraminiferal assemblages in SYBH were vertically structured in response to the abiotic gradients and diversity was higher than in JZB and NWP. This study illustrates the capacity of foraminifera to colonize hostile environments and shows that blue holes are natural laboratories to explore physiological innovation associated with anoxia.
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Affiliation(s)
- Qingxia Li
- Laboratory of Marine Organism Taxonomy and Phylogeny, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yanli Lei
- Laboratory of Marine Organism Taxonomy and Phylogeny, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China.
| | - Raphaёl Morard
- MARUM Center for Marine Environmental Sciences, University of Bremen, Leobener Strasse, 28359, Bremen, Germany
| | - Tiegang Li
- Key Laboratory of Marine Sedimentology and Environmental Geology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, 266061, China.
- Pilot National Laboratory for Marine Science and Technology, Qingdao, 266237, China.
| | - Baodong Wang
- Key Laboratory of Marine Sedimentology and Environmental Geology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, 266061, China
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23
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Gooday AJ, Schoenle A, Dolan JR, Arndt H. Protist diversity and function in the dark ocean - Challenging the paradigms of deep-sea ecology with special emphasis on foraminiferans and naked protists. Eur J Protistol 2020; 75:125721. [PMID: 32575029 DOI: 10.1016/j.ejop.2020.125721] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 05/13/2020] [Accepted: 05/21/2020] [Indexed: 11/27/2022]
Abstract
The dark ocean and the underlying deep seafloor together represent the largest environment on this planet, comprising about 80% of the oceanic volume and covering more than two-thirds of the Earth's surface, as well as hosting a major part of the total biosphere. Emerging evidence suggests that these vast pelagic and benthic habitats play a major role in ocean biogeochemistry and represent an "untapped reservoir" of high genetic and metabolic microbial diversity. Due to its huge volume, the water column of the dark ocean is the largest reservoir of organic carbon in the biosphere and likely plays a major role in the global carbon budget. The dark ocean and the seafloor beneath it are also home to a largely enigmatic food web comprising little-known and sometimes spectacular organisms, mainly prokaryotes and protists. This review considers the globally important role of pelagic and benthic protists across all protistan size classes in the deep-sea realm, with a focus on their taxonomy, diversity, and physiological properties, including their role in deep microbial food webs. We argue that, given the important contribution that protists must make to deep-sea biodiversity and ecosystem processes, they should not be overlooked in biological studies of the deep ocean.
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Affiliation(s)
- Andrew J Gooday
- National Oceanography Centre, University of Southampton Waterfront Campus, Southampton, UK; Life Sciences Department, Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Alexandra Schoenle
- University of Cologne, Institute of Zoology, General Ecology, 50674 Cologne, Germany
| | - John R Dolan
- Sorbonne Université, CNRS UMR 7093, Laboratoroire d'Océanographie de Villefranche-sur-Mer, Villefranche-sur-Mer, France
| | - Hartmut Arndt
- University of Cologne, Institute of Zoology, General Ecology, 50674 Cologne, Germany.
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24
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Caron DA, Hu SK. Are We Overestimating Protistan Diversity in Nature? Trends Microbiol 2018; 27:197-205. [PMID: 30455081 DOI: 10.1016/j.tim.2018.10.009] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 10/04/2018] [Accepted: 10/25/2018] [Indexed: 12/30/2022]
Abstract
Documenting the immense diversity of single-celled, eukaryotic organisms (protists) has been a formidable challenge for ecologists. These species were originally defined by morphological criteria, but shortcomings of the morphospecies concept, and a bewildering array of sizes and cellular attributes, has made constructing a taxonomy that is useful for ecologists nearly impossible. Consequently, physiological and genetic information has been integrated to address these shortcomings, and to develop the framework of a unifying taxonomy. DNA sequence information, in particular, has revolutionized studies of protistan diversity. However, the exponential increase in sequence-based protistan species richness published from field surveys in recent years raises the question of whether we have moved beyond characterizing species-level diversity and begun to reveal intraspecies diversity. The answer to that question appears to be 'yes', at least for some protistan lineages. The need to document such microdiversity may be justified, but it is important for protistologists to recognize and acknowledge that possibility, and its consequences.
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Affiliation(s)
- David A Caron
- Department of Biological Sciences, 3616 Trousdale Parkway, University of Southern California, Los Angeles, CA 90089-0371, USA.
| | - Sarah K Hu
- Department of Biological Sciences, 3616 Trousdale Parkway, University of Southern California, Los Angeles, CA 90089-0371, USA
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25
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Pawlowski J, Kelly-Quinn M, Altermatt F, Apothéloz-Perret-Gentil L, Beja P, Boggero A, Borja A, Bouchez A, Cordier T, Domaizon I, Feio MJ, Filipe AF, Fornaroli R, Graf W, Herder J, van der Hoorn B, Iwan Jones J, Sagova-Mareckova M, Moritz C, Barquín J, Piggott JJ, Pinna M, Rimet F, Rinkevich B, Sousa-Santos C, Specchia V, Trobajo R, Vasselon V, Vitecek S, Zimmerman J, Weigand A, Leese F, Kahlert M. The future of biotic indices in the ecogenomic era: Integrating (e)DNA metabarcoding in biological assessment of aquatic ecosystems. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 637-638:1295-1310. [PMID: 29801222 DOI: 10.1016/j.scitotenv.2018.05.002] [Citation(s) in RCA: 197] [Impact Index Per Article: 32.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 04/11/2018] [Accepted: 05/01/2018] [Indexed: 05/05/2023]
Abstract
The bioassessment of aquatic ecosystems is currently based on various biotic indices that use the occurrence and/or abundance of selected taxonomic groups to define ecological status. These conventional indices have some limitations, often related to difficulties in morphological identification of bioindicator taxa. Recent development of DNA barcoding and metabarcoding could potentially alleviate some of these limitations, by using DNA sequences instead of morphology to identify organisms and to characterize a given ecosystem. In this paper, we review the structure of conventional biotic indices, and we present the results of pilot metabarcoding studies using environmental DNA to infer biotic indices. We discuss the main advantages and pitfalls of metabarcoding approaches to assess parameters such as richness, abundance, taxonomic composition and species ecological values, to be used for calculation of biotic indices. We present some future developments to fully exploit the potential of metabarcoding data and improve the accuracy and precision of their analysis. We also propose some recommendations for the future integration of DNA metabarcoding to routine biomonitoring programs.
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Affiliation(s)
- Jan Pawlowski
- Department of Genetics and Evolution, University of Geneva, CH-1211 Geneva, Switzerland.
| | - Mary Kelly-Quinn
- School of Biology & Environmental Science, University College Dublin, Ireland
| | - Florian Altermatt
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Department of Aquatic Ecology, Überlandstrasse 133, CH-8600 Dübendorf, Switzerland(;) Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | | | - Pedro Beja
- CIBIO/InBIO-Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Rua Padre Armando Quintas, 4485-601 Vairão, Portugal; CEABN/InBIO-Centro de Estudos Ambientais 'Prof. Baeta Neves', Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, 1349-017 Lisboa, Portugal
| | - Angela Boggero
- LifeWatch, Italy and CNR-Institute of Ecosystem Study (CNR-ISE), Largo Tonolli 50, 28922 Verbania Pallanza, Italy
| | - Angel Borja
- AZTI, Marine Research Division, Herrera Kaia, Portualdea s/n, 20110 Pasaia, Spain
| | - Agnès Bouchez
- INRA, UMR42 CARRTEL, 75bis Avenue de Corzent, 74203 Thonon les Bains Cedex, France
| | - Tristan Cordier
- Department of Genetics and Evolution, University of Geneva, CH-1211 Geneva, Switzerland
| | - Isabelle Domaizon
- INRA, UMR42 CARRTEL, 75bis Avenue de Corzent, 74203 Thonon les Bains Cedex, France
| | - Maria Joao Feio
- Marine and Environmental Sciences Centre, Faculty of Sciences and Technology, Department of Life Sciences, University of Coimbra, Portugal
| | - Ana Filipa Filipe
- CIBIO/InBIO-Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Rua Padre Armando Quintas, 4485-601 Vairão, Portugal; CEABN/InBIO-Centro de Estudos Ambientais 'Prof. Baeta Neves', Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, 1349-017 Lisboa, Portugal
| | - Riccardo Fornaroli
- University of Milano Bicocca, Department of Earth and Environmental Sciences(DISAT), Piazza della Scienza 1,20126 Milano, Italy
| | - Wolfram Graf
- Institute of Hydrobiology and Aquatic Ecosystem Management (IHG), 1180 Vienna, Austria
| | - Jelger Herder
- RAVON, Postbus 1413, Nijmegen 6501 BK, The Netherlands
| | | | - J Iwan Jones
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Marketa Sagova-Mareckova
- Crop Research Institute, Epidemiology and Ecology of Microorganisms, Drnovska 507, 16106 Praha 6, Czechia
| | - Christian Moritz
- ARGE Limnologie GesmbH, Hunoldstraße 14, 6020 Innsbruck, Austria
| | - Jose Barquín
- Environmental Hydraulics Institute "IHCantabria", Universidad de Cantabria, C/ Isabel Torres n°15, Parque Científico y Tecnológico de Cantabria, 39011 Santander, Spain
| | - Jeremy J Piggott
- Department of Zoology, School of Natural Sciences, Trinity College Dublin, the University of Dublin, College Green, Dublin 2, Ireland; Department of Zoology, University of Otago, 340 Great King Street, Dunedin 9016, New Zealand
| | - Maurizio Pinna
- Department of Biological and Environmental Sciences and Technologies, University of Salento, S.P. Lecce-Monteroni, 73100 Lecce, Italy
| | - Frederic Rimet
- INRA, UMR42 CARRTEL, 75bis Avenue de Corzent, 74203 Thonon les Bains Cedex, France
| | - Buki Rinkevich
- Israel Oceanographic and Limnological Research, Tel- Shikmona, Haifa 31080, Israel
| | - Carla Sousa-Santos
- MARE - Marine and Environmental Sciences Centre, ISPA - Instituto Universitário, Rua Jardim do Tabaco 34, 1149-041 Lisboa, Portugal
| | - Valeria Specchia
- Department of Biological and Environmental Sciences and Technologies, University of Salento, S.P. Lecce-Monteroni, 73100 Lecce, Italy
| | - Rosa Trobajo
- IRTA, Institute of Agriculture and Food Research and Technology, Marine and Continental Waters Program, Carretera Poble Nou Km 5.5, E-43540 St. Carles de la Ràpita, Catalonia, Spain
| | - Valentin Vasselon
- INRA, UMR42 CARRTEL, 75bis Avenue de Corzent, 74203 Thonon les Bains Cedex, France
| | - Simon Vitecek
- Department of Limnology and Bio-Oceanography, Faculty of Life Sciences, University of Vienna, Althanstraße 14, 1090 Vienna, Austria; Senckenberg Research Institute and Natural History Museum, Senckenberganlage 25, 60325 Frankfurt am Main, Germany
| | - Jonas Zimmerman
- Botanic Garden and Botanical Museum Berlin-Dahlem, Freie Universität Berlin, Königin-Luise-Str. 6-8, 14195 Berlin, Germany
| | - Alexander Weigand
- University of Duisburg-Essen, Aquatic Ecosystem Research, Universitaetsstrasse 5, 45141 Essen, Germany; Musée National d'Histoire Naturelle, 25 Rue Münster, 2160 Luxembourg, Luxembourg
| | - Florian Leese
- University of Duisburg-Essen, Aquatic Ecosystem Research, Universitaetsstrasse 5, 45141 Essen, Germany
| | - Maria Kahlert
- Swedish University of Agricultural Sciences, Department of Aquatic Sciences and Assessment, PO Box 7050, SE - 750 07 Uppsala, Sweden
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Frontalini F, Greco M, Di Bella L, Lejzerowicz F, Reo E, Caruso A, Cosentino C, Maccotta A, Scopelliti G, Nardelli MP, Losada MT, Armynot du Châtelet E, Coccioni R, Pawlowski J. Assessing the effect of mercury pollution on cultured benthic foraminifera community using morphological and eDNA metabarcoding approaches. MARINE POLLUTION BULLETIN 2018; 129:512-524. [PMID: 29033170 DOI: 10.1016/j.marpolbul.2017.10.022] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Revised: 09/14/2017] [Accepted: 10/09/2017] [Indexed: 06/07/2023]
Abstract
Mercury (Hg) is a highly toxic element for living organisms and is known to bioaccumulate and biomagnify. Here, we analyze the response of benthic foraminifera communities cultured in mesocosm and exposed to different concentrations of Hg. Standard morphological analyses and environmental DNA metabarcoding show evidence that Hg pollution has detrimental effects on benthic foraminifera. The molecular analysis provides a more complete view of foraminiferal communities including the soft-walled single-chambered monothalamiids and small-sized hard-shelled rotaliids and textulariids than the morphological one. Among these taxa that are typically overlooked in morphological studies we found potential bioindicators of Hg pollution. The mesocosm approach proves to be an effective method to study benthic foraminiferal responses to various types and concentrations of pollutants over time. This study further supports foraminiferal metabarcoding as a complementary and/or alternative method to standard biomonitoring program based on the morphological identification of species communities.
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Affiliation(s)
- Fabrizio Frontalini
- Department of Pure and Applied Sciences, University of Urbino, 61029 Urbino, Italy.
| | | | - Letizia Di Bella
- Department of Earth Science, Rome University "Sapienza", 00185 Roma, Italy
| | - Franck Lejzerowicz
- Department of Genetics and Evolution, University of Geneva, 1211 Genève, Switzerland
| | - Emanuela Reo
- Department of Genetics and Evolution, University of Geneva, 1211 Genève, Switzerland
| | - Antonio Caruso
- Dipartimento di Scienze della Terra e del Mare (DiSTeM), Università di Palermo, 90123 Palermo, Italy
| | - Claudia Cosentino
- Dipartimento di Scienze della Terra e del Mare (DiSTeM), Università di Palermo, 90123 Palermo, Italy
| | - Antonella Maccotta
- Dipartimento di Scienze della Terra e del Mare (DiSTeM), Università di Palermo, 90123 Palermo, Italy
| | - Giovanna Scopelliti
- Dipartimento di Scienze della Terra e del Mare (DiSTeM), Università di Palermo, 90123 Palermo, Italy
| | | | - Maria Teresa Losada
- Departamento de Zooloxía e Antropoloxía Física, Universidade de Santiago de Compostela, 27002 Lugo, Spain
| | - Eric Armynot du Châtelet
- Univ. Lille, CNRS, Univ. Littoral Cote d'Opale, UMR 8187, LOG, Laboratoire d'Océanologie et de Géosciences, F 59 000 Lille, France
| | - Rodolfo Coccioni
- Department of Pure and Applied Sciences, University of Urbino, 61029 Urbino, Italy
| | - Jan Pawlowski
- Department of Genetics and Evolution, University of Geneva, 1211 Genève, Switzerland
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27
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Cordier T, Esling P, Lejzerowicz F, Visco J, Ouadahi A, Martins C, Cedhagen T, Pawlowski J. Predicting the Ecological Quality Status of Marine Environments from eDNA Metabarcoding Data Using Supervised Machine Learning. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2017; 51:9118-9126. [PMID: 28665601 DOI: 10.1021/acs.est.7b01518] [Citation(s) in RCA: 89] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Monitoring biodiversity is essential to assess the impacts of increasing anthropogenic activities in marine environments. Traditionally, marine biomonitoring involves the sorting and morphological identification of benthic macro-invertebrates, which is time-consuming and taxonomic-expertise demanding. High-throughput amplicon sequencing of environmental DNA (eDNA metabarcoding) represents a promising alternative for benthic monitoring. However, an important fraction of eDNA sequences remains unassigned or belong to taxa of unknown ecology, which prevent their use for assessing the ecological quality status. Here, we show that supervised machine learning (SML) can be used to build robust predictive models for benthic monitoring, regardless of the taxonomic assignment of eDNA sequences. We tested three SML approaches to assess the environmental impact of marine aquaculture using benthic foraminifera eDNA, a group of unicellular eukaryotes known to be good bioindicators, as features to infer macro-invertebrates based biotic indices. We found similar ecological status as obtained from macro-invertebrates inventories. We argue that SML approaches could overcome and even bypass the cost and time-demanding morpho-taxonomic approaches in future biomonitoring.
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Affiliation(s)
- Tristan Cordier
- Department of Genetics and Evolution, University of Geneva , Boulevard d'Yvoy 4, CH 1205 Geneva, Switzerland
| | - Philippe Esling
- IRCAM, UMR 9912, Université Pierre et Marie Curie , 4 place Jussieu, 75005 Paris, France
| | - Franck Lejzerowicz
- Department of Genetics and Evolution, University of Geneva , Boulevard d'Yvoy 4, CH 1205 Geneva, Switzerland
| | - Joana Visco
- ID-Gene ecodiagnostics, Ltd. , chemin des Aulx 14, 1228 Plan-les-Ouates, Switzerland
| | - Amine Ouadahi
- Department of Genetics and Evolution, University of Geneva , Boulevard d'Yvoy 4, CH 1205 Geneva, Switzerland
| | - Catarina Martins
- Marine Harvest ASA , Sandviksboder 77AB, Bergen, 5035 Bergen, Norway
| | - Tomas Cedhagen
- Department of Bioscience, Section of Aquatic Biology, University of Aarhus , Building 1135, Ole Worms allé 1, DK-8000 Aarhus, Denmark
| | - Jan Pawlowski
- Department of Genetics and Evolution, University of Geneva , Boulevard d'Yvoy 4, CH 1205 Geneva, Switzerland
- ID-Gene ecodiagnostics, Ltd. , chemin des Aulx 14, 1228 Plan-les-Ouates, Switzerland
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28
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Laroche O, Wood SA, Tremblay LA, Lear G, Ellis JI, Pochon X. Metabarcoding monitoring analysis: the pros and cons of using co-extracted environmental DNA and RNA data to assess offshore oil production impacts on benthic communities. PeerJ 2017; 5:e3347. [PMID: 28533985 PMCID: PMC5437860 DOI: 10.7717/peerj.3347] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 04/22/2017] [Indexed: 11/20/2022] Open
Abstract
Sequencing environmental DNA (eDNA) is increasingly being used as an alternative to traditional morphological-based identification to characterize biological assemblages and monitor anthropogenic impacts in marine environments. Most studies only assess eDNA which, compared to eRNA, can persist longer in the environment after cell death. Therefore, eRNA may provide a more immediate census of the environment due to its relatively weaker stability, leading some researchers to advocate for the use of eRNA as an additional, or perhaps superior proxy for portraying ecological changes. A variety of pre-treatment techniques for screening eDNA and eRNA derived operational taxonomic units (OTUs) have been employed prior to statistical analyses, including removing singleton taxa (i.e., OTUs found only once) and discarding those not present in both eDNA and eRNA datasets. In this study, we used bacterial (16S ribosomal RNA gene) and eukaryotic (18S ribosomal RNA gene) eDNA- and eRNA-derived data from benthic communities collected at increasing distances along a transect from an oil production platform (Taranaki, New Zealand). Macro-infauna (visual classification of benthic invertebrates) and physico-chemical data were analyzed in parallel. We tested the effect of removing singleton taxa, and removing taxa not present in the eDNA and eRNA libraries from the same environmental sample (trimmed by shared OTUs), by comparing the impact of the oil production platform on alpha- and beta-diversity of the eDNA/eRNA-based biological assemblages, and by correlating these to the morphologically identified macro-faunal communities and the physico-chemical data. When trimmed by singletons, presence/absence information from eRNA data represented the best proxy to detect changes on species diversity for both bacteria and eukaryotes. However, assessment of quantitative beta-diversity from read abundance information of bacteria eRNA did not, contrary to eDNA, reveal any impact from the oil production activity. Overall, the data appeared more robust when trimmed by shared OTUs, showing a greater effect of the platform on alpha- and beta-diversity. Trimming by shared OTUs likely removes taxa derived from legacy DNA and technical artefacts introduced through reverse transcriptase, polymerase-chain-reaction and sequencing. Findings from our scoping study suggest that metabarcoding-based biomonitoring surveys should, if funds, time and expertise allow, be assessed using both eDNA and eRNA products.
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Affiliation(s)
- Olivier Laroche
- School of Biological Sciences, University of Auckland, Auckland, New Zealand.,Environmental Technologies, Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
| | - Susanna A Wood
- Environmental Technologies, Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand.,Environmental Research Institute, University of Waikato, Hamilton, New Zealand
| | - Louis A Tremblay
- School of Biological Sciences, University of Auckland, Auckland, New Zealand.,Environmental Technologies, Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
| | - Gavin Lear
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Joanne I Ellis
- Red Sea Research Centre, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Xavier Pochon
- Environmental Technologies, Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand.,Institute of Marine Science, University of Auckland, Auckland, New Zealand
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Novel benthic foraminifera are abundant and diverse in an area of the abyssal equatorial Pacific licensed for polymetallic nodule exploration. Sci Rep 2017; 7:45288. [PMID: 28382941 PMCID: PMC5382569 DOI: 10.1038/srep45288] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Accepted: 02/15/2017] [Indexed: 11/10/2022] Open
Abstract
The benthic biota of the Clarion–Clipperton Zone (CCZ, abyssal eastern equatorial Pacific) is the focus of a major research effort linked to possible future mining of polymetallic nodules. Within the framework of ABYSSLINE, a biological baseline study conducted on behalf of Seabed Resources Development Ltd. in the UK-1 exploration contract area (eastern CCZ, ~4,080 m water depth), we analysed foraminifera (testate protists), including ‘live’ (Rose Bengal stained) and dead tests, in 5 cores (0–1 cm layer, >150-μm fraction) recovered during separate megacorer deployments inside a 30 by 30 km seafloor area. In both categories (live and dead) we distinguished between complete and fragmented specimens. The outstanding feature of these assemblages is the overwhelming predominance of monothalamids, a group often ignored in foraminiferal studies. These single-chambered foraminifera, which include agglutinated tubes, spheres and komokiaceans, represented 79% of 3,607 complete tests, 98% of 1,798 fragments and 76% of the 416 morphospecies (live and dead combined) in our samples. Only 3.1% of monothalamid species and 9.8% of all species in the UK-1 assemblages are scientifically described and many are rare (29% singletons). Our results emphasise how little is known about foraminifera in abyssal areas that may experience major impacts from future mining activities.
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Guardiola M, Wangensteen OS, Taberlet P, Coissac E, Uriz MJ, Turon X. Spatio-temporal monitoring of deep-sea communities using metabarcoding of sediment DNA and RNA. PeerJ 2016; 4:e2807. [PMID: 28028473 PMCID: PMC5180584 DOI: 10.7717/peerj.2807] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 11/20/2016] [Indexed: 11/20/2022] Open
Abstract
We assessed spatio-temporal patterns of diversity in deep-sea sediment communities using metabarcoding. We chose a recently developed eukaryotic marker based on the v7 region of the 18S rRNA gene. Our study was performed in a submarine canyon and its adjacent slope in the Northwestern Mediterranean Sea, sampled along a depth gradient at two different seasons. We found a total of 5,569 molecular operational taxonomic units (MOTUs), dominated by Metazoa, Alveolata and Rhizaria. Among metazoans, Nematoda, Arthropoda and Annelida were the most diverse. We found a marked heterogeneity at all scales, with important differences between layers of sediment and significant changes in community composition with zone (canyon vs slope), depth, and season. We compared the information obtained from metabarcoding DNA and RNA and found more total MOTUs and more MOTUs per sample with DNA (ca. 20% and 40% increase, respectively). Both datasets showed overall similar spatial trends, but most groups had higher MOTU richness with the DNA template, while others, such as nematodes, were more diverse in the RNA dataset. We provide metabarcoding protocols and guidelines for biomonitoring of these key communities in order to generate information applicable to management efforts.
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Affiliation(s)
- Magdalena Guardiola
- Department of Marine Ecology, Centre for Advanced Studies of Blanes (CEAB-CSIC) , Blanes , Spain
| | - Owen S Wangensteen
- Department of Animal Biology and Biodiversity Research Institute (IRBIO), University of Barcelona, Barcelona, Spain; Ecosystems & Environment Research Centre, School of Environment & Life Sciences, University of Salford, Salford, United Kingdom
| | - Pierre Taberlet
- Laboratoire d'Ecologie Alpine (LECA), Centre National de la Recherche Scientifique and Université Grenoble-Alpes , Grenoble , France
| | - Eric Coissac
- Laboratoire d'Ecologie Alpine (LECA), Centre National de la Recherche Scientifique and Université Grenoble-Alpes , Grenoble , France
| | - María Jesús Uriz
- Department of Marine Ecology, Centre for Advanced Studies of Blanes (CEAB-CSIC) , Blanes , Spain
| | - Xavier Turon
- Department of Marine Ecology, Centre for Advanced Studies of Blanes (CEAB-CSIC) , Blanes , Spain
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Laroche O, Wood SA, Tremblay LA, Ellis JI, Lejzerowicz F, Pawlowski J, Lear G, Atalah J, Pochon X. First evaluation of foraminiferal metabarcoding for monitoring environmental impact from an offshore oil drilling site. MARINE ENVIRONMENTAL RESEARCH 2016; 120:225-235. [PMID: 27595900 DOI: 10.1016/j.marenvres.2016.08.009] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 08/12/2016] [Accepted: 08/23/2016] [Indexed: 06/06/2023]
Abstract
At present, environmental impacts from offshore oil and gas activities are partly determined by measuring changes in macrofauna diversity. Morphological identification of macrofauna is time-consuming, expensive and dependent on taxonomic expertise. In this study, we evaluated the applicability of using foraminiferal-specific metabarcoding for routine monitoring. Sediment samples were collected along distance gradients from two oil platforms off Taranaki (New Zealand) and their physico-chemical properties, foraminiferal environmental DNA/RNA, and macrofaunal composition analyzed. Macrofaunal and foraminiferal assemblages showed similar shifts along impact gradients, but responded differently to environmental perturbations. Macrofauna were affected by hypoxia, whereas sediment grain size appeared to drive shifts in foraminifera. We identified eight foraminiferal molecular operational taxonomic units that have potential to be used as bioindicator taxa. Our results show that metabarcoding represents an effective tool for assessing foraminiferal communities near offshore oil and gas platforms, and that it can be used to complement current monitoring techniques.
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Affiliation(s)
- Olivier Laroche
- Environmental Technologies, Coastal and Freshwater Group, Cawthron Institute, Private Bag 2, Nelson 7042, New Zealand; School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand.
| | - Susanna A Wood
- Environmental Technologies, Coastal and Freshwater Group, Cawthron Institute, Private Bag 2, Nelson 7042, New Zealand; Environmental Research Institute, University of Waikato, Private Bag 3105, Hamilton 3240, New Zealand
| | - Louis A Tremblay
- Environmental Technologies, Coastal and Freshwater Group, Cawthron Institute, Private Bag 2, Nelson 7042, New Zealand; School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - Joanne I Ellis
- Red Sea Research Centre, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | | | - Jan Pawlowski
- Department of Genetics and Evolution, University of Geneva, Switzerland
| | - Gavin Lear
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - Javier Atalah
- Environmental Technologies, Coastal and Freshwater Group, Cawthron Institute, Private Bag 2, Nelson 7042, New Zealand
| | - Xavier Pochon
- Environmental Technologies, Coastal and Freshwater Group, Cawthron Institute, Private Bag 2, Nelson 7042, New Zealand; Institute of Marine Science, University of Auckland, Private Bag 349, Warkworth 0941, New Zealand
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Protist metabarcoding and environmental biomonitoring: Time for change. Eur J Protistol 2016; 55:12-25. [DOI: 10.1016/j.ejop.2016.02.003] [Citation(s) in RCA: 99] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Revised: 01/29/2016] [Accepted: 02/12/2016] [Indexed: 01/06/2023]
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Bacteria and Archaea diversity within the hot springs of Lake Magadi and Little Magadi in Kenya. BMC Microbiol 2016; 16:136. [PMID: 27388368 PMCID: PMC4936230 DOI: 10.1186/s12866-016-0748-x] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Accepted: 06/15/2016] [Indexed: 02/02/2023] Open
Abstract
Background Lake Magadi and little Magadi are hypersaline, alkaline lakes situated in the southern part of Kenyan Rift Valley. Solutes are supplied mainly by a series of alkaline hot springs with temperatures as high as 86 °C. Previous culture-dependent and culture-independent studies have revealed diverse groups of microorganisms thriving under these conditions. Previous culture independent studies were based on the analysis of 16S rDNA but were done on less saline lakes. For the first time, this study combined illumina sequencing and analysis of amplicons of both total community rDNA and 16S rRNA cDNA to determine the diversity and community structure of bacteria and archaea within 3 hot springs of L. Magadi and little Magadi. Methods Water, wet sediments and microbial mats were collected from springs in the main lake at a temperature of 45.1 °C and from Little Magadi “Nasikie eng’ida” (temperature of 81 °C and 83.6 °C). Total community DNA and RNA were extracted from samples using phenol-chloroform and Trizol RNA extraction protocols respectively. The 16S rRNA gene variable region (V4 – V7) of the extracted DNA and RNA were amplified and library construction performed following Illumina sequencing protocol. Sequences were analyzed done using QIIME while calculation of Bray-Curtis dissimilarities between datasets, hierarchical clustering, Non Metric Dimensional Scaling (NMDS) redundancy analysis (RDA) and diversity indices were carried out using the R programming language and the Vegan package. Results Three thousand four hundred twenty-six and one thousand nine hundred thirteen OTUs were recovered from 16S rDNA and 16S rRNA cDNA respectively. Uncultured diversity accounted for 89.35 % 16S rDNA and 87.61 % 16S rRNA cDNA reads. The most abundant phyla in both the 16S rDNA and 16S rRNA cDNA datasets included: Proteobacteria (8.33–50 %), Firmicutes 3.52–28.92 %, Bacteroidetes (3.45–26.44 %), Actinobacteria (0.98–28.57 %) and Euryarchaeota (3.55–34.48 %) in all samples. NMDS analyses of taxonomic composition clustered the taxa into three groups according to sample types (i.e. wet sediments, mats and water samples) with evident overlap of clusters between wet sediments and microbial mats from the three sample types in both DNA and cDNA datasets. The hot spring (45.1 °C) contained less diverse populations compared to those in Little Magadi (81–83 °C). Conclusion There were significant differences in microbial community structure at 95 % level of confidence for both total diversity (P value, 0.009) based on 16S rDNA analysis and active microbial diversity (P value, 0.01) based on 16S rRNA cDNA analysis, within the three hot springs. Differences in microbial composition and structure were observed as a function of sample type and temperature, with wet sediments harboring the highest diversity. Electronic supplementary material The online version of this article (doi:10.1186/s12866-016-0748-x) contains supplementary material, which is available to authorized users.
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Pochon X, Wood SA, Keeley NB, Lejzerowicz F, Esling P, Drew J, Pawlowski J. Accurate assessment of the impact of salmon farming on benthic sediment enrichment using foraminiferal metabarcoding. MARINE POLLUTION BULLETIN 2015; 100:370-382. [PMID: 26337228 DOI: 10.1016/j.marpolbul.2015.08.022] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2015] [Revised: 08/09/2015] [Accepted: 08/11/2015] [Indexed: 06/05/2023]
Abstract
Assessing the environmental impact of salmon farms on benthic systems is traditionally undertaken using biotic indices derived from microscopic analyses of macrobenthic infaunal (MI) communities. In this study, we tested the applicability of using foraminiferal-specific high-throughput sequencing (HTS) metabarcoding for monitoring these habitats. Sediment samples and physico-chemical data were collected along an enrichment gradient radiating out from three Chinook salmon (Oncorhynchus tshawytscha) farms in New Zealand. HTS of environmental DNA and RNA (eDNA/eRNA) resulted in 1,875,300 sequences that clustered into 349 Operational Taxonomic Units. Strong correlations were observed among various biotic indices calculated from MI data and normalized fourth-root transformed HTS data. Correlations were stronger using eRNA compared to eDNA data. Quantile regression spline analyses identified 12 key foraminiferal taxa that have potential to be used as bioindicator species. This study demonstrates the huge potential for using this method for biomonitoring of fish-farming and other marine industrial activities.
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Affiliation(s)
- X Pochon
- Environmental Technologies, Coastal and Freshwater Group, Cawthron Institute, Private Bag 2, Nelson 7042, New Zealand; Institute of Marine Science, University of Auckland, Private Bag 349, Warkworth 0941, New Zealand.
| | - S A Wood
- Environmental Technologies, Coastal and Freshwater Group, Cawthron Institute, Private Bag 2, Nelson 7042, New Zealand; Environmental Research Institute, University of Waikato, Private Bag 3105, Hamilton 3240, New Zealand
| | - N B Keeley
- Environmental Technologies, Coastal and Freshwater Group, Cawthron Institute, Private Bag 2, Nelson 7042, New Zealand; Institute of Marine Research, PO Box 1870, Bergen 5817, Norway
| | - F Lejzerowicz
- Department of Genetics and Evolution, University of Geneva, Switzerland
| | - P Esling
- Department of Genetics and Evolution, University of Geneva, Switzerland; IRCAM, UMR 9912, Université Pierre et Marie Curie, Paris, France
| | - J Drew
- Environmental Technologies, Coastal and Freshwater Group, Cawthron Institute, Private Bag 2, Nelson 7042, New Zealand
| | - J Pawlowski
- Department of Genetics and Evolution, University of Geneva, Switzerland
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Guardiola M, Uriz MJ, Taberlet P, Coissac E, Wangensteen OS, Turon X. Deep-Sea, Deep-Sequencing: Metabarcoding Extracellular DNA from Sediments of Marine Canyons. PLoS One 2015; 10:e0139633. [PMID: 26436773 PMCID: PMC4593591 DOI: 10.1371/journal.pone.0139633] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2015] [Accepted: 09/14/2015] [Indexed: 12/22/2022] Open
Abstract
Marine sediments are home to one of the richest species pools on Earth, but logistics and a dearth of taxonomic work-force hinders the knowledge of their biodiversity. We characterized α- and β-diversity of deep-sea assemblages from submarine canyons in the western Mediterranean using an environmental DNA metabarcoding. We used a new primer set targeting a short eukaryotic 18S sequence (ca. 110 bp). We applied a protocol designed to obtain extractions enriched in extracellular DNA from replicated sediment corers. With this strategy we captured information from DNA (local or deposited from the water column) that persists adsorbed to inorganic particles and buffered short-term spatial and temporal heterogeneity. We analysed replicated samples from 20 localities including 2 deep-sea canyons, 1 shallower canal, and two open slopes (depth range 100–2,250 m). We identified 1,629 MOTUs, among which the dominant groups were Metazoa (with representatives of 19 phyla), Alveolata, Stramenopiles, and Rhizaria. There was a marked small-scale heterogeneity as shown by differences in replicates within corers and within localities. The spatial variability between canyons was significant, as was the depth component in one of the canyons where it was tested. Likewise, the composition of the first layer (1 cm) of sediment was significantly different from deeper layers. We found that qualitative (presence-absence) and quantitative (relative number of reads) data showed consistent trends of differentiation between samples and geographic areas. The subset of exclusively benthic MOTUs showed similar patterns of β-diversity and community structure as the whole dataset. Separate analyses of the main metazoan phyla (in number of MOTUs) showed some differences in distribution attributable to different lifestyles. Our results highlight the differentiation that can be found even between geographically close assemblages, and sets the ground for future monitoring and conservation efforts on these bottoms of ecological and economic importance.
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Affiliation(s)
- Magdalena Guardiola
- Department of Marine Ecology, Center for Advanced Studies of Blanes (CEAB-CSIC), Girona, Spain
| | - María Jesús Uriz
- Department of Marine Ecology, Center for Advanced Studies of Blanes (CEAB-CSIC), Girona, Spain
| | - Pierre Taberlet
- Université Grenoble Alpes, Laboratoire d’Ecologie Alpine (LECA), F-38000, Grenoble, France
- Centre National de la Recherche Scientifique (CNRS), Laboratoire d’Ecologie Alpine (LECA), F-38000, Grenoble, France
| | - Eric Coissac
- Université Grenoble Alpes, Laboratoire d’Ecologie Alpine (LECA), F-38000, Grenoble, France
- Centre National de la Recherche Scientifique (CNRS), Laboratoire d’Ecologie Alpine (LECA), F-38000, Grenoble, France
| | - Owen Simon Wangensteen
- Department of Marine Ecology, Center for Advanced Studies of Blanes (CEAB-CSIC), Girona, Spain
- Department of Animal Biology, University of Barcelona, Barcelona, Spain
| | - Xavier Turon
- Department of Marine Ecology, Center for Advanced Studies of Blanes (CEAB-CSIC), Girona, Spain
- * E-mail:
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Visco JA, Apothéloz-Perret-Gentil L, Cordonier A, Esling P, Pillet L, Pawlowski J. Environmental Monitoring: Inferring the Diatom Index from Next-Generation Sequencing Data. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2015; 49:7597-7605. [PMID: 26052741 DOI: 10.1021/es506158m] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Diatoms are widely used as bioindicators for the assessment of water quality in rivers and streams. Classically, the diatom biotic indices are based on the relative abundance of morphologically identified species weighted by their autoecological value. Obtaining such indices is time-consuming, costly, and requires excellent taxonomic expertise, which is not always available. Here we tested the possibility to overcome these limitations using a next-generation sequencing (NGS) approach to identify and quantify diatoms found in environmental DNA and RNA samples. We analyzed 27 river sites in the Geneva area (Switzerland), in order to compare the values of the Swiss Diatom Index (DI-CH) computed either by microscopic quantification of diatom species or directly from NGS data. Despite gaps in the reference database and variations in relative abundance of analyzed species, the diatom index shows a significant correlation between morphological and molecular data indicating similar biological quality status for the majority of sites. This proof-of-concept study demonstrates the potential of the NGS approach for identification and quantification of diatoms in environmental samples, opening new avenues toward the routine application of genetic tools for bioassessment and biomonitoring of aquatic ecosystems.
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Affiliation(s)
- Joana Amorim Visco
- †Department of Genetics and Evolution, University of Geneva, Boulevard d'Yvoy 4, CH 1205 Geneva, Switzerland
| | | | - Arielle Cordonier
- ‡Water Ecology Service, Department of Environment, Transports and Agriculture, Canton of Geneva, CH 1205 Geneva, Switzerland
| | - Philippe Esling
- †Department of Genetics and Evolution, University of Geneva, Boulevard d'Yvoy 4, CH 1205 Geneva, Switzerland
- §IRCAM, UMR 9912, Université Pierre et Marie Curie, 4 place Jussieu, 75005 Paris, France
| | - Loïc Pillet
- †Department of Genetics and Evolution, University of Geneva, Boulevard d'Yvoy 4, CH 1205 Geneva, Switzerland
- ∥CNRS, UMR 7144, Laboratoire Adaptation et Diversité en Milieu Marin, Place Georges Teissier, CS90074, 29688 Roscoff, France
| | - Jan Pawlowski
- †Department of Genetics and Evolution, University of Geneva, Boulevard d'Yvoy 4, CH 1205 Geneva, Switzerland
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Geisen S, Laros I, Vizcaíno A, Bonkowski M, de Groot GA. Not all are free-living: high-throughput DNA metabarcoding reveals a diverse community of protists parasitizing soil metazoa. Mol Ecol 2015; 24:4556-69. [DOI: 10.1111/mec.13238] [Citation(s) in RCA: 102] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Revised: 04/28/2015] [Accepted: 05/06/2015] [Indexed: 01/02/2023]
Affiliation(s)
- S. Geisen
- Department of Terrestrial Ecology; Netherlands Institute of Ecology (NIOO-KNAW); PO Box 50 6700 AB Wageningen, the Netherlands
- Department of Terrestrial Ecology; Institute of Zoology; University of Cologne; Zülpicher Str 47b, 50674 Cologne Germany
| | - I. Laros
- ALTERRA - Wageningen UR; P.O. Box 47 6700 AA Wageningen The Netherlands
| | - A. Vizcaíno
- AllGenetics, Ed. de Servicios Centrales de Investigación; Campus de Elviña s/n E-15071 A Coruña Spain
| | - M. Bonkowski
- Department of Terrestrial Ecology; Institute of Zoology; University of Cologne; Zülpicher Str 47b, 50674 Cologne Germany
| | - G. A. de Groot
- ALTERRA - Wageningen UR; P.O. Box 47 6700 AA Wageningen The Netherlands
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Morard R, Darling KF, Mahé F, Audic S, Ujiié Y, Weiner AKM, André A, Seears HA, Wade CM, Quillévéré F, Douady CJ, Escarguel G, de Garidel-Thoron T, Siccha M, Kucera M, de Vargas C. PFR2: a curated database of planktonic foraminifera 18S ribosomal DNA as a resource for studies of plankton ecology, biogeography and evolution. Mol Ecol Resour 2015; 15:1472-85. [DOI: 10.1111/1755-0998.12410] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Revised: 03/25/2015] [Accepted: 03/27/2015] [Indexed: 11/29/2022]
Affiliation(s)
- Raphaël Morard
- Centre National de la Recherche Scientifique; UMR 7144; EPEP; Station Biologique de Roscoff; 29680 Roscoff France
- Sorbonne Universités; UPMC Univ Paris 06; UMR 7144; Station Biologique de Roscoff; 29680 Roscoff France
- MARUM Center for Marine Environmental Sciences; University of Bremen; Leobener Strasse 28359 Bremen Germany
| | - Kate F. Darling
- School of GeoSciences; University of Edinburgh; Edinburgh EH9 3JW UK
- School of Geography and GeoSciences; University of St Andrews; Fife KY16 9AL UK
| | - Frédéric Mahé
- Department of Ecology; Technische Universität Kaiserslautern; 67663 Kaiserslautern Germany
| | - Stéphane Audic
- Centre National de la Recherche Scientifique; UMR 7144; EPEP; Station Biologique de Roscoff; 29680 Roscoff France
- Sorbonne Universités; UPMC Univ Paris 06; UMR 7144; Station Biologique de Roscoff; 29680 Roscoff France
| | - Yurika Ujiié
- Department of Biology; Shinshu University; Asahi3-1-1 Matsumoto Nagano 390-8621 Japan
| | - Agnes K. M. Weiner
- MARUM Center for Marine Environmental Sciences; University of Bremen; Leobener Strasse 28359 Bremen Germany
| | - Aurore André
- CNRS UMR 5276; Laboratoire de Géologie de Lyon: Terre, Planètes, Environnement; Université Claude Bernard Lyon 1; 69622 Villeurbanne France
- UFR Sciences Exactes et Naturelles; Université de Reims-Champagne-Ardenne; Campus Moulin de la Housse Batiment 18 51100 Reims France
| | - Heidi A. Seears
- School of Life Sciences; University of Nottingham; University Park Nottingham NG7 2RD UK
- Department of Biological Sciences; Lehigh University; Iacocca Hall 111 Research Drive Bethlehem PA 18105 USA
| | - Christopher M. Wade
- School of Life Sciences; University of Nottingham; University Park Nottingham NG7 2RD UK
| | - Frédéric Quillévéré
- CNRS UMR 5276; Laboratoire de Géologie de Lyon: Terre, Planètes, Environnement; Université Claude Bernard Lyon 1; 69622 Villeurbanne France
| | - Christophe J. Douady
- UMR5023 Ecologie des Hydrosystèmes Naturels et Anthropisés; Université Lyon 1; ENTPE; CNRS; Université de Lyon; 6 rue Raphaël Dubois 69622 Villeurbanne France
- Institut Universitaire de France; 103 Boulevard Saint-Michel 75005 Paris France
| | - Gilles Escarguel
- CNRS UMR 5276; Laboratoire de Géologie de Lyon: Terre, Planètes, Environnement; Université Claude Bernard Lyon 1; 69622 Villeurbanne France
| | | | - Michael Siccha
- MARUM Center for Marine Environmental Sciences; University of Bremen; Leobener Strasse 28359 Bremen Germany
| | - Michal Kucera
- MARUM Center for Marine Environmental Sciences; University of Bremen; Leobener Strasse 28359 Bremen Germany
| | - Colomban de Vargas
- Centre National de la Recherche Scientifique; UMR 7144; EPEP; Station Biologique de Roscoff; 29680 Roscoff France
- Sorbonne Universités; UPMC Univ Paris 06; UMR 7144; Station Biologique de Roscoff; 29680 Roscoff France
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