1
|
Kaleli A, Gozde Ozbayram E, Akcaalan R. Environmental DNA metabarcoding reveals diverse phytoplankton assemblages and potentially harmful algal distribution along the urban coasts of Türkiye. MARINE ENVIRONMENTAL RESEARCH 2024; 199:106623. [PMID: 38917660 DOI: 10.1016/j.marenvres.2024.106623] [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: 03/26/2024] [Revised: 06/13/2024] [Accepted: 06/21/2024] [Indexed: 06/27/2024]
Abstract
Marine phytoplankton are widely used to monitor the state of the water column due to their rapid changes in response to environmental conditions. In this study, we aimed to investigate the coastal phytoplankton assemblages, including bloom-forming species using high-throughput sequencing of 18S rRNA genes targeting the V4 region and their relationship with environmental variables along the Istanbul coasts of the Sea of Marmara. A total of 118 genera belonging to six phyla were detected. Among them, Dinoflagellata (36) and Bacillariophyta (26) were represented with the highest number of genera. According to the relative abundance of DNA reads, the most abundant taxa were Dinoflagellata_phylum (18.1%), Emiliania (8.4%), Biecheleria (8.4), and Noctiluca (8.1%). The ANOSIM test showed that there was a significant temporal difference in the assemblages, while the driving environmental factors were pH, water temperature, and salinity. According to the TRIX index, the trophic state of the coasts was highly mesotrophic and eutrophic. In addition, 45 bloom-forming and HAB taxa were detected and two species of Noctiluca and Emiliania, which frequently cause blooms in the area, were recorded in high abundance. Our results provide insight into the phytoplankton assemblages along the urbanized coastlines by analysing the V4 region of 18S rRNA. This data can support future studies that use both traditional methods and metabarcoding, employing various primers and targeting different genes and regions.
Collapse
Affiliation(s)
- Aydın Kaleli
- Istanbul University, Faculty of Aquatic Sciences, Department of Marine and Freshwater Resources Management, 34134, Istanbul, Türkiye.
| | - Emine Gozde Ozbayram
- Istanbul University, Faculty of Aquatic Sciences, Department of Marine and Freshwater Resources Management, 34134, Istanbul, Türkiye.
| | - Reyhan Akcaalan
- Istanbul University, Faculty of Aquatic Sciences, Department of Marine and Freshwater Resources Management, 34134, Istanbul, Türkiye.
| |
Collapse
|
2
|
Cohen Y, Johnke J, Abed-Rabbo A, Pasternak Z, Chatzinotas A, Jurkevitch E. Unbalanced predatory communities and a lack of microbial degraders characterize the microbiota of a highly sewage-polluted Eastern-Mediterranean stream. FEMS Microbiol Ecol 2024; 100:fiae069. [PMID: 38684474 PMCID: PMC11099661 DOI: 10.1093/femsec/fiae069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 03/10/2024] [Accepted: 04/25/2024] [Indexed: 05/02/2024] Open
Abstract
Wastewater pollution of water resources takes a heavy toll on humans and on the environment. In highly polluted water bodies, self-purification is impaired, as the capacity of the riverine microbes to regenerate the ecosystem is overwhelmed. To date, information on the composition, dynamics and functions of the microbial communities in highly sewage-impacted rivers is limited, in particular in arid and semi-arid environments. In this year-long study of the highly sewage-impacted Al-Nar/Kidron stream in the Barr al-Khalil/Judean Desert east of Jerusalem, we show, using 16S and 18S rRNA gene-based community analysis and targeted qPCR, that both the bacterial and micro-eukaryotic communities, while abundant, exhibited low stability and diversity. Hydrolyzers of organics compounds, as well as nitrogen and phosphorus recyclers were lacking, pointing at reduced potential for regeneration. Furthermore, facultative bacterial predators were almost absent, and the obligate predators Bdellovibrio and like organisms were found at very low abundance. Finally, the micro-eukaryotic predatory community differed from those of other freshwater environments. The lack of essential biochemical functions may explain the stream's inability to self-purify, while the very low levels of bacterial predators and the disturbed assemblages of micro-eukaryote predators present in Al-Nar/Kidron may contribute to community instability and disfunction.
Collapse
Affiliation(s)
- Yossi Cohen
- Department of Plant Pathology and Microbiology, Institute of Environmental Sciences, Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, 76100, Israel
- Presently at DayTwo, Rehovot, Israel
| | - Julia Johnke
- Evolutionary Ecology and Genetics, Zoological Institute, University of Kiel, Kiel, Germany
| | | | - Zohar Pasternak
- Department of Plant Pathology and Microbiology, Institute of Environmental Sciences, Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, 76100, Israel
- Presently at the Division of Identification and Forensic Science, Israel Police, National Headquarters
| | - Antonis Chatzinotas
- Department of Applied Microbial Ecology, Helmholtz Centre for Environmental Research - UFZ, Permoserstrasse 15, 04318 Leipzig, Germany
- Institute of Biology, Leipzig University, Talstrasse 33, 04103 Leipzig, Germany
- Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstrasse 4, 04103 Leipzig, Germany
| | - Edouard Jurkevitch
- Department of Plant Pathology and Microbiology, Institute of Environmental Sciences, Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, 76100, Israel
| |
Collapse
|
3
|
Bilbao J, Pavloudi C, Blanco-Rayón E, Franco J, Madariaga I, Seoane S. Phytoplankton community composition in relation to environmental variability in the Urdaibai estuary (SE Bay of Biscay): Microscopy and eDNA metabarcoding. MARINE ENVIRONMENTAL RESEARCH 2023; 191:106175. [PMID: 37717336 DOI: 10.1016/j.marenvres.2023.106175] [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: 06/21/2023] [Revised: 09/06/2023] [Accepted: 09/07/2023] [Indexed: 09/19/2023]
Abstract
Phytoplankton monitoring is essential for the global understanding of aquatic ecosystems. The present research studies the phytoplankton community of the Urdaibai estuary, combining microscopy and eDNA metabarcoding for the first time in the area. The main aims were to describe the phytoplankton community composition in relation to the environmental conditions of the estuary, and to compare the two methods used. Diatoms Minutocellus polymorphus and Chaetoceros tenuissimus dominated the outer estuary, being replaced by Teleaulax acuta (cryptophyte), Kryptoperidinium foliaceum (dinoflagellate) and Cyclotella spp. (diatom) towards the inner area. This change was mainly prompted by salinity and nutrients. Metabarcoding revealed the presence of 223 species that were not observed by microscopy in previous studies in the estuary. However, several characteristic species (e.g., K. foliaceum) were only detected with microscopy. Additionally, microscopy covered the limitations of eDNA metabarcoding concerning quantification. Thus, to give a full insight, a combination of techniques is recommended.
Collapse
Affiliation(s)
- Jone Bilbao
- Department of Plant Biology and Ecology, Faculty of Science and Technology, University of the Basque Country, UPV/EHU, Leioa, Spain; Research Centre for Experimental Marine Biology and Biotechnology (Plentzia Marine Station, PiE- UPV/EHU), University of the Basque Country, UPV/EHU, Plentzia, Spain.
| | - Christina Pavloudi
- Institute of Marine Biology, Biotechnology, Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR), Heraklion, Crete, Greece; Department of Biological Sciences, The George Washington University, District of Columbia, USA
| | - Esther Blanco-Rayón
- Research Centre for Experimental Marine Biology and Biotechnology (Plentzia Marine Station, PiE- UPV/EHU), University of the Basque Country, UPV/EHU, Plentzia, Spain
| | | | - Iosu Madariaga
- Department of Plant Biology and Ecology, Faculty of Science and Technology, University of the Basque Country, UPV/EHU, Leioa, Spain
| | - Sergio Seoane
- Department of Plant Biology and Ecology, Faculty of Science and Technology, University of the Basque Country, UPV/EHU, Leioa, Spain; Research Centre for Experimental Marine Biology and Biotechnology (Plentzia Marine Station, PiE- UPV/EHU), University of the Basque Country, UPV/EHU, Plentzia, Spain
| |
Collapse
|
4
|
Hwang J, Kang HW, Moon SJ, Hyung JH, Lee ES, Park J. Metagenomic Analysis of the Species Composition and Seasonal Distribution of Marine Dinoflagellate Communities in Four Korean Coastal Regions. Microorganisms 2022; 10:1459. [PMID: 35889179 PMCID: PMC9320301 DOI: 10.3390/microorganisms10071459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 07/14/2022] [Accepted: 07/18/2022] [Indexed: 12/10/2022] Open
Abstract
Biomonitoring of dinoflagellate communities in marine ecosystems is essential for efficient water quality management and limiting ecosystem disturbances. Current identification and monitoring of toxic dinoflagellates, which cause harmful algal blooms, primarily involves light or scanning electron microscopy; however, these techniques are limited in their ability to monitor dinoflagellates and plankton, leaving an incomplete analysis. In this study, we analyzed the species composition and seasonal distribution of the dinoflagellate communities in four Korean coastal regions using 18S rRNA amplicon sequencing. The results showed significantly high diversity in the dinoflagellate communities in all regions and seasons. Furthermore, we found seasonally dominant species and causative species of harmful algal blooms (Cochlodinium sp., Alexandrium sp., Dinophysis sp., and Gymnodinium sp.). Moreover, dominant species were classified by region and season according to the difference in geographical and environmental parameters. The molecular analysis of the dinoflagellate community based on metagenomics revealed more diverse species compositions that could not be identified by microscopy and revealed potentially harmful or recently introduced dinoflagellate species. In conclusion, metagenomic analysis of dinoflagellate communities was more precise and obtained results faster than microscopic analysis, and could improve the existing monitoring techniques for community analysis.
Collapse
Affiliation(s)
- Jinik Hwang
- West Sea Fisheries Research Institute, National Institute of Fisheries Science, Incheon 22383, Korea; (J.H.); (H.W.K.)
| | - Hee Woong Kang
- West Sea Fisheries Research Institute, National Institute of Fisheries Science, Incheon 22383, Korea; (J.H.); (H.W.K.)
| | - Seung Joo Moon
- Environment and Resource Convergence Center, Advanced Institute of Convergence Technology, Suwon 16229, Korea; (S.J.M.); (J.-H.H.); (E.S.L.)
| | - Jun-Ho Hyung
- Environment and Resource Convergence Center, Advanced Institute of Convergence Technology, Suwon 16229, Korea; (S.J.M.); (J.-H.H.); (E.S.L.)
| | - Eun Sun Lee
- Environment and Resource Convergence Center, Advanced Institute of Convergence Technology, Suwon 16229, Korea; (S.J.M.); (J.-H.H.); (E.S.L.)
| | - Jaeyeon Park
- Environment and Resource Convergence Center, Advanced Institute of Convergence Technology, Suwon 16229, Korea; (S.J.M.); (J.-H.H.); (E.S.L.)
| |
Collapse
|
5
|
Choi TJ, Malik A, An HE, Kim JI, Dinh Do T, Kim CB. Seasonal Diversity of Microeukaryotes in the Han River, Korea Through 18S rRNA Gene Metabarcoding. Evol Bioinform Online 2022; 18:11769343221074688. [PMID: 35095269 PMCID: PMC8793432 DOI: 10.1177/11769343221074688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 12/21/2021] [Indexed: 11/15/2022] Open
Abstract
Freshwater ecosystems contain a large diversity of microeukaryotes that play important roles in maintaining their structure. Microeukaryote communities vary in composition and abundance on the basis of temporal and environmental variables and may serve as useful bioindicators of environmental changes. In the present study, 18S rRNA metabarcoding was employed to investigate the seasonal diversity of microeukaryote communities during four seasons in the Han River, Korea. In total, 882 unique operational taxonomic units (OTUs) were detected, including various diatoms, metazoans (e.g., arthropods and rotifers), chlorophytes, and fungi. Although alpha diversity revealed insignificant differences based on seasons, beta diversity exhibited a prominent variation in the community composition as per seasons. The analysis revealed that the diversity of microeukaryotes was primarily driven by seasonal changes in the prevailing conditions of environmental water temperature and dissolved oxygen. Moreover, potential indicator OTUs belonging to diatoms and chlorophytes were associated with seasonal and environmental factors. This analysis was a preliminary study that established a continuous monitoring system using metabarcoding. This approach could be an effective tool to manage the Han River along with other freshwater ecosystems in Korea.
Collapse
Affiliation(s)
- Tae-June Choi
- Department of Biotechnology, Sangmyung University, Seoul, Republic of Korea
| | - Adeel Malik
- Institute of Intelligence Informatics Technology, Sangmyung University, Seoul, Republic of Korea
| | - Hyung-Eun An
- Department of Biotechnology, Sangmyung University, Seoul, Republic of Korea
| | - Jung-Il Kim
- Department of Biotechnology, Sangmyung University, Seoul, Republic of Korea
| | - Thinh Dinh Do
- Department of Biotechnology, Sangmyung University, Seoul, Republic of Korea
| | - Chang-Bae Kim
- Department of Biotechnology, Sangmyung University, Seoul, Republic of Korea
- Chang-Bae Kim, Department of Biotechnology, Sangmyung University, Seoul, 03016 Republic of Korea.
| |
Collapse
|