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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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2
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Greco M, Al-Enezi E, Amao A, Francescangeli F, Cavaliere M, Bucci C, Toscanesi M, Trifuoggi M, Pawlowski J, Frontalini F. Deciphering the impact of decabromodiphenyl ether (BDE-209) on benthic foraminiferal communities: Insights from Cell-Tracker Green staining and eDNA metabarcoding. JOURNAL OF HAZARDOUS MATERIALS 2024; 466:133652. [PMID: 38309158 DOI: 10.1016/j.jhazmat.2024.133652] [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: 11/06/2023] [Revised: 01/11/2024] [Accepted: 01/26/2024] [Indexed: 02/05/2024]
Abstract
This study investigates the ecotoxicological effects of BDE-209, a persistent organic pollutant (POP) prevalent in Kuwait's coastal-industrial areas, on benthic foraminiferal communities. We conducted a mesocosm experiment in which we exposed benthic foraminiferal communities sampled from the coastal-industrial areas of Kuwait to a gradient of BDE-209 concentrations (0.01 to 20 mg/kg). The impact of exposure was assessed using live-staining and metabarcoding techniques. Despite the significantly different taxonomic compositions detected by the two techniques, our results show that BDE-209 significantly affects foraminiferal communities, with moderately high concentrations leading to reduced α-diversity and considerable taxonomic shifts in both molecular and morphological assemblages. At concentrations of 10 and 20 mg/kg, no living foraminifera were detected after 8 weeks, suggesting a threshold for their survival under BDE-209 exposure. The parallel responses of molecular and morphological communities confirm the reliability of both assessment methods. This study is the first to investigate the reaction of eukaryotic communities, specifically foraminifera, to POPs such as BDE-209, generating valuable insights that have the potential to enhance field studies and aid the refinement of sediment quality guidelines.
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Affiliation(s)
- Mattia Greco
- Institut de Ciències del Mar, Passeig Marítim de la Barceloneta, 37-49, Barcelona, Spain.
| | - Eqbal Al-Enezi
- Environment & Life Sciences Research Center, Kuwait Institute for Scientific Research, P.O. Box 24885, Safat 13109, Kuwait.
| | - Abduljamiu Amao
- Center for Integrative Petroleum Research, College of Petroleum Engineering and Geosciences, King Fahd University of Petroleum and Minerals, P.O. Box 5070, 31261 Dhahran, Saudi Arabia.
| | - Fabio Francescangeli
- Department of Geosciences, University of Fribourg, Chemin du Musée 6, 1700 Fribourg/Freiburg, Switzerland.
| | - Marco Cavaliere
- Department of Pure and Applied Sciences, Urbino University, Campus Scientifico, via Ca le Suore 2/4, 61029 Urbino, Italy.
| | - Carla Bucci
- Department of Pure and Applied Sciences, Urbino University, Campus Scientifico, via Ca le Suore 2/4, 61029 Urbino, Italy.
| | - Maria Toscanesi
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia 21, 80126 Naples, Italy.
| | - Marco Trifuoggi
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia 21, 80126 Naples, Italy.
| | - Jan Pawlowski
- ID-Gene ecodiagnostics Ltd, 109 ch. du Pont-du-Centenaire, 1228 Plan-les-Ouates, Switzerland; Institute of Oceanology, Polish Academy of Sciences, Powstańców Warszawy 55, Sopot 81-712, Poland.
| | - Fabrizio Frontalini
- Department of Pure and Applied Sciences, Urbino University, Campus Scientifico, via Ca le Suore 2/4, 61029 Urbino, Italy.
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3
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Rishan ST, Kline RJ, Rahman MS. Exploitation of environmental DNA (eDNA) for ecotoxicological research: A critical review on eDNA metabarcoding in assessing marine pollution. CHEMOSPHERE 2024; 351:141238. [PMID: 38242519 DOI: 10.1016/j.chemosphere.2024.141238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 01/05/2024] [Accepted: 01/15/2024] [Indexed: 01/21/2024]
Abstract
The rise in worldwide population has led to a noticeable spike in the production, consumption, and transportation of energy and food, contributing to elevated environmental pollution. Marine pollution is a significant global environmental issue with ongoing challenges, including plastic waste, oil spills, chemical pollutants, and nutrient runoff, threatening marine ecosystems, biodiversity, and human health. Pollution detection and assessment are crucial to understanding the state of marine ecosystems. Conventional approaches to pollution evaluation usually represent laborious and prolonged physical and chemical assessments, constraining their efficacy and expansion. The latest advances in environmental DNA (eDNA) are valuable methods for the detection and surveillance of pollution in the environment, offering enhanced sensibility, efficacy, and involvement. Molecular approaches allow genetic information extraction from natural resources like water, soil, or air. The application of eDNA enables an expanded evaluation of the environmental condition by detecting both identified and unidentified organisms and contaminants. eDNA methods are valuable for assessing community compositions, providing indirect insights into the intensity and quality of marine pollution through their effects on ecological communities. While eDNA itself is not direct evidence of pollution, its analysis offers a sensitive tool for monitoring changes in biodiversity, serving as an indicator of environmental health and allowing for the indirect estimation of the impact and extent of marine pollution on ecosystems. This review explores the potential of eDNA metabarcoding techniques for detecting and identifying marine pollutants. This review also provides evidence for the efficacy of eDNA assessment in identifying a diverse array of marine pollution caused by oil spills, harmful algal blooms, heavy metals, ballast water, and microplastics. In this report, scientists can expand their knowledge and incorporate eDNA methodologies into ecotoxicological research.
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Affiliation(s)
- Sakib Tahmid Rishan
- Biochemistry and Molecular Biology Program, School of Integrative Biological and Chemical Sciences, University of Texas Rio Grande Valley, Brownsville, Texas, USA
| | - Richard J Kline
- Biochemistry and Molecular Biology Program, School of Integrative Biological and Chemical Sciences, University of Texas Rio Grande Valley, Brownsville, Texas, USA; School of Earth, Environmental, and Marine Sciences, University of Texas Rio Grande Valley, Brownsville, Texas, USA
| | - Md Saydur Rahman
- Biochemistry and Molecular Biology Program, School of Integrative Biological and Chemical Sciences, University of Texas Rio Grande Valley, Brownsville, Texas, USA; School of Earth, Environmental, and Marine Sciences, University of Texas Rio Grande Valley, Brownsville, Texas, USA.
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4
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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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5
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Papaioannou C, Geladakis G, Kommata V, Batargias C, Lagoumintzis G. Insights in Pharmaceutical Pollution: The Prospective Role of eDNA Metabarcoding. TOXICS 2023; 11:903. [PMID: 37999555 PMCID: PMC10675236 DOI: 10.3390/toxics11110903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 10/30/2023] [Accepted: 11/02/2023] [Indexed: 11/25/2023]
Abstract
Environmental pollution is a growing threat to natural ecosystems and one of the world's most pressing concerns. The increasing worldwide use of pharmaceuticals has elevated their status as significant emerging contaminants. Pharmaceuticals enter aquatic environments through multiple pathways related to anthropogenic activity. Their high consumption, insufficient waste treatment, and the incapacity of organisms to completely metabolize them contribute to their accumulation in aquatic environments, posing a threat to all life forms. Various analytical methods have been used to quantify pharmaceuticals. Biotechnology advancements based on next-generation sequencing (NGS) techniques, like eDNA metabarcoding, have enabled the development of new methods for assessing and monitoring the ecotoxicological effects of pharmaceuticals. eDNA metabarcoding is a valuable biomonitoring tool for pharmaceutical pollution because it (a) provides an efficient method to assess and predict pollution status, (b) identifies pollution sources, (c) tracks changes in pharmaceutical pollution levels over time, (d) assesses the ecological impact of pharmaceutical pollution, (e) helps prioritize cleanup and mitigation efforts, and (f) offers insights into the diversity and composition of microbial and other bioindicator communities. This review highlights the issue of aquatic pharmaceutical pollution while emphasizing the importance of using modern NGS-based biomonitoring actions to assess its environmental effects more consistently and effectively.
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Affiliation(s)
- Charikleia Papaioannou
- Department of Biology, University of Patras, 26504 Patras, Greece; (C.P.); (G.G.); (V.K.)
| | - George Geladakis
- Department of Biology, University of Patras, 26504 Patras, Greece; (C.P.); (G.G.); (V.K.)
| | - Vasiliki Kommata
- Department of Biology, University of Patras, 26504 Patras, Greece; (C.P.); (G.G.); (V.K.)
| | - Costas Batargias
- Department of Biology, University of Patras, 26504 Patras, Greece; (C.P.); (G.G.); (V.K.)
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6
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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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7
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Wang Z, Liu L, Tang Y, Li A, Liu C, Xie C, Xiao L, Lu S. Phytoplankton community and HAB species in the South China Sea detected by morphological and metabarcoding approaches. HARMFUL ALGAE 2022; 118:102297. [PMID: 36195422 DOI: 10.1016/j.hal.2022.102297] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 07/23/2022] [Accepted: 08/01/2022] [Indexed: 06/16/2023]
Abstract
The southern Chinese coast is one of the most developed regions in China and is an area where harmful algal blooms (HABs) have occurred frequently. In this study, differences in the phytoplankton community between microscopic observations and 18S rDNA metabarcoding were compared in 89 surface water samples collected from the southern Chinese coast and the western South China Sea (SCS). This is the first report investigating the phytoplankton community and HAB species using a combination of morphological and metabarcoding approaches in this sea area. There were substantial differences in phytoplankton community structure detected by the two methods. Microscopic observation revealed diatom predominance in the phytoplankton community, while metabarcoding indicated dinoflagellate dominance. The phytoplankton community structure obtained by microscopic observation better reflects the real situation in the water column. Metabarcoding annotated more species than morphospecies observed by microscopy. Haptophyta and Cryptophyta were the specific phyla detected in metabarcoding but were missed in microscopy due to their small size. Conversely, some taxa were found in microscopic analysis alone, such as species in Dinophysis, Prorocentrum, and Scrippsiella, suggesting some biases during metabarcoding and gaps in sequence databases. Metabarcoding is superior for detecting morphologically cryptic, small-sized and HAB taxa, such as unarmored dinoflagellates, nanosized hatophytes and chlorophytes, as well as multiple species in Alexandrium, Pseudonitzschia, and Chaetoceros in our study. A total of 62 HAB taxa were identified in this study, including blooming and potentially toxic species. Diatom abundances generally decreased southward, while those of dinoflagellates and haptophytes showed the opposite trend. Chlorophytes were mainly distributed in coastal waters, especially in the Pearl River Estuary. Phytoplankton community structures were shaped by nutrients and salinity, and phosphorus was the most limiting factor for phytoplankton growth. The phytoplankton community in the western SCS showed unique characteristics away from those in the coastal sea areas. The results suggest that the combination of morphological and metabarcoding approaches comprehensively reveals the phytoplankton community structure and diversity of HAB species.
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Affiliation(s)
- Zhaohui Wang
- College of Life Science and Technology, Jinan University, Guangzhou, 510632, China.
| | - Lei Liu
- College of Life Science and Technology, Jinan University, Guangzhou, 510632, China
| | - Yali Tang
- College of Life Science and Technology, Jinan University, Guangzhou, 510632, China
| | - Aifeng Li
- College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China
| | - Chao Liu
- College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China
| | - Changliang Xie
- College of Life Science and Technology, Jinan University, Guangzhou, 510632, China
| | - Lijuan Xiao
- College of Life Science and Technology, Jinan University, Guangzhou, 510632, China.
| | - Songhui Lu
- College of Life Science and Technology, Jinan University, Guangzhou, 510632, China.
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8
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Greco M, Lejzerowicz F, Reo E, Caruso A, Maccotta A, Coccioni R, Pawlowski J, Frontalini F. Environmental RNA outperforms eDNA metabarcoding in assessing impact of marine pollution: A chromium-spiked mesocosm test. CHEMOSPHERE 2022; 298:134239. [PMID: 35292278 DOI: 10.1016/j.chemosphere.2022.134239] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 02/09/2022] [Accepted: 03/04/2022] [Indexed: 06/14/2023]
Abstract
Environmental (e)DNA metabarcoding holds great promise for biomonitoring and ecotoxicological applications. However, few studies have compared the performance of eDNA versus eRNA metabarcoding in assessing organismal response to marine pollution, in experimental conditions. Here, we performed a chromium (Cr)-spiked mesocosm experimental test on benthic foraminiferal community to investigate the effects on species diversity by analysing both eDNA and eRNA metabarcoding data across different Cr concentrations in the sediment. Foraminiferal diversity in the eRNA data showed a significant negative correlation with the Cr concentration in the sediment, while a positive response was observed in the eDNA data. The foraminiferal OTUs exhibited a higher turnover rate in eRNA than in the eDNA-derived community. Furthermore, in the eRNA samples, OTUs abundance was significantly affected by the Cr gradient in the sediment (Pseudo-R2 = 0.28, p = 0.05), while no significant trend was observed in the eDNA samples. The correlation between Cr concentration and foraminiferal diversity in eRNA datasets was stronger when the less abundant OTUs (<100 reads) were removed and the analyses were conducted exclusively on OTUs shared between eRNA and eDNA datasets. This indicates the importance of metabarcoding data filtering to capture ecological impacts, in addition to using the putatively active organisms in the eRNA dataset. The comparative analyses on foraminiferal diversity revealed that eRNA-based metabarcoding can better assess the response to heavy metal exposure in presence of subtle concentrations of the pollutant. Furthermore, our results suggest that to unlock the full potential for ecosystem assessment, eDNA and eRNA should be studied in parallel to control for potential sequence artifacts in routine ecosystem surveys.
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Affiliation(s)
- Mattia Greco
- Institute of Oceanology, Polish Academy of Sciences, 81-712, Sopot, Poland.
| | - Franck Lejzerowicz
- Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA.
| | - Emanuela Reo
- Department of Genetics and Evolution, University of Geneva, Genève, Switzerland.
| | - Antonio Caruso
- Dipartimento di Scienze della Terra e del Mare (DiSTeM), Università di Palermo, Palermo, Italy.
| | - Antonella Maccotta
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche (STEBICEF), Università di Palermo, Palermo, Italy.
| | | | - Jan Pawlowski
- Institute of Oceanology, Polish Academy of Sciences, 81-712, Sopot, Poland; Department of Genetics and Evolution, University of Geneva, Genève, Switzerland; ID-Gene Ecodiagnostics, Chemin du Pont-du-Centenaire 109, CH-1228, Plan-les-Ouates, Switzerland.
| | - Fabrizio Frontalini
- Dipartimento di Scienze Pure e Applicate, University of Urbino, Urbino, Italy.
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9
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Mailli AA, Jakt LM, Reiss H, Kopp ME, Moum TB. Exploring the potential of mRNA for taxonomic delineation of marine benthic eukaryotes. Mar Genomics 2022; 62:100934. [DOI: 10.1016/j.margen.2022.100934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 02/08/2022] [Accepted: 02/08/2022] [Indexed: 10/19/2022]
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10
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Thakur R, Collens A, Greco M, Sleith RS, Grattepanche JD, Katz LA. Newly designed foraminifera primers identify habitat-specific lineages through metabarcoding analyses. J Eukaryot Microbiol 2022; 69:e12913. [PMID: 35332619 DOI: 10.1111/jeu.12913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Foraminifera include diverse shell-building lineages found in a wide array of aquatic habitats from the deep-sea to intertidal zones to brackish and freshwater ecosystems. Recent estimates of morphological and molecular foraminifera diversity have increased the knowledge of foraminiferal diversity, which is critical as these lineages are used as bioindicators of past and present environmental perturbation. However, a comparative analysis of foraminiferal biodiversity between their major habitats (freshwater, brackish, intertidal, and marine) is underexplored, particularly using molecular tools. Here, we present metabarcoding survey of foraminiferal diversity across different ecosystems using newly designed foraminifera-specific primers that target the hypervariable regions of the foraminifera SSU-rRNA gene (~250-300bp long). We tested these primer sets on four foraminifera species and then across several environments: the intertidal zone, coastal ecosystems, and freshwater vernal pools. We retrieved 655 operational taxonomic units (OTUs); the majority are undetermined taxa that have no closely-matching sequences in the database. Furthermore, we identified 163 OTUs with distinct habitat preferences. Most of the observed OTUs belonged to lineages of single-chambered foraminifera, including poorly explored freshwater foraminifera which encompass a clade of Reticulomyxa-like forms. Our pilot study provides the community with an additional set of newly designed and taxon-specific primers to elucidate foraminiferal diversity across different habitats.
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Affiliation(s)
- Rabindra Thakur
- Smith College, Department of Biological Science, Northampton, Massachusetts, USA.,University of Massachusetts Amherst, Program in Organismic and Evolutionary Biology, Amherst, Massachusetts, USA
| | - Adena Collens
- Smith College, Department of Biological Science, Northampton, Massachusetts, USA
| | - Mattia Greco
- Smith College, Department of Biological Science, Northampton, Massachusetts, USA.,Temple University, Department of Biology, Philadelphia, Pennsylvania, USA
| | - Robin S Sleith
- Smith College, Department of Biological Science, Northampton, Massachusetts, USA
| | - Jean-David Grattepanche
- Smith College, Department of Biological Science, Northampton, Massachusetts, USA.,Institute of Oceanology, Polish Academy of Sciences, Sopot, Poland
| | - Laura A Katz
- Smith College, Department of Biological Science, Northampton, Massachusetts, USA.,University of Massachusetts Amherst, Program in Organismic and Evolutionary Biology, Amherst, Massachusetts, USA
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11
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Beentjes KK, Barmentlo SH, Cieraad E, Schilthuizen M, van der Hoorn BB, Speksnijder AGCL, Trimbos KB. Environmental DNA metabarcoding reveals comparable responses to agricultural stressors on different trophic levels of a freshwater community. Mol Ecol 2021; 31:1430-1443. [PMID: 34908199 PMCID: PMC9306904 DOI: 10.1111/mec.16326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 11/17/2021] [Accepted: 12/06/2021] [Indexed: 11/29/2022]
Abstract
Freshwater habitats are under stress from agricultural land use, most notably the influx of neonicotinoid pesticides and increased nutrient pressure from fertilizer. Traditional studies investigating the effects of stressors on freshwater systems are often limited to a narrow range of taxa, depending heavily on morphological expertise. Additionally, disentanglement of multiple simultaneous stressors can be difficult in field studies, whereas controlled laboratory conditions do not accurately reflect natural conditions and food webs. To overcome these drawbacks, we investigated the impacts of two agricultural stressors (the neonicotinoid insecticide thiacloprid and fertilizer) in full‐factorial design in a semi‐natural research site, using environmental DNA sampling to study three different taxonomic groups representing three trophic levels: bacteria (decomposers), phytoplankton (primary producers), and chironomids (consumers). The results show considerable impact of both stressors across trophic levels, with an additive effect of fertilizer and thiacloprid on community composition at all levels. These findings suggest that agricultural stressors affect the entire food web, either directly or through cascade reactions. They are also consistent with morphological assessments that were performed in the same study site, even at a lower number of replicates. The study presented shows that the use of multimarker environmental DNA provides a more comprehensive assessment of stressor impacts across multiple trophic levels, at a higher taxonomic resolution than traditional surveys. Additionally, many putative novel bioindicators for both agricultural stressors were discovered. We encourage further investigations into stressors impacts at different trophic levels, which will lead to more effective monitoring and management of freshwater systems.
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Affiliation(s)
- Kevin K Beentjes
- Naturalis Biodiversity Center, Leiden, The Netherlands.,Institute of Biology Leiden, Leiden University, Leiden, The Netherlands
| | - S Henrik Barmentlo
- Institute of Environmental Sciences, Leiden University, Leiden, The Netherlands.,Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Ellen Cieraad
- Institute of Environmental Sciences, Leiden University, Leiden, The Netherlands.,Nelson-Marlborough Institute of Technology, Nelson, New Zealand
| | - Menno Schilthuizen
- Naturalis Biodiversity Center, Leiden, The Netherlands.,Institute of Biology Leiden, Leiden University, Leiden, The Netherlands
| | | | | | - Krijn B Trimbos
- Institute of Environmental Sciences, Leiden University, Leiden, The Netherlands
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12
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Dully V, Rech G, Wilding TA, Lanzén A, MacKichan K, Berrill I, Stoeck T. Comparing sediment preservation methods for genomic biomonitoring of coastal marine ecosystems. MARINE POLLUTION BULLETIN 2021; 173:113129. [PMID: 34784523 DOI: 10.1016/j.marpolbul.2021.113129] [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: 10/07/2021] [Revised: 11/04/2021] [Accepted: 11/06/2021] [Indexed: 06/13/2023]
Abstract
To avoid loss of genetic information in environmental DNA (eDNA) field samples, the preservation of nucleic acids during field sampling is a critical step. In the development of standard operating procedures (SOPs) for eDNA-based compliance monitoring, the effect of different routinely used sediment preservations on biological community structures serving as bioindicators has gone untested. We compared eDNA metabarcoding results of marine bacterial communities from sample aliquots that were treated with a nucleic acid preservation solution (treated samples) and aliquots that were frozen without further treatment (non-treated samples). Sediment samples were obtained from coastal locations subjected to different stressors (aquaculture, urbanization, industry). DNA extraction efficiency, bacterial community profiles, and measures of alpha- and beta-diversity were highly congruent between treated and non-treated samples. As both preservation methods provide the same relevant information to environmental managers and regulators, we recommend the inclusion of both methods into SOPs for biomonitoring in marine coastal environments.
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Affiliation(s)
- Verena Dully
- Technische Universität Kaiserslautern, Ecology, D-67663 Kaiserslautern, Germany
| | - Giulia Rech
- Technische Universität Kaiserslautern, Ecology, D-67663 Kaiserslautern, Germany
| | - Thomas A Wilding
- Scottish Association for Marine Science, Scottish Marine Institute, Oban, Scotland, United Kingdom
| | - Anders Lanzén
- AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), Pasaia, Gipuzkoa, Spain; IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
| | | | - Iain Berrill
- Scottish Salmon Producers Organization, Edinburgh, Scotland, United Kingdom
| | - Thorsten Stoeck
- Technische Universität Kaiserslautern, Ecology, D-67663 Kaiserslautern, Germany.
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13
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Distribution Patterns of Benthic Foraminifera in Fish Farming Areas (Corsica, France): Implications for the Implementation of Biotic Indices in Biomonitoring Studies. WATER 2021. [DOI: 10.3390/w13202821] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Corsican marine aquaculture is one of the highest contributors of fish production in France, which may result in environmental perturbations caused by organic matter (OM) accumulation under fish farms and impacting natural communities. This study aimed to (1) characterise the environmental conditions at two different fish farms, (2) monitor the response of benthic foraminiferal species to this activity, and (3) assess the accuracy of existing foraminiferal biotic indices. In 2017, sea floor sediment was sampled in transects from two Corsican fish farms for living foraminiferal and sedimentary analyses. Four indices were calculated and compared: exp(H′bc), Foram-AMBI, Foram Stress Index and TSI-Med. A significant increase in total organic carbon (TOC) has been shown, mainly below the fish cages. Communities were characterized by a shift from high density, opportunistic and tolerant species under the cages to lower densities and more sensitive species further away. According to their distribution patterns along the TOC gradient, we propose to update the ecological group classification of seven species to improve Foram-AMBI’s accuracy and sensitivity: Triloculina oblonga and Quinqueloculina lamarckiana to Ecological Group (EG) I; Rosalina bradyi to EGIII; and Bolivina dilatata, Bulimina aculeata and Quinqueloculina stalkeri to EGIV. We recommend prioritising the use of TSI-Med and Foram-AMBI with the updated list to assess ecological quality in coastal waters of the Mediterranean Sea.
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14
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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: 15] [Impact Index Per Article: 5.0] [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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15
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Cordier T, Alonso‐Sáez L, Apothéloz‐Perret‐Gentil L, Aylagas E, Bohan DA, Bouchez A, Chariton A, Creer S, Frühe L, Keck F, Keeley N, Laroche O, Leese F, Pochon X, Stoeck T, Pawlowski J, Lanzén A. Ecosystems monitoring powered by environmental genomics: A review of current strategies with an implementation roadmap. Mol Ecol 2021; 30:2937-2958. [PMID: 32416615 PMCID: PMC8358956 DOI: 10.1111/mec.15472] [Citation(s) in RCA: 76] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 04/25/2020] [Accepted: 05/06/2020] [Indexed: 01/02/2023]
Abstract
A decade after environmental scientists integrated high-throughput sequencing technologies in their toolbox, the genomics-based monitoring of anthropogenic impacts on the biodiversity and functioning of ecosystems is yet to be implemented by regulatory frameworks. Despite the broadly acknowledged potential of environmental genomics to this end, technical limitations and conceptual issues still stand in the way of its broad application by end-users. In addition, the multiplicity of potential implementation strategies may contribute to a perception that the routine application of this methodology is premature or "in development", hence restraining regulators from binding these tools into legal frameworks. Here, we review recent implementations of environmental genomics-based methods, applied to the biomonitoring of ecosystems. By taking a general overview, without narrowing our perspective to particular habitats or groups of organisms, this paper aims to compare, review and discuss the strengths and limitations of four general implementation strategies of environmental genomics for monitoring: (a) Taxonomy-based analyses focused on identification of known bioindicators or described taxa; (b) De novo bioindicator analyses; (c) Structural community metrics including inferred ecological networks; and (d) Functional community metrics (metagenomics or metatranscriptomics). We emphasise the utility of the three latter strategies to integrate meiofauna and microorganisms that are not traditionally utilised in biomonitoring because of difficult taxonomic identification. Finally, we propose a roadmap for the implementation of environmental genomics into routine monitoring programmes that leverage recent analytical advancements, while pointing out current limitations and future research needs.
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Affiliation(s)
- Tristan Cordier
- Department of Genetics and EvolutionScience IIIUniversity of GenevaGenevaSwitzerland
| | - Laura Alonso‐Sáez
- AZTIMarine ResearchBasque Research and Technology Alliance (BRTA)Spain
| | | | - Eva Aylagas
- Red Sea Research Center (RSRC)Biological and Environmental Sciences and Engineering (BESE)King Abdullah University of Science and Technology (KAUST)ThuwalSaudi Arabia
| | - David A. Bohan
- AgroécologieINRAEUniversity of BourgogneUniversity Bourgogne Franche‐ComtéDijonFrance
| | | | - Anthony Chariton
- Department of Biological SciencesMacquarie UniversitySydneyNSWAustralia
| | - Simon Creer
- School of Natural SciencesBangor UniversityGwyneddUK
| | - Larissa Frühe
- Department of EcologyTechnische Universität KaiserslauternKaiserslauternGermany
| | | | - Nigel Keeley
- Benthic Resources and Processes GroupInstitute of Marine ResearchTromsøNorway
| | - Olivier Laroche
- Benthic Resources and Processes GroupInstitute of Marine ResearchTromsøNorway
| | - Florian Leese
- Aquatic Ecosystem ResearchFaculty of BiologyUniversity of Duisburg‐EssenEssenGermany
- Centre for Water and Environmental Research (ZWU)University of Duisburg‐EssenEssenGermany
| | - Xavier Pochon
- Coastal & Freshwater GroupCawthron InstituteNelsonNew Zealand
- Institute of Marine ScienceUniversity of AucklandWarkworthNew Zealand
| | - Thorsten Stoeck
- Department of EcologyTechnische Universität KaiserslauternKaiserslauternGermany
| | - Jan Pawlowski
- Department of Genetics and EvolutionScience IIIUniversity of GenevaGenevaSwitzerland
- ID‐Gene EcodiagnosticsGenevaSwitzerland
- Institute of OceanologyPolish Academy of SciencesSopotPoland
| | - Anders Lanzén
- AZTIMarine ResearchBasque Research and Technology Alliance (BRTA)Spain
- Basque Foundation for ScienceIKERBASQUEBilbaoSpain
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16
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He X, Gilmore SR, Sutherland TF, Hajibabaei M, Miller KM, Westfall KM, Pawlowski J, Abbott CL. Biotic signals associated with benthic impacts of salmon farms from eDNA metabarcoding of sediments. Mol Ecol 2021; 30:3158-3174. [PMID: 33481325 DOI: 10.1111/mec.15814] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 12/06/2020] [Accepted: 01/15/2021] [Indexed: 01/04/2023]
Abstract
Environmental DNA (eDNA) metabarcoding can rapidly characterize the composition and diversity of benthic communities, thus it has high potential utility for routine assessments of benthic impacts of marine finfish farming. In this study, 126 sediment grab samples from 42 stations were collected at six salmon farms in British Columbia, Canada. Benthic community changes were assessed by both eDNA metabarcoding of metazoans and macrofaunal polychaete surveys. The latter was done by analysing 11,466 individuals using a combination of morphology-based taxonomy and DNA barcoding. Study objectives were to: (i) compare biotic signals associated with benthic impacts of salmon farming in the two data sources, and (ii) identify potential eDNA indicators to facilitate monitoring in Canada. Alpha diversity parameters were consistently reduced near fish cage edge and negatively correlated with pore-water sulphide concentration, with coefficients ranging from -0.62 to -0.48. Although Polychaeta are a common indicator group, the negative correlation with pore-water sulphide concentration was much stronger for Nematoda OTU richness (correlation coefficient: -0.86) than for Polychaeta (correlation coefficient: -0.38). Presence/absence of Capitella generally agreed well between the two methods despite that they differed in the volume of sediments sampled and the molecular marker used. Multiple approaches were used to identify OTUs related to organic enrichment statuses. We demonstrate that eDNA metabarcoding generates biotic signals that could be leveraged for environmental assessment of benthic impacts of fish farms in multiple ways: both alpha diversity and Nematoda OTU richness could be used to assess the spatial extent of impact, and OTUs related to organic enrichment could be used to develop local biotic indices.
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Affiliation(s)
- Xiaoping He
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, BC, Canada
| | - Scott R Gilmore
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, BC, Canada
| | - Terri F Sutherland
- Pacific Science Enterprise Centre, Fisheries and Oceans Canada, West Vancouver, BC, Canada
| | - Mehrdad Hajibabaei
- Department of Integrative Biology & Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Kristina M Miller
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, BC, Canada
| | - Kristen M Westfall
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, BC, Canada
| | - Jan Pawlowski
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland.,Institute of Oceanology, Polish Academy of Sciences, Sopot, Poland.,ID-Gene Ecodiagnostics, Geneva, Switzerland
| | - Cathryn L Abbott
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, BC, Canada
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17
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Metabarcoding on both environmental DNA and RNA highlights differences between fungal communities sampled in different habitats. PLoS One 2020; 15:e0244682. [PMID: 33378355 PMCID: PMC7773206 DOI: 10.1371/journal.pone.0244682] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 12/14/2020] [Indexed: 12/14/2022] Open
Abstract
In recent years, metabarcoding has become a key tool to describe microbial communities from natural and artificial environments. Thanks to its high throughput nature, metabarcoding efficiently explores microbial biodiversity under different conditions. It can be performed on environmental (e)DNA to describe so-called total microbial community, or from environmental (e)RNA to describe active microbial community. As opposed to total microbial communities, active ones exclude dead or dormant organisms. For what concerns Fungi, which are mostly filamentous microorganisms, the relationship between DNA-based (total) and RNA-based (active) communities is unclear. In the present study, we evaluated the consequences of performing metabarcoding on both soil and wood-extracted eDNA and eRNA to delineate molecular operational taxonomic units (MOTUs) and differentiate fungal communities according to the environment they originate from. DNA and RNA-based communities differed not only in their taxonomic composition, but also in the relative abundances of several functional guilds. From a taxonomic perspective, we showed that several higher taxa are globally more represented in either “active” or “total” microbial communities. We also observed that delineation of MOTUs based on their co-occurrence among DNA and RNA sequences highlighted differences between the studied habitats that were overlooked when all MOTUs were considered, including those identified exclusively by eDNA sequences. We conclude that metabarcoding on eRNA provides original functional information on the specific roles of several taxonomic or functional groups that would not have been revealed using eDNA alone.
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18
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Aylagas E, Borja A, Pochon X, Zaiko A, Keeley N, Bruce K, Hong P, Ruiz GM, Stein ED, Theroux S, Geraldi N, Ortega A, Gajdzik L, Coker DJ, Katan Y, Hikmawan T, Saleem A, Alamer S, Jones BH, Duarte CM, Pearman J, Carvalho S. Translational Molecular Ecology in practice: Linking DNA-based methods to actionable marine environmental management. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 744:140780. [PMID: 32693276 DOI: 10.1016/j.scitotenv.2020.140780] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 07/02/2020] [Accepted: 07/04/2020] [Indexed: 06/11/2023]
Abstract
Molecular-based approaches can provide timely biodiversity assessments, showing an immense potential to facilitate decision-making in marine environmental management. However, the uptake of molecular data into environmental policy remains minimal. Here, we showcase a selection of local to global scale studies applying molecular-based methodologies for environmental management at various stages of implementation. Drawing upon lessons learned from these case-studies, we provide a roadmap to facilitate applications of DNA-based methods to marine policies and to overcome the existing challenges. The main impediment identified is the need for standardized protocols to guarantee data comparison across spatial and temporal scales. Adoption of Translational Molecular Ecology - the sustained collaboration between molecular ecologists and stakeholders, will enhance consensus with regards to the objectives, methods, and outcomes of environmental management projects. Establishing a sustained dialogue among stakeholders is key to accelerating the adoption of molecular-based approaches for marine monitoring and assessment.
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Affiliation(s)
- Eva Aylagas
- Red Sea Research Center (RSRC), Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia.
| | - Angel Borja
- AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), Herrera Kaia, Portualdea s/n, 20110 Pasaia, Spain
| | - Xavier Pochon
- 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
| | - Anastasija Zaiko
- 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
| | - Nigel Keeley
- Benthic Resources and Processors Group, Institute of Marine Research, Postboks 6606 Langnes, 9296 Tromsø, Norway
| | - Kat Bruce
- Nature Metrics Ltd, CABI site, Bakeham Lane, Egham TW20 9TY, United Kingdom
| | - Peiying Hong
- Water Desalination and Reuse Center, Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Gregory M Ruiz
- Smithsonian Environmental Research Center, 647 Contees Wharf Road, Edgewater, MD 21037, USA; Aquatic Bioinvasion Research and Policy Institute, Environmental Science and Management, Portland State University, Portland, OR 97201, USA
| | - Eric D Stein
- Southern California Coastal Water Research Project, 3535 Harbor Blvd., Suite 110, Costa Mesa, CA 92626-1437, USA
| | - Susanna Theroux
- Southern California Coastal Water Research Project, 3535 Harbor Blvd., Suite 110, Costa Mesa, CA 92626-1437, USA
| | - Nathan Geraldi
- Red Sea Research Center (RSRC), Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Alejandra Ortega
- Red Sea Research Center (RSRC), Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Laura Gajdzik
- Red Sea Research Center (RSRC), Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Darren J Coker
- Red Sea Research Center (RSRC), Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Yasser Katan
- Environmental Protection Department, Saudi Aramco, Dhahran 3131, Saudi Arabia
| | - Tyas Hikmawan
- Environmental Protection Department, Saudi Aramco, Dhahran 3131, Saudi Arabia
| | - Ammar Saleem
- The General Authority of Meteorology and Environmental Protection, The Ministry of Environment, Water and Agriculture, Saudi Arabia
| | - Sultan Alamer
- The General Authority of Meteorology and Environmental Protection, The Ministry of Environment, Water and Agriculture, Saudi Arabia
| | - Burton H Jones
- Red Sea Research Center (RSRC), Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Carlos M Duarte
- Red Sea Research Center (RSRC), Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - John Pearman
- Coastal and Freshwater Group, Cawthron Institute, Private Bag 2, Nelson 7042, New Zealand
| | - Susana Carvalho
- Red Sea Research Center (RSRC), Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
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19
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Mauffrey F, Cordier T, Apothéloz-Perret-Gentil L, Cermakova K, Merzi T, Delefosse M, Blanc P, Pawlowski J. Benthic monitoring of oil and gas offshore platforms in the North Sea using environmental DNA metabarcoding. Mol Ecol 2020; 30:3007-3022. [PMID: 33070453 DOI: 10.1111/mec.15698] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 09/15/2020] [Accepted: 10/09/2020] [Indexed: 12/12/2022]
Abstract
Since 2010, considerable efforts have been undertaken to monitor the environmental status of European marine waters and ensuring the development of methodological standards for the evaluation of this status. However, the current routine biomonitoring implicates time-consuming and costly manual sorting and morphological identification of benthic macrofauna. Environmental DNA (eDNA) metabarcoding represents an alternative to the traditional monitoring method with very promising results. Here, we tested it further by performing eDNA metabarcoding of benthic eukaryotic communities in the vicinity of two offshore oil and gas platforms in the North Sea. Three different genetic markers (18S V1V2, 18S V9 and COI) were used to assess the environmental pressures induced by the platforms. All markers showed patterns of alpha and beta diversity consistent with morphology-based macrofauna analyses. In particular, the communities' structure inferred from metabarcoding and morphological data significantly changed along distance gradients from the platforms. The impact of the operational discharges was also detected by the variation of biotic index values, AMBI index showing the best correlation between morphological and eDNA data sets. Finally, the sediment physicochemical parameters were used to build a local de novo pressure index that served as benchmark to test the potential of a taxonomy-free approach. Our study demonstrates that metabarcoding approach outperforms morphology-based approach and can be used as a cost and time-saving alternative solution to the traditional morphology-based monitoring in order to monitor more efficiently the impact of industrial activities on marine biodiversity.
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Affiliation(s)
- Florian Mauffrey
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland.,ID-Gene Ecodiagnostics, Campus Biotech Innovation Park, Geneva, Switzerland
| | - Tristan Cordier
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland.,ID-Gene Ecodiagnostics, Campus Biotech Innovation Park, Geneva, Switzerland
| | - Laure Apothéloz-Perret-Gentil
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland.,ID-Gene Ecodiagnostics, Campus Biotech Innovation Park, Geneva, Switzerland
| | - Kristina Cermakova
- ID-Gene Ecodiagnostics, Campus Biotech Innovation Park, Geneva, Switzerland
| | - Thomas Merzi
- Total SA, Centre Scientifique et Technique Jean Feger, Pau, France
| | | | - Philippe Blanc
- Total SA, Centre Scientifique et Technique Jean Feger, Pau, France
| | - Jan Pawlowski
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland.,ID-Gene Ecodiagnostics, Campus Biotech Innovation Park, Geneva, Switzerland.,Institute of Oceanology, Polish Academy of Sciences, Sopot, Poland
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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: 19] [Impact Index Per Article: 4.8] [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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Pearman JK, Keeley NB, Wood SA, Laroche O, Zaiko A, Thomson-Laing G, Biessy L, Atalah J, Pochon X. Comparing sediment DNA extraction methods for assessing organic enrichment associated with marine aquaculture. PeerJ 2020; 8:e10231. [PMID: 33194417 PMCID: PMC7597629 DOI: 10.7717/peerj.10231] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 10/02/2020] [Indexed: 12/21/2022] Open
Abstract
Marine sediments contain a high diversity of micro- and macro-organisms which are important in the functioning of biogeochemical cycles. Traditionally, anthropogenic perturbation has been investigated by identifying macro-organism responses along gradients. Environmental DNA (eDNA) analyses have recently been advocated as a rapid and cost-effective approach to measuring ecological impacts and efforts are underway to incorporate eDNA tools into monitoring. Before these methods can replace or complement existing methods, robustness and repeatability of each analytical step has to be demonstrated. One area that requires further investigation is the selection of sediment DNA extraction method. Environmental DNA sediment samples were obtained along a disturbance gradient adjacent to a Chinook (Oncorhynchus tshawytscha) salmon farm in Otanerau Bay, New Zealand. DNA was extracted using four extraction kits (Qiagen DNeasy PowerSoil, Qiagen DNeasy PowerSoil Pro, Qiagen RNeasy PowerSoil Total RNA/DNA extraction/elution and Favorgen FavorPrep Soil DNA Isolation Midi Kit) and three sediment volumes (0.25, 2, and 5 g). Prokaryotic and eukaryotic communities were amplified using primers targeting the 16S and 18S ribosomal RNA genes, respectively, and were sequenced on an Illumina MiSeq. Diversity and community composition estimates were obtained from each extraction kit, as well as their relative performance in established metabarcoding biotic indices. Differences were observed in the quality and quantity of the extracted DNA amongst kits with the two Qiagen DNeasy PowerSoil kits performing best. Significant differences were observed in both prokaryotes and eukaryotes (p < 0.001) richness among kits. A small proportion of amplicon sequence variants (ASVs) were shared amongst the kits (~3%) although these shared ASVs accounted for the majority of sequence reads (prokaryotes: 59.9%, eukaryotes: 67.2%). Differences were observed in the richness and relative abundance of taxonomic classes revealed with each kit. Multivariate analysis showed that there was a significant interaction between "distance" from the farm and "kit" in explaining the composition of the communities, with the distance from the farm being a stronger determinant of community composition. Comparison of the kits against the bacterial and eukaryotic metabarcoding biotic index suggested that all kits showed similar patterns along the environmental gradient. Overall, we advocate for the use of Qiagen DNeasy PowerSoil kits for use when characterizing prokaryotic and eukaryotic eDNA from marine farm sediments. We base this conclusion on the higher DNA quality values and richness achieved with these kits compared to the other kits/amounts investigated in this study. The additional advantage of the PowerSoil Kits is that DNA extractions can be performed using an extractor robot, offering additional standardization and reproducibility of results.
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Affiliation(s)
- John K. Pearman
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
| | | | - Susanna A. Wood
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
| | | | - Anastasija Zaiko
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
- Institute of Marine Science, University of Auckland, Auckland, New Zealand
| | | | - Laura Biessy
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
| | - Javier Atalah
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
| | - Xavier Pochon
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
- Institute of Marine Science, University of Auckland, Auckland, New Zealand
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22
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Fang J, Samuelsen OB, Strand Ø, Hansen PK, Jansen H. The effects of teflubenzuron on mortality, physiology and accumulation in Capitella sp. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2020; 203:111029. [PMID: 32888609 DOI: 10.1016/j.ecoenv.2020.111029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 07/08/2020] [Accepted: 07/10/2020] [Indexed: 06/11/2023]
Abstract
The chitin synthesis inhibitor teflubenzuron (TFB) is a feed antiparasitic agents used to impede molting of the salmon lice, an ecto-parasite that severely affects the salmon industry. Low absorption of oral administered TFB may cause elevated concentrations in the feces discharged from the salmon into the benthic environment. The polychaete Capitella sp. are often dominant in such habitats and consume organic waste deposited on the sediment. In the present study, Capitella sp. were exposed to doses of TFB in salmon feed of 1, 2 and 4 g TFB kg-1 (0 g TFB kg-1 in control group) over an experimental period of 32 days. Cumulative mortality was 12%-15% in both treatment groups with 1 and 2 g TFB kg-1 and reached 27% in the group with 4 g TFB kg-1. Only the highest dose (4 g TFB kg-1) negatively affected feed intake, growth and respiration of the polychaetes while food conversion efficiency was not affected. At the end of the experiment, the concentrations of TFB in the Capitella sp. were high, in the range of 9.24-10.32 μg g-1 for the three treatment groups. It was suggested that a maximum level of absorption rate was reached, also for the lowest dose. High concentrations of TFB in the Capitella sp. might pose a risk to crustaceans that forage for polychaetes in the vicinity of fish farms. We conclude that the effects of TFB on Capitella sp. may therefore primarily be to the predators rather than the Capitella sp.
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Affiliation(s)
- Jinghui Fang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, PR China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, PR China.
| | - Ole B Samuelsen
- Institute of Marine Research, P.O. Box 1870 Nordnes, Bergen, N-5817, Norway.
| | - Øivind Strand
- Institute of Marine Research, P.O. Box 1870 Nordnes, Bergen, N-5817, Norway
| | - Pia Kupka Hansen
- Institute of Marine Research, P.O. Box 1870 Nordnes, Bergen, N-5817, Norway
| | - Henrice Jansen
- Institute of Marine Research, P.O. Box 1870 Nordnes, Bergen, N-5817, Norway; Wageningen Marine Research, Yerseke, 4401 NT, the Netherlands
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23
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Broman E, Bonaglia S, Norkko A, Creer S, Nascimento FJA. High throughput shotgun sequencing of eRNA reveals taxonomic and derived functional shifts across a benthic productivity gradient. Mol Ecol 2020; 30:3023-3039. [PMID: 32706485 DOI: 10.1111/mec.15561] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 06/29/2020] [Accepted: 07/18/2020] [Indexed: 01/04/2023]
Abstract
Benthic macrofauna is regularly used in monitoring programmes, however the vast majority of benthic eukaryotic biodiversity lies mostly in microscopic organisms, such as meiofauna (invertebrates < 1 mm) and protists, that rapidly responds to environmental change. These communities have traditionally been hard to sample and handle in the laboratory, but DNA sequencing has made such work less time consuming. While DNA sequencing captures both alive and dead organisms, environmental RNA (eRNA) better targets living organisms or organisms of recent origin in the environment. Here, we assessed the biodiversity of three known bioindicator microeukaryote groups (nematodes, foraminifera, and ciliates) in sediment samples collected at seven coastal sites along an organic carbon (OC) gradient. We aimed to investigate if eRNA shotgun sequencing can be used to simultaneously detect differences in (i) biodiversity of multiple microeukaryotic communities; and (ii) functional feeding traits of nematodes. Results showed that biodiversity was lower for nematodes and foraminifera in high OC (6.2%-6.9%), when compared to low OC sediments (1.2%-2.8%). Dissimilarity in community composition increased for all three groups between Low OC and High OC, as well as the classified feeding type of nematode genera (with more nonselective deposit feeders in high OC sediment). High relative abundant genera included nematode Sabatieria and foraminifera Elphidium in high OC, and Cryptocaryon-like ciliates in low OC sediments. Considering that future sequencing technologies are likely to decrease in cost, the use of eRNA shotgun sequencing to assess biodiversity of benthic microeukaryotes could be a powerful tool in recurring monitoring programmes.
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Affiliation(s)
- Elias Broman
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden.,Baltic Sea Centre, Stockholm University, Stockholm, Sweden
| | - Stefano Bonaglia
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden.,Nordcee, Department of Biology, University of Southern Denmark, Odense, Denmark.,Department of Marine Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Alf Norkko
- Baltic Sea Centre, Stockholm University, Stockholm, Sweden.,Tvärminne Zoological Station, University of Helsinki, Hanko, Finland
| | - Simon Creer
- Molecular Ecology and Fisheries Genetics Laboratory, School of Natural Sciences, Bangor University, Bangor, UK
| | - Francisco J A Nascimento
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden.,Baltic Sea Centre, Stockholm University, Stockholm, Sweden
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24
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Frühe L, Cordier T, Dully V, Breiner HW, Lentendu G, Pawlowski J, Martins C, Wilding TA, Stoeck T. Supervised machine learning is superior to indicator value inference in monitoring the environmental impacts of salmon aquaculture using eDNA metabarcodes. Mol Ecol 2020; 30:2988-3006. [PMID: 32285497 DOI: 10.1111/mec.15434] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 03/17/2020] [Accepted: 03/31/2020] [Indexed: 01/02/2023]
Abstract
Increasing anthropogenic impact and global change effects on natural ecosystems has prompted the development of less expensive and more efficient bioassessments methodologies. One promising approach is the integration of DNA metabarcoding in environmental monitoring. A critical step in this process is the inference of ecological quality (EQ) status from identified molecular bioindicator signatures that mirror environmental classification based on standard macroinvertebrate surveys. The most promising approaches to infer EQ from biotic indices (BI) are supervised machine learning (SML) and the calculation of indicator values (IndVal). In this study we compared the performance of both approaches using DNA metabarcodes of bacteria and ciliates as bioindicators obtained from 152 samples collected from seven Norwegian salmon farms. Results from standard macroinvertebrate-monitoring of the same samples were used as reference to compare the accuracy of both approaches. First, SML outperformed the IndVal approach to infer EQ from eDNA metabarcodes. The Random Forest (RF) algorithm appeared to be less sensitive to noisy data (a typical feature of massive environmental sequence data sets) and uneven data coverage across EQ classes (a typical feature of environmental compliance monitoring scheme) compared to a widely used method to infer IndVals for the calculation of a BI. Second, bacteria allowed for a more accurate EQ assessment than ciliate eDNA metabarcodes. For the implementation of DNA metabarcoding into routine monitoring programmes to assess EQ around salmon aquaculture cages, we therefore recommend bacterial DNA metabarcodes in combination with SML to classify EQ categories based on molecular signatures.
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Affiliation(s)
- Larissa Frühe
- Ecology Group, Technische Universität Kaiserslautern, Kaiserslautern, Germany
| | - Tristan Cordier
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
| | - Verena Dully
- Ecology Group, Technische Universität Kaiserslautern, Kaiserslautern, Germany
| | - Hans-Werner Breiner
- Ecology Group, Technische Universität Kaiserslautern, Kaiserslautern, Germany
| | - Guillaume Lentendu
- Ecology Group, Technische Universität Kaiserslautern, Kaiserslautern, Germany
| | - Jan Pawlowski
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland.,ID-Gene Ecodiagnostics Ltd, Geneva, Switzerland.,Institute of Oceanology, Polish Academy of Sciences, Sopot, Poland
| | | | - Thomas A Wilding
- Scottish Marine Institute, Scottish Association for Marine Science, Oban, Scotland
| | - Thorsten Stoeck
- Ecology Group, Technische Universität Kaiserslautern, Kaiserslautern, Germany
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25
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Damak M, Fourati R, Elleuch B, Kallel M. Environmental quality assessment of the fish farms' impact in the Monastir Bay (eastern of Tunisia, Central Mediterranean): a benthic foraminiferal perspective. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2020; 27:9059-9074. [PMID: 31912392 DOI: 10.1007/s11356-019-07523-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 12/25/2019] [Indexed: 06/10/2023]
Abstract
Offshore fish farms have been active inside the Monastir Bay, Hammemet Gulf for over 10 years, but their environmental impact is still unknown. This study focuses on the evaluation of the fish farming activity impact in the Monastir Bay as revealed by geochemical and benthic foraminiferal data. Samples were collected around three fish cages at different water depths. Total organic carbon (TOC) and total phosphate (TP) in the sediment show higher values beneath the fish cages and decrease proportionally with distance from the cages. Living foraminiferal assemblages around fish farms are dominated by stress-tolerant species with higher abundances of Ammonia tepida, Rosalina bradyi, Elphidium crispum, and Peneroplis planatus. On the basis of our results, A. tepida and Quinqueloculina seminula are confirmed to be tolerant to elevated nutriment content, while Ammonia parkinsoniana seems to be more sensitive to organic enrichment. We also test the Foram-AMBI that is revealed to be a very promising tool by which evaluating the ecological quality status of marine sediment. The results of the present study confirm the suitability of living benthic foraminifera as bioindicators of organic enrichment induced by aquaculture activities.
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Affiliation(s)
- Mohamed Damak
- Laboratoire de Génie de l'Environnement et Écotechnologie (GEET), École National des Ingénieurs Sfax ENIS, Université de Sfax, BP 1173, 3038, Sfax, Tunisia.
- Association Notre Grand Bleu (NGO), Cap Marina, 5000, Monastir, Tunisia.
| | - Rania Fourati
- Laboratoire de Génie de l'Environnement et Écotechnologie (GEET), École National des Ingénieurs Sfax ENIS, Université de Sfax, BP 1173, 3038, Sfax, Tunisia
| | - Boubaker Elleuch
- Laboratoire de Génie de l'Environnement et Écotechnologie (GEET), École National des Ingénieurs Sfax ENIS, Université de Sfax, BP 1173, 3038, Sfax, Tunisia
| | - Monem Kallel
- Laboratoire de Génie de l'Environnement et Écotechnologie (GEET), École National des Ingénieurs Sfax ENIS, Université de Sfax, BP 1173, 3038, Sfax, Tunisia
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26
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Cordier T, Lanzén A, Apothéloz-Perret-Gentil L, Stoeck T, Pawlowski J. Embracing Environmental Genomics and Machine Learning for Routine Biomonitoring. Trends Microbiol 2019; 27:387-397. [DOI: 10.1016/j.tim.2018.10.012] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 10/17/2018] [Accepted: 10/30/2018] [Indexed: 01/28/2023]
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27
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He X, Sutherland TF, Pawlowski J, Abbott CL. Responses of foraminifera communities to aquaculture‐derived organic enrichment as revealed by environmental
DNA
metabarcoding. Mol Ecol 2019; 28:1138-1153. [DOI: 10.1111/mec.15007] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 11/28/2018] [Accepted: 12/26/2018] [Indexed: 01/19/2023]
Affiliation(s)
- Xiaoping He
- Pacific Biological Station, Fisheries and Oceans Canada Nanaimo British Columbia Canada
| | - Terri F. Sutherland
- Pacific Science Enterprise Centre, Fisheries and Oceans Canada West Vancouver British Columbia Canada
| | - Jan Pawlowski
- Department of Genetics and Evolution University of Geneva Geneva Switzerland
| | - Cathryn L. Abbott
- Pacific Biological Station, Fisheries and Oceans Canada Nanaimo British Columbia Canada
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28
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Cordier T, Frontalini F, Cermakova K, Apothéloz-Perret-Gentil L, Treglia M, Scantamburlo E, Bonamin V, Pawlowski J. Multi-marker eDNA metabarcoding survey to assess the environmental impact of three offshore gas platforms in the North Adriatic Sea (Italy). MARINE ENVIRONMENTAL RESEARCH 2019; 146:24-34. [PMID: 30890270 DOI: 10.1016/j.marenvres.2018.12.009] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 12/18/2018] [Accepted: 12/18/2018] [Indexed: 06/09/2023]
Abstract
The environmental DNA (eDNA) metabarcoding represents a new promising tool for biomonitoring and environmental impact assessment. One of the main advantages of eDNA metabarcoding, compared to the traditional morphotaxonomy-based methods, is to provide a more holistic biodiversity information that includes inconspicuous morphologically non-identifiable taxa. Here, we use eDNA metabarcoding to survey marine biodiversity in the vicinity of the three offshore gas platforms in North Adriatic Sea (Italy). We isolated eDNA from 576 water and sediment samples collected at 32 sampling sites situated along four axes at increasing distances from the gas platforms. We obtained about 46 million eDNA sequences for 5 markers from nuclear 18S V1V2, 18S V4, 18S 37F and mitochondrial 16S and COI genes that cover a wide diversity of benthic and planktonic eukaryotes. Our results showed some impact of platform activities on benthic and pelagic communities at very close distance (<50 m), while communities for intermediate (125 m, 250 m, 500 m) and reference (1000 m, 2000 m) sites did not show any particular biodiversity changes that could be related to platforms activities. The most significant community change along the distance gradient was obtained with the 18S V1V2 marker targeting benthic eukaryotes, even though other markers showed similar trends, but to a lesser extent. These results were congruent with the AMBI index inferred from the eDNA sequences assigned to benthic macrofauna. We finally explored the relation between various physicochemical parameters, including hydrocarbons, on benthic community in the case of one of the platforms. Our results showed that these communities were not significantly impacted by most of hydrocarbons, but rather by macro-elements and sediment texture.
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Affiliation(s)
- Tristan Cordier
- Department of Genetics and Evolution, University of Geneva, Switzerland.
| | - Fabrizio Frontalini
- Dipartimento di Scienze Pure e Applicate (DiSPeA), Università degli Studi di Urbino "Carlo Bo", 61029, Urbino, Italy
| | - Kristina Cermakova
- ID-Gene ecodiagnostics, Campus Biotech Innovation Park, 1202, Geneva, Switzerland
| | - Laure Apothéloz-Perret-Gentil
- Department of Genetics and Evolution, University of Geneva, Switzerland; ID-Gene ecodiagnostics, Campus Biotech Innovation Park, 1202, Geneva, Switzerland
| | - Mauro Treglia
- SGS Italia S.p.A., 35010, Villafranca Padovana, Italy
| | | | | | - Jan Pawlowski
- Department of Genetics and Evolution, University of Geneva, Switzerland; ID-Gene ecodiagnostics, Campus Biotech Innovation Park, 1202, Geneva, Switzerland
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29
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Adams CIM, Knapp M, Gemmell NJ, Jeunen GJ, Bunce M, Lamare MD, Taylor HR. Beyond Biodiversity: Can Environmental DNA (eDNA) Cut It as a Population Genetics Tool? Genes (Basel) 2019; 10:E192. [PMID: 30832286 PMCID: PMC6470983 DOI: 10.3390/genes10030192] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 02/19/2019] [Accepted: 02/26/2019] [Indexed: 01/23/2023] Open
Abstract
Population genetic data underpin many studies of behavioral, ecological, and evolutionary processes in wild populations and contribute to effective conservation management. However, collecting genetic samples can be challenging when working with endangered, invasive, or cryptic species. Environmental DNA (eDNA) offers a way to sample genetic material non-invasively without requiring visual observation. While eDNA has been trialed extensively as a biodiversity and biosecurity monitoring tool with a strong taxonomic focus, it has yet to be fully explored as a means for obtaining population genetic information. Here, we review current research that employs eDNA approaches for the study of populations. We outline challenges facing eDNA-based population genetic methodologies, and suggest avenues of research for future developments. We advocate that with further optimizations, this emergent field holds great potential as part of the population genetics toolkit.
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Affiliation(s)
- Clare I M Adams
- Department of Anatomy, University of Otago, 270 Great King Street, Dunedin, Otago 9016, New Zealand.
| | - Michael Knapp
- Department of Anatomy, University of Otago, 270 Great King Street, Dunedin, Otago 9016, New Zealand.
| | - Neil J Gemmell
- Department of Anatomy, University of Otago, 270 Great King Street, Dunedin, Otago 9016, New Zealand.
| | - Gert-Jan Jeunen
- Department of Anatomy, University of Otago, 270 Great King Street, Dunedin, Otago 9016, New Zealand.
| | - Michael Bunce
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Bentley, Perth, WA 6102, Australia.
| | - Miles D Lamare
- Department of Marine Science, University of Otago, 310 Castle Street, Dunedin, Otago 9016, New Zealand.
| | - Helen R Taylor
- Department of Anatomy, University of Otago, 270 Great King Street, Dunedin, Otago 9016, New Zealand.
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30
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Past, present, and future perspectives of environmental DNA (eDNA) metabarcoding: A systematic review in methods, monitoring, and applications of global eDNA. Glob Ecol Conserv 2019. [DOI: 10.1016/j.gecco.2019.e00547] [Citation(s) in RCA: 303] [Impact Index Per Article: 60.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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31
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Development and testing of an 18S rRNA phylogenetic microarray for marine sediments. J Microbiol Methods 2018; 154:95-106. [DOI: 10.1016/j.mimet.2018.10.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 04/09/2018] [Accepted: 10/08/2018] [Indexed: 11/22/2022]
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32
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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: 189] [Impact Index Per Article: 31.5] [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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Forster D, Filker S, Kochems R, Breiner HW, Cordier T, Pawlowski J, Stoeck T. A Comparison of Different Ciliate Metabarcode Genes as Bioindicators for Environmental Impact Assessments of Salmon Aquaculture. J Eukaryot Microbiol 2018; 66:294-308. [DOI: 10.1111/jeu.12670] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 06/22/2018] [Accepted: 07/18/2018] [Indexed: 12/20/2022]
Affiliation(s)
- Dominik Forster
- Ecology Group; University of Technology Kaiserslautern; D-67663 Kaiserslautern Germany
| | - Sabine Filker
- Molecular Ecology; University of Technology Kaiserslautern; D-67663 Kaiserslautern Germany
| | - Rebecca Kochems
- Ecology Group; University of Technology Kaiserslautern; D-67663 Kaiserslautern Germany
| | - Hans-Werner Breiner
- Ecology Group; University of Technology Kaiserslautern; D-67663 Kaiserslautern Germany
| | - Tristan Cordier
- Department of Genetics and Evolution; University of Geneva; 1211 Geneva Switzerland
| | - Jan Pawlowski
- Department of Genetics and Evolution; University of Geneva; 1211 Geneva Switzerland
- ID-Gene ecodiagnostics Ltd.; Campus Biotech Innovation Park 1202 Geneva Switzerland
| | - Thorsten Stoeck
- Ecology Group; University of Technology Kaiserslautern; D-67663 Kaiserslautern Germany
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Sample size effects on the assessment of eukaryotic diversity and community structure in aquatic sediments using high-throughput sequencing. Sci Rep 2018; 8:11737. [PMID: 30082688 PMCID: PMC6078945 DOI: 10.1038/s41598-018-30179-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 07/23/2018] [Indexed: 11/30/2022] Open
Abstract
Understanding how biodiversity changes in time and space is vital to assess the effects of environmental change on benthic ecosystems. Due to the limitations of morphological methods, there has been a rapid expansion in the application of high-throughput sequencing methods to study benthic eukaryotic communities. However, the effect of sample size and small-scale spatial variation on the assessment of benthic eukaryotic diversity is still not well understood. Here, we investigate the effect of different sample volumes in the genetic assessment of benthic metazoan and non-metazoan eukaryotic community composition. Accordingly, DNA was extracted from five different cumulative sediment volumes comprising 100% of the top 2 cm of five benthic sampling cores, and used as template for Ilumina MiSeq sequencing of 18 S rRNA amplicons. Sample volumes strongly impacted diversity metrics for both metazoans and non-metazoan eukaryotes. Beta-diversity of treatments using smaller sample volumes was significantly different from the beta-diversity of the 100% sampled area. Overall our findings indicate that sample volumes of 0.2 g (1% of the sampled area) are insufficient to account for spatial heterogeneity at small spatial scales, and that relatively large percentages of sediment core samples are needed for obtaining robust diversity measurement of both metazoan and non-metazoan eukaryotes.
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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: 26] [Impact Index Per Article: 4.3] [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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Laroche O, Wood SA, Tremblay LA, Ellis JI, Lear G, Pochon X. A cross-taxa study using environmental DNA/RNA metabarcoding to measure biological impacts of offshore oil and gas drilling and production operations. MARINE POLLUTION BULLETIN 2018; 127:97-107. [PMID: 29475721 DOI: 10.1016/j.marpolbul.2017.11.042] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 11/16/2017] [Accepted: 11/20/2017] [Indexed: 06/08/2023]
Abstract
Standardized ecosystem-based monitoring surveys are critical for providing information on marine ecosystem health. Environmental DNA/RNA (eDNA/eRNA) metabarcoding may facilitate such surveys by quickly and effectively characterizing multi-trophic levels. In this study, we assessed the suitability of eDNA/eRNA metabarcoding to evaluate changes in benthic assemblages of bacteria, Foraminifera and other eukaryotes along transects at three offshore oil and gas (O&G) drilling and production sites, and compared these to morphologically characterized macro-faunal assemblages. Bacterial communities were the most responsive to O&G activities, followed by Foraminifera, and macro-fauna (the latter assessed by morphology). The molecular approach enabled detection of hydrocarbon degrading taxa such as the bacteria Alcanivorax and Microbulbifer at petroleum impacted stations. Most identified indicator taxa, notably among macro-fauna, were highly specific to site conditions. Based on our results we suggest that eDNA/eRNA metabarcoding can be used as a stand-alone method for biodiversity assessment or as a complement to morphology-based monitoring approaches.
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Affiliation(s)
- Olivier Laroche
- Coastal and Freshwater Group, Cawthron Institute, Private Bag 2, Nelson 7042, New Zealand; School of Biological Sciences, University of Auckland, Private Bag 349, Warkworth 0941, New Zealand.
| | - Susanna A Wood
- Coastal and Freshwater Group, Cawthron Institute, Private Bag 2, Nelson 7042, New Zealand; Environmental Research Institute, The University of Waikato, Private Bag 3105, Hamilton 3240, New Zealand
| | - Louis A Tremblay
- Coastal and Freshwater Group, Cawthron Institute, Private Bag 2, Nelson 7042, New Zealand; School of Biological Sciences, University of Auckland, Private Bag 349, Warkworth 0941, New Zealand
| | - Joanne I Ellis
- King Abdullah University of Science and Technology (KAUST), Red Sea Research Centre, Thuwal 23955-6900, Saudi Arabia
| | - Gavin Lear
- School of Biological Sciences, University of Auckland, Private Bag 349, Warkworth 0941, New Zealand
| | - Xavier Pochon
- 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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37
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Banerji A, Bagley M, Elk M, Pilgrim E, Marinson J, Santo Domingo J. Spatial and temporal dynamics of a freshwater eukaryotic plankton community revealed via 18S rRNA gene metabarcoding. HYDROBIOLOGIA 2018; 818:71-86. [PMID: 31595089 PMCID: PMC6781235 DOI: 10.1007/s10750-018-3593-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
DNA metabarcoding is a sophisticated molecular tool that can enhance biological surveys of freshwater plankton communities by providing broader taxonomic coverage and, for certain groups, higher taxonomic resolution compared to morphological methods. We conducted 18S rRNA gene metabarcoding analyses on 214 water samples collected over a four-month period from multiple sites within a freshwater reservoir. We detected 1,314 unique operational taxonomic units that included various metazoans, protists, chlorophytes, and fungi. Alpha diversity differed among sites, suggesting local habitat variation linked to differing species responses. Strong temporal variation was detected at both daily and monthly scales. Diversity and relative abundance patterns for several protist groups (including dinoflagellates, ciliates, and cryptophytes) differed from arthropods (e.g., cladocerans and copepods), a traditional focus of plankton surveys. This suggests that the protists respond to different environmental dimensions and may therefore provide additional information regarding ecosystem status. Comparison of the sequence-based population survey data to conventional-based data revealed similar trends for taxa that were ranked among the most abundant in both approaches, although some groups were missing in each data set. These results highlight the potential benefit of supplementing conventional biological survey approaches with metabarcoding to obtain a more comprehensive understanding of freshwater plankton community structure and dynamics.
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Affiliation(s)
- A Banerji
- US Environmental Protection Agency, Cincinnati, USA
| | - M Bagley
- US Environmental Protection Agency, Cincinnati, USA
| | - M Elk
- US Environmental Protection Agency, Cincinnati, USA
| | - E Pilgrim
- US Environmental Protection Agency, Cincinnati, USA
| | - J Marinson
- US Environmental Protection Agency, Cincinnati, USA
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Leray M, Knowlton N. Censusing marine eukaryotic diversity in the twenty-first century. Philos Trans R Soc Lond B Biol Sci 2017; 371:rstb.2015.0331. [PMID: 27481783 PMCID: PMC4971183 DOI: 10.1098/rstb.2015.0331] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/26/2016] [Indexed: 11/12/2022] Open
Abstract
The ocean constitutes one of the vastest and richest biomes on our planet. Most recent estimations, all based on indirect approaches, suggest that there are millions of marine eukaryotic species. Moreover, a large majority of these are small (less than 1 mm), cryptic and still unknown to science. However, this knowledge gap, caused by the lack of diagnostic morphological features in small organisms and the limited sampling of the global ocean, is currently being filled, thanks to new DNA-based approaches. The molecular technique of PCR amplification of homologous gene regions combined with high-throughput sequencing, routinely used to census unculturable prokaryotes, is now also being used to characterize whole communities of marine eukaryotes. Here, we review how this methodological advancement has helped to better quantify the magnitude and patterns of marine eukaryotic diversity, with an emphasis on taxonomic groups previously largely overlooked. We then discuss obstacles remaining to achieve a global understanding of marine eukaryotic diversity. In particular, we argue that 18S variable regions do not provide sufficient taxonomic resolution to census marine life, and suggest combining broad eukaryotic surveys targeting the 18S rRNA region with more taxon-focused analyses of hypervariable regions to improve our understanding of the diversity of species, the functional units of marine ecosystems. This article is part of the themed issue ‘From DNA barcodes to biomes’.
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Affiliation(s)
- Matthieu Leray
- National Museum of Natural History, Smithsonian Institution, Washington, DC 20013, USA
| | - Nancy Knowlton
- National Museum of Natural History, Smithsonian Institution, Washington, DC 20013, USA
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39
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Pochon X, Zaiko A, Fletcher LM, Laroche O, Wood SA. Wanted dead or alive? Using metabarcoding of environmental DNA and RNA to distinguish living assemblages for biosecurity applications. PLoS One 2017; 12:e0187636. [PMID: 29095959 PMCID: PMC5667844 DOI: 10.1371/journal.pone.0187636] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 10/23/2017] [Indexed: 11/19/2022] Open
Abstract
High-throughput sequencing metabarcoding studies in marine biosecurity have largely focused on targeting environmental DNA (eDNA). DNA can persist extracellularly in the environment, making discrimination of living organisms difficult. In this study, bilge water samples (i.e., water accumulating on-board a vessel during transit) were collected from 15 small recreational and commercial vessels. eDNA and eRNA molecules were co-extracted and the V4 region of the 18S ribosomal RNA gene targeted for metabarcoding. In total, 62.7% of the Operational Taxonomic Units (OTUs) were identified at least once in the corresponding eDNA and eRNA reads, with 19.5% unique to eDNA and 17.7% to eRNA. There were substantial differences in diversity between molecular compartments; 57% of sequences from eDNA-only OTUs belonged to fungi, likely originating from legacy DNA. In contrast, there was a higher percentage of metazoan (50.2%) and ciliate (31.7%) sequences in the eRNA-only OTUs. Our data suggest that the presence of eRNA-only OTUs could be due to increased cellular activities of some rare taxa that were not identified in the eDNA datasets, unusually high numbers of rRNA transcripts in ciliates, and/or artefacts produced during the reverse transcriptase, PCR and sequencing steps. The proportions of eDNA/eRNA shared and unshared OTUs were highly heterogeneous within individual bilge water samples. Multiple factors including boat type and the activities performed on-board, such as washing of scientific equipment, may play a major role in contributing to this variability. For some marine biosecurity applications analysis, eDNA-only data may be sufficient, however there are an increasing number of instances where distinguishing the living portion of a community is essential. For these circumstances, we suggest only including OTUs that are present in both eDNA and eRNA data. OTUs found only in the eRNA data need to be interpreted with caution until further research provides conclusive evidence for their origin.
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Affiliation(s)
- Xavier Pochon
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
- Institute of Marine Science, University of Auckland, Auckland, New Zealand
- * E-mail:
| | - Anastasija Zaiko
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
- Institute of Marine Science, University of Auckland, Auckland, New Zealand
- Marine Science and Technology Centre, Klaipeda University, Klaipeda, Lithuania
| | | | - Olivier Laroche
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
| | - Susanna A. Wood
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
- Environmental Research Institute, University of Waikato, Hamilton, New Zealand
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40
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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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41
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Wood SA, Zaiko A, Richter I, Inglis GJ, Pochon X. Development of a real-time polymerase chain reaction assay for the detection of the invasive Mediterranean fanworm, Sabella spallanzanii, in environmental samples. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2017; 24:17373-17382. [PMID: 28589279 DOI: 10.1007/s11356-017-9357-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Accepted: 05/23/2017] [Indexed: 06/07/2023]
Abstract
The Mediterranean fanworm, Sabella spallanzanii Gmelin 1791, was first detected in the Southern Hemisphere in the 1990s and is now abundant in many parts of southern Australia and in several locations around northern New Zealand. Once established, it can proliferate rapidly, reaching high densities with potential ecological and economic impacts. Early detection of new S. spallanzanii incursions is important to prevent its spread, guide eradication or control efforts and to increase knowledge on the species' dispersal pathways. In this study, we developed a TaqMan probe real-time polymerase chain reaction assay targeting a region of the mitochondrial cytochrome oxidase I gene. The assay was validated in silico and in vitro using DNA from New Zealand and Australian Sabellidae with no cross-reactivity detected. The assay has a linear range of detection over seven orders of magnitude with a limit of detection reached at 12.4 × 10-4 ng/μL of DNA. We analysed 145 environmental (water, sediment and biofouling) samples and obtained positive detections only from spiked samples and those collected at a port where S. spallanzanii is known to be established. This assay has the potential to enhance current morphological and molecular-based methods, through its ability to rapidly and accurately identify S. spallanzanii in environmental samples.
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Affiliation(s)
- Susanna A Wood
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand.
- Environmental Research Institute, University of Waikato, Hamilton, New Zealand.
| | - Anastasija Zaiko
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
- Marine Science and Technology Centre, Klaipeda University, Klaipeda, Lithuania
| | - Ingrid Richter
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
| | - Graeme J Inglis
- National Institute of Water and Atmospheric Research Ltd, Christchurch, New Zealand
| | - Xavier Pochon
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
- Institute of Marine Science, University of Auckland, Auckland, New Zealand
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42
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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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43
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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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Lanzén A, Lekang K, Jonassen I, Thompson EM, Troedsson C. High-throughput metabarcoding of eukaryotic diversity for environmental monitoring of offshore oil-drilling activities. Mol Ecol 2016; 25:4392-406. [DOI: 10.1111/mec.13761] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Revised: 06/20/2016] [Accepted: 07/13/2016] [Indexed: 10/21/2022]
Affiliation(s)
- Anders Lanzén
- Department of Conservation of Natural Resources; NEIKER Tecnalia; Bizkaia Technology Park 48160 Derio Spain
| | - Katrine Lekang
- Department of Biology; University of Bergen; Box 7800 5020 Bergen Norway
| | - Inge Jonassen
- Computational Biology Unit; Department of Informatics; University of Bergen; Bergen Norway
| | - Eric M. Thompson
- Department of Biology; University of Bergen; Box 7800 5020 Bergen Norway
- Sars International Centre for Marine Molecular Biology; University of Bergen; Bergen Norway
- Uni Research Environment; Uni Research AS; 5020 Bergen Norway
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45
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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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Zaiko A, Schimanski K, Pochon X, Hopkins GA, Goldstien S, Floerl O, Wood SA. Metabarcoding improves detection of eukaryotes from early biofouling communities: implications for pest monitoring and pathway management. BIOFOULING 2016; 32:671-684. [PMID: 27212415 DOI: 10.1080/08927014.2016.1186165] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 04/26/2016] [Indexed: 06/05/2023]
Abstract
In this experimental study the patterns in early marine biofouling communities and possible implications for surveillance and environmental management were explored using metabarcoding, viz. 18S ribosomal RNA gene barcoding in combination with high-throughput sequencing. The community structure of eukaryotic assemblages and the patterns of initial succession were assessed from settlement plates deployed in a busy port for one, five and 15 days. The metabarcoding results were verified with traditional morphological identification of taxa from selected experimental plates. Metabarcoding analysis identified > 400 taxa at a comparatively low taxonomic level and morphological analysis resulted in the detection of 25 taxa at varying levels of resolution. Despite the differences in resolution, data from both methods were consistent at high taxonomic levels and similar patterns in community shifts were observed. A high percentage of sequences belonging to genera known to contain non-indigenous species (NIS) were detected after exposure for only one day.
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Affiliation(s)
- Anastasija Zaiko
- a Coastal and Freshwater Group , Cawthron Institute , Nelson , New Zealand
- b Marine Science and Technology Center , Klaipeda University , Klaipeda , Lithuania
| | - Kate Schimanski
- a Coastal and Freshwater Group , Cawthron Institute , Nelson , New Zealand
- c School of Biological Sciences , University of Canterbury , Christchurch , New Zealand
| | - Xavier Pochon
- a Coastal and Freshwater Group , Cawthron Institute , Nelson , New Zealand
- d Institute of Marine Science , University of Auckland , Auckland , New Zealand
| | - Grant A Hopkins
- a Coastal and Freshwater Group , Cawthron Institute , Nelson , New Zealand
| | - Sharyn Goldstien
- c School of Biological Sciences , University of Canterbury , Christchurch , New Zealand
| | - Oliver Floerl
- a Coastal and Freshwater Group , Cawthron Institute , Nelson , New Zealand
| | - Susanna A Wood
- a Coastal and Freshwater Group , Cawthron Institute , Nelson , New Zealand
- e Environmental Research Institute , Waikato University , Hamilton , New Zealand
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Dowle EJ, Pochon X, C. Banks J, Shearer K, Wood SA. Targeted gene enrichment and high-throughput sequencing for environmental biomonitoring: a case study using freshwater macroinvertebrates. Mol Ecol Resour 2015; 16:1240-54. [DOI: 10.1111/1755-0998.12488] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Revised: 11/12/2015] [Accepted: 11/12/2015] [Indexed: 11/29/2022]
Affiliation(s)
- Eddy J. Dowle
- Cawthron Institute; 98 Halifax Street 7010 Nelson New Zealand
- Department of Entomology; Kansas State University; Waters Hall Manhattan KS 66502 USA
| | - Xavier Pochon
- Cawthron Institute; 98 Halifax Street 7010 Nelson New Zealand
- Institute of Marine Science; University of Auckland; PO Box 349 Warkworth 0941 New Zealand
| | | | - Karen Shearer
- Cawthron Institute; 98 Halifax Street 7010 Nelson New Zealand
| | - Susanna A. Wood
- Cawthron Institute; 98 Halifax Street 7010 Nelson New Zealand
- Environmental Research Insitute University of Waikato; Private Bag 3105 3240 Hamilton New Zealand
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