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Gardoki J, Cearreta A, Irabien MJ, Gómez-Arozamena J, Villasante-Marcos V, García-Artola A, Bessa F. Recent environmental and morphosedimentary evolution of the mining-impacted Nalón Estuary (Asturias, N Spain): Disentangling natural and anthropogenic processes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 943:173792. [PMID: 38851337 DOI: 10.1016/j.scitotenv.2024.173792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 05/22/2024] [Accepted: 06/03/2024] [Indexed: 06/10/2024]
Abstract
Distinguishing between natural and anthropogenic processes in sedimentary records from estuaries with legacy pollutants is an essential task, as it provides baselines to predict future environmental trajectories of coastal areas. Here, we have addressed the recent transformation history of the mining-impacted Nalón Estuary (Asturias, N Spain). Surface and core sediment records from marshes and tidal flats were examined through a broad multidisciplinary approach, involving micropaleontological (benthic foraminifera), sedimentological (grain-size), geochemical (trace metals, major element Al and total organic carbon), physical (magnetic susceptibility, frequency-dependent magnetic susceptibility and large microplastics) and radioisotopic (210Pb, 137Cs and 239+240Pu) proxies. Results suggest that the interplay between natural (high fluvial influence and extreme hydrological events) and anthropogenic (coal and mercury mining disposals) factors induced strong sedimentation-erosion processes, further shaping the recent evolution of the estuary. Short-time scale and intense sedimentation processes were revealed by overall high sediment accumulation rates, the dilution of some geological signatures and the rapid formation of a marsh in the lower estuary bay. The increasing mining fingerprints during the 20th century were shortly interrupted by the catastrophic riverine flooding of 1938. Conversely, current erosional processes by fluvial influence led to the remobilization of contaminated sedimentary materials and exposure of mining-legacy Hg levels in tidal flats from the middle sector. Fluvial activity, floodings and taphonomic biases exerted a major control on benthic foraminifera since the 19th century, although Hg ecotoxicological effects on modern assemblages at certain areas within the estuary cannot be discarded. These findings, along with the documented enhanced erosion of marshes with 'trapped' pollutants (Hg, coal microparticles and microplastics), highlight the importance of monitoring the environmental and geomorphic processes taking place in historically-contaminated estuaries.
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Affiliation(s)
- Jon Gardoki
- Departamento de Geología, Facultad de Ciencia y Tecnología, Universidad del País Vasco UPV/EHU, Barrio Sarriena s/n, 48940 Leioa, Spain.
| | - Alejandro Cearreta
- Departamento de Geología, Facultad de Ciencia y Tecnología, Universidad del País Vasco UPV/EHU, Barrio Sarriena s/n, 48940 Leioa, Spain.
| | - María Jesús Irabien
- Departamento de Geología, Facultad de Ciencia y Tecnología, Universidad del País Vasco UPV/EHU, Barrio Sarriena s/n, 48940 Leioa, Spain.
| | - José Gómez-Arozamena
- Departamento de Ciencias Médicas y Quirúrgicas, Facultad de Medicina, Universidad de Cantabria, Avenida Herrera Oria s/n, 39011 Santander, Spain.
| | - Víctor Villasante-Marcos
- Laboratorio de Magnetismo de Materiales y Magnetismo Ambiental, Instituto Geográfico Nacional, Real Observatorio de Madrid, C/Alfonso XII 3, 28014 Madrid, Spain.
| | - Ane García-Artola
- Departamento de Geología, Facultad de Ciencia y Tecnología, Universidad del País Vasco UPV/EHU, Barrio Sarriena s/n, 48940 Leioa, Spain.
| | - Filipa Bessa
- Centre for Functional Ecology - Science for People & the Planet (CFE), Associate Laboratory TERRA, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal.
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Girard EB, Didaskalou EA, Pratama AMA, Rattner C, Morard R, Renema W. Quantitative assessment of reef foraminifera community from metabarcoding data. Mol Ecol Resour 2024:e14000. [PMID: 39041197 DOI: 10.1111/1755-0998.14000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 06/20/2024] [Accepted: 07/15/2024] [Indexed: 07/24/2024]
Abstract
Describing living community compositions is essential to monitor ecosystems in a rapidly changing world, but it is challenging to produce fast and accurate depiction of ecosystems due to methodological limitations. Morphological methods provide absolute abundances with limited throughput, whereas metabarcoding provides relative abundances of genes that may not correctly represent living communities from environmental DNA assessed with morphological methods. However, it has the potential to deliver fast descriptions of living communities provided that it is interpreted with validated species-specific calibrations and reference databases. Here, we developed a quantitative approach to retrieve from metabarcoding data the assemblages of living large benthic foraminifera (LBF), photosymbiotic calcifying protists, from Indonesian coral reefs that are under increasing anthropogenic pressure. To depict the diversity, we calculated taxon-specific correction factors to reduce biological biases by comparing surface area, biovolume and calcite volume, and the number of mitochondrial gene copies in seven common LBF species. To validate the approach, we compared calibrated datasets of morphological communities from mock samples with bulk reef sediment; both sample types were metabarcoded. The calibration of the data significantly improved the estimations of genus relative abundance, with a difference of ±5% on average, allowing for comparison of past morphological datasets with future molecular ones. Our results also highlight the application of our quantitative approach to support reef monitoring operations by capturing fine-scale processes, such as seasonal and pollution-driven dynamics, that require high-throughput sampling treatment.
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Affiliation(s)
- Elsa B Girard
- Naturalis Biodiversity Center, Leiden, The Netherlands
- IBED, University of Amsterdam, Amsterdam, The Netherlands
| | | | - Andi M A Pratama
- Marine Science Department, Faculty of Marine Science and Fisheries, Hasanuddin University, Makassar, Indonesia
| | | | | | - Willem Renema
- Naturalis Biodiversity Center, Leiden, The Netherlands
- IBED, University of Amsterdam, Amsterdam, The Netherlands
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3
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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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4
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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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5
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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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6
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Barrenechea Angeles I, Nguyen NL, Greco M, Tan KS, Pawlowski J. Assigning the unassigned: A signature-based classification of rDNA metabarcodes reveals new deep-sea diversity. PLoS One 2024; 19:e0298440. [PMID: 38422100 PMCID: PMC10903905 DOI: 10.1371/journal.pone.0298440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 01/23/2024] [Indexed: 03/02/2024] Open
Abstract
Environmental DNA metabarcoding reveals a vast genetic diversity of marine eukaryotes. Yet, most of the metabarcoding data remain unassigned due to the paucity of reference databases. This is particularly true for the deep-sea meiofauna and eukaryotic microbiota, whose hidden diversity is largely unexplored. Here, we tackle this issue by using unique DNA signatures to classify unknown metabarcodes assigned to deep-sea foraminifera. We analyzed metabarcoding data obtained from 311 deep-sea sediment samples collected in the Clarion-Clipperton Fracture Zone, an area of potential polymetallic nodule exploitation in the Eastern Pacific Ocean. Using the signatures designed in the 37F hypervariable region of the 18S rRNA gene, we were able to classify 802 unassigned metabarcodes into 61 novel lineages, which have been placed in 27 phylogenetic clades. The comparison of new lineages with other foraminiferal datasets shows that most novel lineages are widely distributed in the deep sea. Five lineages are also present in the shallow-water datasets; however, phylogenetic analysis of these lineages separates deep-sea and shallow-water metabarcodes except in one case. While the signature-based classification does not solve the problem of gaps in reference databases, this taxonomy-free approach provides insight into the distribution and ecology of deep-sea species represented by unassigned metabarcodes, which could be useful in future applications of metabarcoding for environmental monitoring.
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Affiliation(s)
- Inès Barrenechea Angeles
- Department of Earth Sciences, University of Geneva, Geneva, Switzerland
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
- Department of Geosciences, UiT-The Arctic University of Norway, Tromsø, Norway
| | - Ngoc-Loi Nguyen
- Institute of Oceanology, Polish Academy of Sciences, Sopot, Poland
| | - Mattia Greco
- Institute of Oceanology, Polish Academy of Sciences, Sopot, Poland
- Institute of Marine Sciences, Spanish National Research Council, Barcelona, Spain
| | - Koh Siang Tan
- Tropical Marine Science Institute, National University of Singapore, Singapore, Singapore
| | - Jan Pawlowski
- Institute of Oceanology, Polish Academy of Sciences, Sopot, Poland
- ID-Gene Ecodiagnostics Ltd., Plan-les-Ouates, Switzerland
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7
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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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8
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Bouchet VMP, Seuront L, Tsujimoto A, Richirt J, Frontalini F, Tsuchiya M, Matsuba M, Nomaki H. Foraminifera and plastic pollution: Knowledge gaps and research opportunities. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 324:121365. [PMID: 36858101 DOI: 10.1016/j.envpol.2023.121365] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Revised: 01/19/2023] [Accepted: 02/25/2023] [Indexed: 06/18/2023]
Abstract
Plastic has become one of the most ubiquitous and environmentally threatening sources of pollution in the Anthropocene. Beyond the conspicuous visual impact and physical damages, plastics both carry and release a cocktail of harmful chemicals, such as monomers, additives and persistent organic pollutants. Here we show through a review of the scientific literature dealing with both plastic pollution and benthic foraminifera (Rhizaria), that despite their critical roles in the structure and function of benthic ecosystems, only 0.4% of studies have investigated the effects of micro- and nano-plastics on this group. Consequently, we urge to consider benthic foraminifera in plastic pollution studies via a tentative roadmap that includes (i) the use of their biological, physiological and behavioral responses that may unveil the effects of microplastics and nanoplastics and (ii) the evaluation of the indicative value of foraminiferal species to serve as proxies for the degree of pollution. This appears particularly timely in the context of the development of management strategies to restore coastal ecosystems.
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Affiliation(s)
- Vincent M P Bouchet
- Univ. Lille, CNRS, Univ. Littoral Côte d'Opale, IRD, UMR8187, LOG, Laboratoire d'Océanologie et de Géosciences, Station Marine de Wimereux, 59000, Lille, France.
| | - Laurent Seuront
- Univ. Lille, CNRS, Univ. Littoral Côte d'Opale, IRD, UMR8187, LOG, Laboratoire d'Océanologie et de Géosciences, Station Marine de Wimereux, 59000, Lille, France; Department of Marine Energy and Resource, Tokyo University of Marine Science and Technology, 4-5-7 Konan, Minato-ku, Tokyo, 108-8477, Japan; Department of Zoology and Entomology, Rhodes University, Grahamstown, 6140, South Africa
| | - Akira Tsujimoto
- Faculty of Education, Shimane University, 1060 Nishikawatsu-cho, Matsue-shi, Shimane, 690-8504, Japan
| | - Julien Richirt
- Univ. Lille, CNRS, Univ. Littoral Côte d'Opale, IRD, UMR8187, LOG, Laboratoire d'Océanologie et de Géosciences, Station Marine de Wimereux, 59000, Lille, France; X-star, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, 237-0061, Japan
| | - Fabrizio Frontalini
- Department of Pure and Applied Sciences, Urbino University, 61029, Urbino, Italy
| | - Masashi Tsuchiya
- Research Institute for Global Change (RIGC), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, 237-0061, Japan
| | - Misako Matsuba
- Biodiversity Division, National Institute of Environmental Studies, 16-2 Onogawa, Tsukuba, Ibaraki, 305-8506, Japan
| | - Hidetaka Nomaki
- X-star, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, 237-0061, Japan
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9
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Rebecchi F, Lattanzi D, Abramovich S, Ambrogini P, Ciacci C, Betti M, Frontalini F. Evaluation of the Effects of Electrical Stimulation: A Pilot Experiment on the Marine Benthic Foraminiferal Species Amphistegina lessonii. Life (Basel) 2023; 13:life13040862. [PMID: 37109392 PMCID: PMC10142474 DOI: 10.3390/life13040862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 03/15/2023] [Accepted: 03/21/2023] [Indexed: 04/29/2023] Open
Abstract
Environmental disturbances resulting from anthropogenic energy pollution are intensely growing and represent a concern for the marine environment. Benthic organisms are the significant fauna exposed to this kind of pollution; among them, foraminifera are largely used as pollution bioindicators in marine environments, but studies on the effects induced by electrical stimulation are not documented. In the present research, we evaluated the effects of short-term different electric current densities on the viability of benthic foraminiferal species Amphistegina lessonii by checking the pseudopodial activity and defined the threshold electrical density range. After 3 days of treatment, A. lessonii stimulated with a constant current showed pseudopodial activity at a lower electric current density (0.29, 0.86 μA/cm2) up to 24 h. With increasing stimulation time, the percentages of pseudopodial activity decreased. The pseudopodial activity was absent at high current densities (5.71, 8.57 μA/cm2). The viability of A. lessonii exposed to a pulsed current was higher at a low and middle electric current density (from 0.29 to 5.71 μA/cm2) than at a high electric current density (from 11.43 to 20 μA/cm2). Based on these preliminary results, the selected benthic foraminiferal species seems to better stand pulsed currents than constant ones. These first experiments might provide useful information for the definition of the appropriate electrical density threshold to avoid side effects on a part of the benthic community.
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Affiliation(s)
- Federica Rebecchi
- Department of Pure and Applied Sciences, Urbino University, 61029 Urbino, Italy
| | - Davide Lattanzi
- Department of Biomolecular Science, Urbino University, 61029 Urbino, Italy
| | - Sigal Abramovich
- Department of Earth and Environmental Sciences, Ben Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Patrizia Ambrogini
- Department of Biomolecular Science, Urbino University, 61029 Urbino, Italy
| | - Caterina Ciacci
- Department of Biomolecular Science, Urbino University, 61029 Urbino, Italy
| | - Michele Betti
- Department of Biomolecular Science, Urbino University, 61029 Urbino, Italy
| | - Fabrizio Frontalini
- Department of Pure and Applied Sciences, Urbino University, 61029 Urbino, Italy
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10
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Girard EB, Macher J, Jompa J, Renema W. COI
metabarcoding of large benthic Foraminifera: Method validation for application in ecological studies. Ecol Evol 2022; 12:e9549. [DOI: 10.1002/ece3.9549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 11/04/2022] [Indexed: 11/24/2022] Open
Affiliation(s)
- Elsa B. Girard
- Naturalis Biodiversity Center Leiden the Netherlands
- IBED University of Amsterdam Amsterdam the Netherlands
| | | | - Jamaluddin Jompa
- Marine Science Department, Faculty of Marine Science and Fisheries Hasanuddin University Makassar Indonesia
| | - Willem Renema
- Naturalis Biodiversity Center Leiden the Netherlands
- IBED University of Amsterdam Amsterdam the Netherlands
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11
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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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12
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Macher JN, Bloska DM, Holzmann M, Girard EB, Pawlowski J, Renema W. Mitochondrial cytochrome c oxidase subunit I (COI) metabarcoding of Foraminifera communities using taxon-specific primers. PeerJ 2022; 10:e13952. [PMID: 36093332 PMCID: PMC9454970 DOI: 10.7717/peerj.13952] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 08/05/2022] [Indexed: 01/19/2023] Open
Abstract
Foraminifera are a species-rich phylum of rhizarian protists that are highly abundant in most marine environments. Molecular methods such as metabarcoding have revealed a high, yet undescribed diversity of Foraminifera. However, so far only one molecular marker, the 18S ribosomal RNA, was available for metabarcoding studies on Foraminifera. Primers that allow amplification of foraminiferal mitochondrial cytochrome oxidase I (COI) and identification of Foraminifera species were recently published. Here we test the performance of these primers for the amplification of whole foraminiferal communities, and compare their performance to that of the highly degenerate LerayXT primers, which amplify the same COI region in a wide range of eukaryotes. We applied metabarcoding to 48 samples taken along three transects spanning a North Sea beach in the Netherlands from dunes to the low tide level, and analysed both sediment samples and meiofauna samples, which contained taxa between 42 µm and 1 mm in body size obtained by decantation from sand samples. We used single-cell metabarcoding (Girard et al., 2022) to generate a COI reference library containing 32 species of Foraminifera, and used this to taxonomically annotate our community metabarcoding data. Our analyses show that the highly degenerate LerayXT primers do not amplify Foraminifera, while the Foraminifera primers are highly Foraminifera- specific, with about 90% of reads assigned to Foraminifera and amplifying taxa from all major groups, i.e., monothalamids, Globothalamea, and Tubothalamea. We identified 176 Foraminifera ASVs and found a change in Foraminifera community composition along the beach transects from high tide to low tide level, and a dominance of single-chambered monothalamid Foraminifera. Our results highlight that COI metabarcoding can be a powerful tool for assessing Foraminiferal communities.
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Affiliation(s)
- Jan-Niklas Macher
- Marine Biodiversity, Naturalis Biodiversity Center, Leiden, The Netherlands
| | | | - Maria Holzmann
- Department of Genetics & Evolution, University of Geneva, Geneva, Switzerland
| | - Elsa B. Girard
- Marine Biodiversity, Naturalis Biodiversity Center, Leiden, The Netherlands,Department of Ecosystem & Landscape Dynamics, University of Amsterdam, Amsterdam, Netherlands
| | - Jan Pawlowski
- Laboratory of Paleoceanography, Institute of Oceanology Polish Academy of Sciences, Sopot, Poland
| | - Willem Renema
- Marine Biodiversity, Naturalis Biodiversity Center, Leiden, The Netherlands,Department of Ecosystem & Landscape Dynamics, University of Amsterdam, Amsterdam, Netherlands
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13
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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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14
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Pawlowski J, Bruce K, Panksep K, Aguirre FI, Amalfitano S, Apothéloz-Perret-Gentil L, Baussant T, Bouchez A, Carugati L, Cermakova K, Cordier T, Corinaldesi C, Costa FO, Danovaro R, Dell'Anno A, Duarte S, Eisendle U, Ferrari BJD, Frontalini F, Frühe L, Haegerbaeumer A, Kisand V, Krolicka A, Lanzén A, Leese F, Lejzerowicz F, Lyautey E, Maček I, Sagova-Marečková M, Pearman JK, Pochon X, Stoeck T, Vivien R, Weigand A, Fazi S. Environmental DNA metabarcoding for benthic monitoring: A review of sediment sampling and DNA extraction methods. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 818:151783. [PMID: 34801504 DOI: 10.1016/j.scitotenv.2021.151783] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 11/06/2021] [Accepted: 11/14/2021] [Indexed: 06/13/2023]
Abstract
Environmental DNA (eDNA) metabarcoding (parallel sequencing of DNA/RNA for identification of whole communities within a targeted group) is revolutionizing the field of aquatic biomonitoring. To date, most metabarcoding studies aiming to assess the ecological status of aquatic ecosystems have focused on water eDNA and macroinvertebrate bulk samples. However, the eDNA metabarcoding has also been applied to soft sediment samples, mainly for assessing microbial or meiofaunal biota. Compared to classical methodologies based on manual sorting and morphological identification of benthic taxa, eDNA metabarcoding offers potentially important advantages for assessing the environmental quality of sediments. The methods and protocols utilized for sediment eDNA metabarcoding can vary considerably among studies, and standardization efforts are needed to improve their robustness, comparability and use within regulatory frameworks. Here, we review the available information on eDNA metabarcoding applied to sediment samples, with a focus on sampling, preservation, and DNA extraction steps. We discuss challenges specific to sediment eDNA analysis, including the variety of different sources and states of eDNA and its persistence in the sediment. This paper aims to identify good-practice strategies and facilitate method harmonization for routine use of sediment eDNA in future benthic monitoring.
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Affiliation(s)
- J Pawlowski
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland; Institute of Oceanology, Polish Academy of Sciences, 81-712 Sopot, Poland; ID-Gene Ecodiagnostics, 1202 Geneva, Switzerland
| | - K Bruce
- NatureMetrics Ltd, CABI Site, Bakeham Lane, Egham TW20 9TY, UK
| | - K Panksep
- Institute of Technology, University of Tartu, Tartu 50411, Estonia; Chair of Hydrobiology and Fishery, Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Tartu, Estonia; Chair of Aquaculture, Institute of Veterinary Medicine and Animal Sciences, Estonian University of Life Sciences, Estonia
| | - F I Aguirre
- Water Research Institute, National Research Council of Italy (IRSA-CNR), Monterotondo, Rome, Italy
| | - S Amalfitano
- Water Research Institute, National Research Council of Italy (IRSA-CNR), Monterotondo, Rome, Italy
| | - L Apothéloz-Perret-Gentil
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland; ID-Gene Ecodiagnostics, 1202 Geneva, Switzerland
| | - T Baussant
- Norwegian Research Center AS, NORCE Environment, Marine Ecology Group, Mekjarvik 12, 4070 Randaberg, Norway
| | - A Bouchez
- INRAE, CARRTEL, 74200 Thonon-les-Bains, France
| | - L Carugati
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, Ancona 60131, Italy
| | - K Cermakova
- ID-Gene Ecodiagnostics, 1202 Geneva, Switzerland
| | - T Cordier
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland; NORCE Climate, NORCE Norwegian Research Centre AS, Bjerknes Centre for Climate Research, Jahnebakken 5, 5007 Bergen, Norway
| | - C Corinaldesi
- Department of Materials, Environmental Sciences and Urban Planning, Polytechnic University of Marche, Via Brecce Bianche, Ancona 60131, Italy
| | - F O Costa
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal; Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - R Danovaro
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, Ancona 60131, Italy
| | - A Dell'Anno
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, Ancona 60131, Italy
| | - S Duarte
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal; Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - U Eisendle
- University of Salzburg, Dept. of Biosciences, 5020 Salzburg, Austria
| | - B J D Ferrari
- Swiss Centre for Applied Ecotoxicology (Ecotox Centre), EPFL ENAC IIE-GE, 1015 Lausanne, Switzerland
| | - F Frontalini
- Department of Pure and Applied Sciences, Urbino University, Urbino, Italy
| | - L Frühe
- Technische Universität Kaiserslautern, Ecology Group, D-67663 Kaiserslautern, Germany
| | - A Haegerbaeumer
- Bielefeld University, Animal Ecology, 33615 Bielefeld, Germany
| | - V Kisand
- Institute of Technology, University of Tartu, Tartu 50411, Estonia
| | - A Krolicka
- Norwegian Research Center AS, NORCE Environment, Marine Ecology Group, Mekjarvik 12, 4070 Randaberg, Norway
| | - A Lanzén
- AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), Pasaia, Gipuzkoa, Spain; IKERBASQUE, Basque Foundation for Science, Bilbao, Bizkaia, Spain
| | - F Leese
- University of Duisburg-Essen, Faculty of Biology, Aquatic Ecosystem Research, Germany
| | - F Lejzerowicz
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA
| | - E Lyautey
- Univ. Savoie Mont Blanc, INRAE, CARRTEL, 74200 Thonon-les-Bains, France
| | - I Maček
- Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000 Ljubljana, Slovenia; Faculty of Mathematics, Natural Sciences and Information Technologies (FAMNIT), University of Primorska, Glagoljaška 8, 6000 Koper, Slovenia
| | - M Sagova-Marečková
- Czech University of Life Sciences, Dept. of Microbiology, Nutrition and Dietetics, Prague, Czech Republic
| | - J K Pearman
- Coastal and Freshwater Group, Cawthron Institute, Private Bag 2, Nelson 7042, New Zealand
| | - X Pochon
- Coastal and Freshwater Group, Cawthron Institute, Private Bag 2, Nelson 7042, New Zealand; Institute of Marine Science, University of Auckland, Warkworth 0941, New Zealand
| | - T Stoeck
- Technische Universität Kaiserslautern, Ecology Group, D-67663 Kaiserslautern, Germany
| | - R Vivien
- Swiss Centre for Applied Ecotoxicology (Ecotox Centre), EPFL ENAC IIE-GE, 1015 Lausanne, Switzerland
| | - A Weigand
- National Museum of Natural History Luxembourg, 25 Rue Münster, L-2160 Luxembourg, Luxembourg
| | - S Fazi
- Water Research Institute, National Research Council of Italy (IRSA-CNR), Monterotondo, Rome, Italy.
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15
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Rostami MA, Frontalini F, Giordano P, Francescangeli F, Alves Martins MV, Dyer L, Spagnoli F. Testing the applicability of random forest modeling to examine benthic foraminiferal responses to multiple environmental parameters. MARINE ENVIRONMENTAL RESEARCH 2021; 172:105502. [PMID: 34638002 DOI: 10.1016/j.marenvres.2021.105502] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 09/25/2021] [Accepted: 10/07/2021] [Indexed: 06/13/2023]
Abstract
The main environmental variables controlling benthic foraminiferal distributions were identified and used to assess their influence on ecological indices developed as predictors of Ecological Quality Status (EcoQS) in marine ecosystems. Gradient forest and random forest models were applied to assess the predictive value of a selection of abiotic (environmental) and biotic (foraminifera) variables in a costal marine area in the central Adriatic Sea (Italy). This approach yields evidence that the predictor variables sand, silt, Pollution Load Index, and TN have the greatest influence on the distribution of benthic foraminifera in this area. In addition, we identify thresholds for the most important environmental variables that influence ecological indices. These findings contribute to efforts to determine how to best improve sediment quality and environmental stability for marine conservation. Further application of these approaches represents a useful tool for policymakers to survey the diversity of marine organisms and to improve the ability to protect and restore marine ecosystems by identifying predictors of diversity and identifying key thresholds in these predictors.
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Affiliation(s)
- Masoud A Rostami
- Department of Biology, University of Nevada, Reno, Reno, NV, 89557, USA.
| | - Fabrizio Frontalini
- Department of Pure and Applied Sciences, Università degli Studi di Urbino "Carlo Bo", 61029, Urbino, Italy
| | - Patrizia Giordano
- Istituto di Scienze Polari, Consiglio Nazionale delle Ricerche, 40129, Bologna, Italy
| | - Fabio Francescangeli
- University of Hamburg, Institute for Geology, Centre for Earth System Research and Sustainability, Bundesstraße, 55, 20146, Hamburg, Germany
| | - Maria Virginia Alves Martins
- Rio de Janeiro State University (UERJ), R. São Francisco Xavier, 524, LabMicro 4037F, Maracanã, Rio de Janeiro, 20550-900, Brazil; Aveiro University, Department of Geosciences, GeoBioTec, Campus de Santiago, 3810-197, Aveiro, Portugal
| | - Lee Dyer
- Department of Biology, University of Nevada, Reno, Reno, NV, 89557, USA
| | - Federico Spagnoli
- Istituto per le Risorse Biologiche e le Biotecnologie Marine, Consiglio Nazionale delle Ricerche, 60125, Ancona, Italy; School of Science and Technology, Geology division, University of Camerino, 62032, Camerino, Italy
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16
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Cavaliere M, Barrenechea Angeles I, Montresor M, Bucci C, Brocani L, Balassi E, Margiotta F, Francescangeli F, Bouchet VMP, Pawlowski J, Frontalini F. Assessing the ecological quality status of the highly polluted Bagnoli area (Tyrrhenian Sea, Italy) using foraminiferal eDNA metabarcoding. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 790:147871. [PMID: 34098278 DOI: 10.1016/j.scitotenv.2021.147871] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Revised: 05/14/2021] [Accepted: 05/14/2021] [Indexed: 06/12/2023]
Abstract
Morphology-based benthic foraminifera indices are increasingly used worldwide for biomonitoring the ecological quality of marine sediments. The recent development of foraminiferal eDNA metabarcoding offers a reliable, time-, and cost-effective alternative to morphology-based foraminiferal biomonitoring. However, the practical applications of these new tools are still highly limited. In the present study, we evaluate the response of benthic foraminifera and define the ecological quality status (EcoQS) in the Bagnoli area (Tyrrhenian Sea, Italy) based on a traditional morphology-based approach and eDNA metabarcoding. The geochemical data show that several sites in front of the former industrial plant contain higher concentrations of potentially toxic elements than the effect range median and are characterized by the highest total organic carbon (TOC) content, whereas the distantly located sites can be considered relatively low- to unpolluted. Significant differences (i.e., diversity and assemblage composition) in both morphological and molecular datasets were found between the relatively low- to unpolluted and the most polluted areas. Similarly, the selected ecological indices of both morphological and molecular datasets strikingly and congruently resulted in a clear separation following the environmental stress gradient. The molecular indices (i.e., g-exp(H'bc), g-Foram AMBI, and g-Foram AMBI-MOTUs) reliably identified poor-to-bad EcoQS in the polluted area in front of the former industrial plant. On the other hand, the Foram-AMBI based on morphology well identified an overall trend but seemed to overestimate the EcoQS if the traditional class boundaries were considered. The congruent and complementary trends between morphological and metabarcoding data observed in the case of the Bagnoli site further support the application of foraminiferal metabarcoding in routine biomonitoring to assess the environmental impacts of heavily polluted marine areas.
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Affiliation(s)
- M Cavaliere
- Dipartimento di Scienze Pure e Applicate, Università degli Studi di Urbino "Carlo Bo", 61029 Urbino, Italy.
| | - I Barrenechea Angeles
- Department of Genetics and Evolution, University of Geneva, 1205 Geneva, Switzerland; Department of Earth Sciences, University of Geneva, 1205 Geneva, Switzerland
| | - M Montresor
- Stazione Zoologica Anton Dohrn, 80122 Naples, Italy
| | - C Bucci
- Dipartimento di Scienze Pure e Applicate, Università degli Studi di Urbino "Carlo Bo", 61029 Urbino, Italy
| | - L Brocani
- Dipartimento di Scienze Pure e Applicate, Università degli Studi di Urbino "Carlo Bo", 61029 Urbino, Italy
| | - E Balassi
- Dipartimento di Scienze Pure e Applicate, Università degli Studi di Urbino "Carlo Bo", 61029 Urbino, Italy
| | - F Margiotta
- Stazione Zoologica Anton Dohrn, 80122 Naples, Italy
| | - F Francescangeli
- University of Hamburg, Institute for Geology, Centre for Earth System Research and Sustainability, 20146 Hamburg, Germany
| | - V M P Bouchet
- University of Lille, CNRS, Univ. Littoral Côte d'Opale, UMR 8187, LOG, Laboratoire d'Océanologie et de Géosciences, Station Marine de Wimereux, F 59000 Lille, France
| | - J Pawlowski
- Department of Genetics and Evolution, University of Geneva, 1205 Geneva, Switzerland; ID-Gene ecodiagnostics, Campus Biotech Innovation Park, 1202 Geneva, Switzerland; Institute of Oceanology, Polish Academy of Sciences, 81-712 Sopot, Poland
| | - F Frontalini
- Dipartimento di Scienze Pure e Applicate, Università degli Studi di Urbino "Carlo Bo", 61029 Urbino, Italy
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17
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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: 84] [Impact Index Per Article: 28.0] [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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18
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Sources and Metal Pollution of Sediments from a Coastal Area of the Central Western Adriatic Sea (Southern Marche Region, Italy). APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app11031118] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Sediments represent a critical compartment of marine coastal ecosystems due to the toxic and long-lasting effects of the contaminants buried therein. Here, we investigated the properties of surficial sediments in front of the Southern Marche Region coast (Central Adriatic Sea, Italy). The grain size of the surficial sediments was determined by X-ray sedigraphy. TN and OC contents were determined by elemental analysis. The concentrations of Al, Fe, Mg, K, S, Ca, Ti, P, Na, Mn, Mg, Li, As, Ba, Ga, Pb, Sr, and Zn were determined by ICP-OES to evaluate their spatial patterns and temporal trends. A Q-mode Factor Analyses was applied and resulted in the identification of three compositional facies (Padanic, Coastal, and Residual) characterized by common biogeochemical, mineralogical, sedimentological properties, transport pathway, and source. Some pollution indicators, such as the enrichment factor, the geoaccumulation index, and the pollution load index were calculated to assess the deviation from the natural background levels. The results showed a pollution by As and Ba due to the human activities in the 20th century. Furthermore, a general decreasing of Al, Ti, P, Co, Cr, Cu, Ga, Ni, Pb, Sc, V, and Y concentrations from the background levels suggested a change in the sedimentation processes during the last decades.
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19
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Sagar N, Sadekov A, Scott P, Jenner T, Vadiveloo A, Moheimani NR, McCulloch M. Geochemistry of large benthic foraminifera Amphisorus hemprichii as a high-resolution proxy for lead pollution in coastal environments. MARINE POLLUTION BULLETIN 2021; 162:111918. [PMID: 33341078 DOI: 10.1016/j.marpolbul.2020.111918] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 11/27/2020] [Accepted: 12/01/2020] [Indexed: 06/12/2023]
Abstract
Anthropogenic lead (Pb) contamination resulting from the rapid growth of industrialization in coastal environments poses significant challenges. In this study, we report a novel approach utilising the large benthic foraminifera Amphisorus hemprichii as a biogeochemical archive for monitoring Pb pollution in tropical to warm-temperate coastal waters. Live juvenile specimens of A. hemprichii were cultured in the laboratory for 16 weeks with a range of seawater Pb concentrations. Lead uptake in both newly grown and pre-existing chambers of individual specimens was characterised using the microanalytical technique, Laser ablation-ICP mass spectrometry. We found that Pb concentration in the tests of cultured foraminifera in the laboratory is proportional to seawater [Pb] with the lead partition coefficient (KDPb) of 8.37 ± 0.3. This calibration together with a new biomineralisation model now enables A. hemprichii to be utilised as a naturally occurring bio-archive to quantitatively monitor anthropogenic Pb pollution in coastal waters.
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Affiliation(s)
- Netramani Sagar
- Oceans Graduate School, The University of Western Australia, Perth, Australia; Australian Research Council Centre of Excellence for Coral Reef Studies, UWA, Australia; School of Earth Sciences, The University of Western Australia, Perth, Australia; CSIR-National Geophysical Research Institute, Hyderabad, India.
| | - Aleksey Sadekov
- Oceans Graduate School, The University of Western Australia, Perth, Australia; Australian Research Council Centre of Excellence for Coral Reef Studies, UWA, Australia
| | - Peter Scott
- Oceans Graduate School, The University of Western Australia, Perth, Australia
| | - Talia Jenner
- School of Earth Sciences, The University of Western Australia, Perth, Australia
| | - Ashiwin Vadiveloo
- Algae R & D Centre, Environmental and Conservation Sciences, College of Science, Health, Engineering and Education School, Murdoch University, Australia
| | - Navid R Moheimani
- Algae R & D Centre, Environmental and Conservation Sciences, College of Science, Health, Engineering and Education School, Murdoch University, Australia
| | - Malcolm McCulloch
- Oceans Graduate School, The University of Western Australia, Perth, Australia; Australian Research Council Centre of Excellence for Coral Reef Studies, UWA, Australia
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20
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Frontalini F, Cordier T, Balassi E, Armynot du Chatelet E, Cermakova K, Apothéloz-Perret-Gentil L, Martins MVA, Bucci C, Scantamburlo E, Treglia M, Bonamin V, Pawlowski J. Benthic foraminiferal metabarcoding and morphology-based assessment around three offshore gas platforms: Congruence and complementarity. ENVIRONMENT INTERNATIONAL 2020; 144:106049. [PMID: 32835923 DOI: 10.1016/j.envint.2020.106049] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 08/07/2020] [Accepted: 08/07/2020] [Indexed: 06/11/2023]
Abstract
Since the 1960 s, there has been a rapid expansion of drilling activities in the central and northern Adriatic Sea to meet the increasing global energy demand. The discharges of organic and inorganic pollutants, as well as the alteration of the sediment substrate, are among the main impacts associated with these activities. In the present study, we evaluate the response of benthic foraminifera to the activities of three gas platforms in the northwestern Adriatic Sea, with a special focus on the Armida A platform for which extensive geochemical data (organic matter, trace elements, polycyclic aromatic hydrocarbons, other hydrocarbons, and volatile organic compounds) are available. The response to disturbance is assessed by analyzing the foraminiferal diversity using the traditional morphology-based approach and by 18S rDNA-based metabarcoding. The two methods give congruent results, showing relatively lower foraminiferal diversity and higher dominance values at stations closer to the platforms (<50 m). The taxonomic compositions of the morphological and metabarcoding datasets are very different, the latter being dominated by monothalamous, mainly soft-walled species. However, compositional changes consistently occur at 50 m from the platform and can be related to variations in sediment grain-size variation and higher concentrations of Ni, Zn, Ba, hydrocarbons and total organic carbon. Additionally, several morphospecies and Molecular Operational Taxonomic Units (MOTUs) show strong correlations with distance from the platform and with environmental parameters extracted from BIOENV analysis. Some of these MOTUs have the potential to become new bioindicators, complementing the assemblage of hard-shelled foraminiferal species detected through microscopic analyses. The congruence and complementarity between metabarcoding and morphological approaches support the application of foraminiferal metabarcoding in routine biomonitoring surveys as a reliable, time- and cost-effective methodology to assess the environmental impacts of marine industries.
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Affiliation(s)
- Fabrizio Frontalini
- Dipartimento di Scienze Pure e Applicate, Università degli Studi di Urbino "Carlo Bo", Urbino, Italy
| | - Tristan Cordier
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
| | - Eszter Balassi
- Dipartimento di Scienze Pure e Applicate, Università degli Studi di Urbino "Carlo Bo", Urbino, Italy
| | - Eric Armynot du Chatelet
- Laboratoire d'Océanologie et de Géosciences UMR 8187 LOG CNRS/Lille/ULCO, Université de Lille, Bât SN5, Cité Scientifique, 59655 Villeneuve d'Ascq, France
| | - Kristina Cermakova
- ID-Gene ecodiagnostics, Campus Biotech Innovation Park, 1202 Geneva, Switzerland
| | - Laure Apothéloz-Perret-Gentil
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland; ID-Gene ecodiagnostics, Campus Biotech Innovation Park, 1202 Geneva, Switzerland
| | - Maria Virginia Alves Martins
- Laboratory of Micropaleontology, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Brazil; Universidade de Aveiro, GeoBioTec, Departamento de Geociências, Aveiro, Portugal
| | - Carla Bucci
- Dipartimento di Scienze Pure e Applicate, Università degli Studi di Urbino "Carlo Bo", Urbino, Italy
| | | | | | | | - Jan Pawlowski
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland; ID-Gene ecodiagnostics, Campus Biotech Innovation Park, 1202 Geneva, Switzerland; Institute of Oceanology, Polish Academy of Sciences, 81-712 Sopot, Poland
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21
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Fan J, Wang S, Li H, Yan Z, Zhang Y, Zheng X, Wang P. Modeling the ecological status response of rivers to multiple stressors using machine learning: A comparison of environmental DNA metabarcoding and morphological data. WATER RESEARCH 2020; 183:116004. [PMID: 32622231 DOI: 10.1016/j.watres.2020.116004] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Revised: 05/29/2020] [Accepted: 05/30/2020] [Indexed: 06/11/2023]
Abstract
Understanding the ecological status response of rivers to multiple stressors is a precondition for river restoration and management. However, this requires the collection of appropriate data, including environmental variables and the status of aquatic organisms, and analysis via a suitable model that captures the nonlinear relationships between ecological status and various stressors. The morphological approach has been the standard data collection method employed for establishing the status of aquatic organisms. However, this approach is very laborious and restricted to a specific set of organisms. Recently, an environmental DNA (eDNA) metabarcoding data approach has been developed that is far more efficient than the morphological approach and potentially applicable to an unlimited set of organisms. However, it remains unclear how well eDNA metabarcoding data reflects the impacts of environmental stressors on aquatic ecosystems compared with morphological data, which is essential for clarifying the potential applications of eDNA metabarcoding data in the ecological monitoring and management of rivers. The present work addresses this issue by modeling organism diversity based on three indices with respect to multiple environmental variables in both the catchment and reach scales. This is done by corresponding support vector machine (SVM) models constructed from eDNA metabarcoding and morphological data on 24 sampling locations in the Taizi River basin, China. According to the mean absolute percent error (MAPE) between the measured diversity index values and the index values predicted by the SVM models, the SVM models constructed from eDNA metabarcoding data (MAPE = 3.87) provide more accurate predictions than the SVM models constructed from morphological data (MAPE = 28.36), revealing that the eDNA metabarcoding data better reflects environmental conditions. In addition, the sensitivity of SVM model predictions of the ecological indices for both catchment-scale and reach-scale stressors is evaluated, and the stressors having the greatest impact on the ecological status of rivers are identified. The results demonstrate that the ecological status of rivers is more sensitive to environmental stressors at the reach scale than to stressors at the catchment scale. Therefore, our study is helpful in exploring the potential applications of eDNA metabarcoding data and SVM modeling in the ecological monitoring and management of rivers.
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Affiliation(s)
- Juntao Fan
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Shuping Wang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Hong Li
- Lancaster Environment Centre, Lancaster University, LA1 4YQ, UK; UK Centre for Ecology & Hydrology, MacLean Building, Wallingford, OX108 BB, UK
| | - Zhenguang Yan
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China.
| | - Yizhang Zhang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China; Chinese Research Academy of Environmental Sciences Tianjin Branch, Tianjin, 300457, China
| | - Xin Zheng
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Pengyuan Wang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
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22
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Boehnert S, Birkelund AR, Schmiedl G, Kuhnert H, Kuhn G, Hass HC, Hebbeln D. Test deformation and chemistry of foraminifera as response to anthropogenic heavy metal input. MARINE POLLUTION BULLETIN 2020; 155:111112. [PMID: 32469760 DOI: 10.1016/j.marpolbul.2020.111112] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 03/19/2020] [Accepted: 03/25/2020] [Indexed: 06/11/2023]
Abstract
Benthic foraminifera are sensitive to environmental changes and widely used as tools to monitor pollution. Rising numbers of deformed tests are often used as indicator for elevated levels of heavy metals, but little is known about the relation between heavy metal incorporation into foraminiferal tests and the formation of test deformities. Here, two sediment cores from the south-eastern North Sea are compared, regarding the occurrence of deformed foraminiferal tests, foraminiferal test chemistry (ICP-MS) and bulk sediment Pb content (XRF). The total abundance of deformed foraminiferal tests seems not to align temporarily with historical heavy metal pollution. Therefore, we suggest that foraminifera react with test deformation to other environmental stressors than the studied heavy metals. Test chemistry reflects historical increased bulk sediment heavy metal content, despite a slight temporal offset. We propose that Pb (and Cd) are only incorporated into foraminiferal tests above a yet to be defined threshold of pollution.
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Affiliation(s)
- S Boehnert
- MARUM - Centre for Marine Environmental Sciences, University of Bremen, Leobener Straße 8, 28359 Bremen, Germany.
| | - A R Birkelund
- Department of Geosciences, University of Oslo, P.O. box 1028 Blindern, 0316 Oslo, Norway
| | - G Schmiedl
- Center for Earth System Research and Sustainability, Institute for Geology, University of Hamburg, Bundesstraße 55, 20146 Hamburg, Germany
| | - H Kuhnert
- MARUM - Centre for Marine Environmental Sciences, University of Bremen, Leobener Straße 8, 28359 Bremen, Germany
| | - G Kuhn
- Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- und Meeresforschung, Am Alten Hafen 26, 27568 Bremerhaven, Germany
| | - H C Hass
- Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- und Meeresforschung, Hafenstraße 43, 25992 List/Sylt, Germany
| | - D Hebbeln
- MARUM - Centre for Marine Environmental Sciences, University of Bremen, Leobener Straße 8, 28359 Bremen, Germany.
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23
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Ben-Eliahu N, Herut B, Rahav E, Abramovich S. Shell Growth of Large Benthic Foraminifera under Heavy Metals Pollution: Implications for Geochemical Monitoring of Coastal Environments. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2020; 17:ijerph17103741. [PMID: 32466246 PMCID: PMC7277671 DOI: 10.3390/ijerph17103741] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Revised: 05/20/2020] [Accepted: 05/21/2020] [Indexed: 11/16/2022]
Abstract
This study was promoted by the recent efforts using larger benthic foraminiferal (LBF) shells geochemistry for the monitoring of heavy metals (HMs) pollution in the marine environment. The shell itself acts as a recorder of the ambient water chemistry in low to extreme HMs-polluted environments, allowing the monitoring of recent-past pollution events. This concept, known as sclerochronology, requires the addition of new parts (i.e., new shell) even in extreme pollution events. We evaluated the physiological resilience of three LBF species with different shell types and symbionts to enriched concentrations of Cd, Cu, and Pb at levels several folds higher than the ecological criteria maximum concentration (CMC) (165-166, 33-43, 1001-1206 µg L-1, respectively), which is derived from aquatic organisms' toxicity tests. The physiological response of the holobiont was expressed by growth rates quantified by the addition of new chambers (new shell parts), and by the chlorophyll a of the algal symbionts. The growth rate decrease varied between 0% and 30% compared to the unamended control for all HMs tested, whereas the algal symbionts exhibited a general non-fatal but significant response to Pb and Cu. Our results highlight that shell growth inhibition of LBF is predicted in extreme concentrations of 57 × CMC of Cu and 523 × CMC of Cd, providing a proof of concept for shell geochemistry monitoring, which is currently not used in the regulatory sectors.
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Affiliation(s)
- Nir Ben-Eliahu
- Department of Earth and Environmental Science, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel;
| | - Barak Herut
- National Institute of Oceanography, Israel Oceanographic and Limnological Research, Haifa 31080, Israel; (B.H.); (E.R.)
| | - Eyal Rahav
- National Institute of Oceanography, Israel Oceanographic and Limnological Research, Haifa 31080, Israel; (B.H.); (E.R.)
| | - Sigal Abramovich
- Department of Earth and Environmental Science, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel;
- Correspondence:
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24
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Assessing the Cadmium Effects on the Benthic Foraminifer Ammonia cf. parkinsoniana: An Acute Toxicity Test. WATER 2020. [DOI: 10.3390/w12041018] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Heavy metals are one of the most hazardous pollutants in marine environments because of their bioaccumulation and biomagnification capabilities. Among them, cadmium (Cd) has been considered as one of the most dangerous for marine organisms. Here we incubated Ammonia cf. parkinsoniana specimens, a benthic foraminiferal taxon used in previous experiments, for up to 48 h in natural seawater with different concentrations of Cd to unravel the physiological change. We document a reduced pseudopodial activity of the Cd-treated specimens at concentrations >10–100 ppb in comparison with the control specimens. Moreover, confocal images of Cd-treated specimens using Nile Red as a fluorescent probe reveal an enhanced intracellular neutral lipid accumulation in the form of lipid droplets at 6 h and 12 h. This bioassay experiment allows for the direct evaluation of Cd-dose to A. cf. parkinsoniana-response relationships under laboratory controlled conditions and provides complementary information to field observations as well as to water quality guidelines and thresholds.
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25
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Developing an ANFIS-PSO Model to Predict Mercury Emissions in Combustion Flue Gases. MATHEMATICS 2019. [DOI: 10.3390/math7100965] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Accurate prediction of mercury content emitted from fossil-fueled power stations is of the utmost importance for environmental pollution assessment and hazard mitigation. In this paper, mercury content in the output gas of power stations’ boilers was predicted using an adaptive neuro-fuzzy inference system (ANFIS) method integrated with particle swarm optimization (PSO). The input parameters of the model included coal characteristics and the operational parameters of the boilers. The dataset was collected from 82 sample points in power plants and employed to educate and examine the proposed model. To evaluate the performance of the proposed hybrid model of the ANFIS-PSO, the statistical meter of MARE% was implemented, which resulted in 0.003266 and 0.013272 for training and testing, respectively. Furthermore, relative errors between the acquired data and predicted values were between −0.25% and 0.1%, which confirm the accuracy of the model to deal non-linearity and represent the dependency of flue gas mercury content into the specifications of coal and the boiler type.
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26
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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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27
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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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28
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Frontalini F, Semprucci F, Di Bella L, Caruso A, Cosentino C, Maccotta A, Scopelliti G, Sbrocca C, Bucci C, Balsamo M, Martins MV, Armynot du Châtelet E, Coccioni R. The response of cultured meiofaunal and benthic foraminiferal communities to lead exposure: Results from mesocosm experiments. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY 2018; 37:2439-2447. [PMID: 29920754 DOI: 10.1002/etc.4207] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 03/27/2018] [Accepted: 06/12/2018] [Indexed: 06/08/2023]
Abstract
Lead (Pb) is regarded as a highly toxic element that poses a serious threat to biota. A mesocosm experiment was performed to assess the influence of Pb on meiofaunal (metazoans within 45-500 μm) and benthic foraminiferal (protozoan) communities. To this end, sediments bearing such communities were incubated in mesocosms, exposed to different levels of Pb in seawater, and monitored for up to 8 wk. Concentrations of Pb <1 ppm in water did not promote a significant increase of this metal in sediments. Relatively high concentrations of Pb seemed to affect meiofaunal and benthic foraminiferal communities by reducing their richness or diversity, and the abundance of the most sensitive taxa. The mesocosm approach can be considered an effective method to document the responses of meiofaunal and benthic foraminiferal communities to various kinds and concentrations of pollutants over time. This approach allows the evaluation of dose-response relationships, validates the outcomes of field studies, and possibly confirms the sediment quality guidelines and thresholds. Environ Toxicol Chem 2018;37:2439-2447. © 2018 SETAC.
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Affiliation(s)
- Fabrizio Frontalini
- Department of Pure and Applied Sciences, University of Urbino, Urbino, Italy
| | - Federica Semprucci
- Department of Biomolecular Sciences, University of Urbino, Urbino, Italy
| | - Letizia Di Bella
- Department of Earth Science, Rome University Sapienza, Roma, Italy
| | - Antonio Caruso
- Dipartimento di Scienze della Terra e del Mare, Università di Palermo, Palermo, Italy
| | - Claudia Cosentino
- Dipartimento di Scienze della Terra e del Mare, Università di Palermo, Palermo, Italy
| | - Antonella Maccotta
- Dipartimento di Scienze della Terra e del Mare, Università di Palermo, Palermo, Italy
| | - Giovanna Scopelliti
- Dipartimento di Scienze della Terra e del Mare, Università di Palermo, Palermo, Italy
| | - Claudia Sbrocca
- Department of Biomolecular Sciences, University of Urbino, Urbino, Italy
| | - Carla Bucci
- Department of Pure and Applied Sciences, University of Urbino, Urbino, Italy
| | - Maria Balsamo
- Department of Biomolecular Sciences, University of Urbino, Urbino, Italy
| | - Maria Virginia Martins
- Laboratory of Micropaleontology, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Brazil
- GeoBioTec, Departamento de Geociências, Universidade de Aveiro, Campus de Santiago, Aveiro, Portugal
| | - Eric Armynot du Châtelet
- Laboratoire d'Océanologie et de Géosciences, Université Littoral Côte d'Opale, Université de Lille, Conseil National de la Recherche Scientifique, Lille, France
| | - Rodolfo Coccioni
- Department of Pure and Applied Sciences, University of Urbino, Urbino, Italy
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29
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Cordier T, Forster D, Dufresne Y, Martins CIM, Stoeck T, Pawlowski J. Supervised machine learning outperforms taxonomy-based environmental DNA metabarcoding applied to biomonitoring. Mol Ecol Resour 2018; 18:1381-1391. [DOI: 10.1111/1755-0998.12926] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 06/14/2018] [Accepted: 06/25/2018] [Indexed: 11/27/2022]
Affiliation(s)
- Tristan Cordier
- Department of Genetics and Evolution; University of Geneva; Geneva Switzerland
| | - Dominik Forster
- Ecology Group; University of Kaiserslautern; Kaiserslautern Germany
| | - Yoann Dufresne
- Department of Genetics and Evolution; University of Geneva; Geneva Switzerland
- Institut Pasteur - Hub of Bioinformatics and Biostatistics - C3BI; USR 3756 IP CNRS; Paris France
| | | | - Thorsten Stoeck
- Ecology Group; University of Kaiserslautern; Kaiserslautern Germany
| | - Jan Pawlowski
- Department of Genetics and Evolution; University of Geneva; Geneva Switzerland
- ID-Gene ecodiagnostics, Ltd; Plan-les-Ouates Switzerland
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