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Luo L, Ma X, Guo R, Jiang T, Wang T, Shao H, He H, Wang H, Liang Y, McMinn A, Guo C, Wang M. Characterization and genomic analysis of a novel Synechococcus phage S-H9-2 belonging to Bristolvirus genus isolated from the Yellow Sea. Virus Res 2023; 328:199072. [PMID: 36781075 DOI: 10.1016/j.virusres.2023.199072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 02/08/2023] [Accepted: 02/10/2023] [Indexed: 02/15/2023]
Abstract
Cyanophages are known to influence the population dynamics and community structure of cyanobacteria and thus play an important role in biogeochemical cycles in aquatic ecosystems. In this study, a novel Synechococcus phage S-H9-2 infecting Synechococcus sp. WH 8102 was isolated from the coastal water of the Yellow Sea. Synechococcus phage S-H9-2 contains a 187,320 bp genome of double-stranded DNA with a G + C content of 40.3%, 202 potential open reading frames (ORFs), and 15 tRNAs. Phylogenetic analysis and nucleotide-based intergenomic similarity suggest that Synechococcus phage S-H9-2 belongs to the Bristolvirus genus under the family Kyanoviridae. Homologs of the S-H9-2 open reading frame can be found in a variety of marine environments, as shown by the results of mapping the genome sequence of S-H9-2 to the Global Ocean Viromes 2.0 dataset. The presence of auxiliary metabolic genes (AMGs) related to photosynthesis, carbon metabolism, and phosphorus assimilation, as well as phylogenetic relationships based on complete genome sequences, reflect the mechanism of phage-host interaction and host-specific strategies for adaptation to environmental conditions. This study enriches the current genomic database of cyanophage and contributed to our understanding of the virus-host interactions and their adaption to the environment.
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Affiliation(s)
- Lin Luo
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Xiaohong Ma
- Department of Pediatrics, Qingdao Municipal Hospital, Qingdao266011, China
| | - Ruizhe Guo
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Tong Jiang
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Tiancong Wang
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Hongbing Shao
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China; UMT-OUC Joint Centre for Marine Studies, Qingdao 266003, China
| | - Hui He
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China; UMT-OUC Joint Centre for Marine Studies, Qingdao 266003, China
| | - Hualong Wang
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China; UMT-OUC Joint Centre for Marine Studies, Qingdao 266003, China
| | - Yantao Liang
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China; UMT-OUC Joint Centre for Marine Studies, Qingdao 266003, China
| | - Andrew McMinn
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China; Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS 7001, SA
| | - Cui Guo
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China; UMT-OUC Joint Centre for Marine Studies, Qingdao 266003, China.
| | - Min Wang
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China; UMT-OUC Joint Centre for Marine Studies, Qingdao 266003, China; The Affiliated Hospital of Qingdao University, Qingdao 266000, China.
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Labban A, Shibl AA, Calleja ML, Hong PY, Morán XAG. Growth dynamics and transcriptional responses of a Red Sea Prochlorococcus strain to varying temperatures. Environ Microbiol 2022; 25:1007-1021. [PMID: 36567447 DOI: 10.1111/1462-2920.16326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 12/11/2022] [Indexed: 12/27/2022]
Abstract
Prochlorococcus play a crucial role in the ocean's biogeochemical cycling, but it remains controversial how they will respond to global warming. Here we assessed the response to temperature (22-30°C) of the growth dynamics and gene expression profiles of a Red Sea Prochlorococcus strain (RSP50) in a non-axenic culture. Both the specific growth rate (0.55-0.80 day-1 ) and cell size (0.04-0.07 μm3 ) of Prochlorococcus increased significantly with temperature. The primary production released extracellularly ranged from 20% to 34%, with humic-like fluorescent compounds increasing up to fivefold as Prochlorococcus reached its maximum abundance. At 30°C, genes involved in carbon fixation such as CsoS2 and CsoS3 and photosynthetic electron transport including PTOX were downregulated, suggesting a cellular homeostasis and energy saving mechanism response. In contrast, PTOX was found upregulated at 22°C and 24°C. Similar results were found for transaldolase, related to carbon metabolism, and citrate synthase, an important enzyme in the TCA cycle. Our data suggest that in spite of the currently warm temperatures of the Red Sea, Prochlorococcus can modulate its gene expression profiles to permit growth at temperatures lower than its optimum temperature (28°C) but is unable to cope with temperatures exceeding 30°C.
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Affiliation(s)
- Abbrar Labban
- Marine Science, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia.,Environmental Science and Engineering, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia
| | - Ahmed A Shibl
- Genetic Heritage Group, Biology Program, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates.,Public Health Research Center, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Maria Ll Calleja
- Climate Geochemistry Department, Max Plank Institute for Chemistry, Mainz, Germany
| | - Pei-Ying Hong
- Environmental Science and Engineering, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia
| | - Xosé Anxelu G Morán
- Marine Science, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia.,Centro Oceanográfico de Gijón/Xixón, Instituto Español de Oceanografía (IEO-CSIC), Gijón/Xixón, Spain
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3
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Ashok A, Agusti S. Contrasting sensitivity among oligotrophic marine microbial communities to priority PAHs. CHEMOSPHERE 2022; 309:136490. [PMID: 36210574 DOI: 10.1016/j.chemosphere.2022.136490] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 09/14/2022] [Accepted: 09/15/2022] [Indexed: 06/16/2023]
Abstract
Oligotrophic areas represent a large proportion of the oceans, wherein microbial food webs largely determine carbon flux dynamics and biogeochemical cycles. However, little is known regarding the sensitivity of microbial planktonic communities to pollutants in such areas. Organic pollutants such as polycyclic aromatic hydrocarbons (PAH/s) are toxic oil derivatives that occur as complex mixtures and reach marine environments through different sources. Therefore, our study analyzed the PAH tolerance of natural photosynthetic and heterotrophic bacteria and eukaryotes from the oligotrophic Red Sea, which is uniquely susceptible to high oil contamination. Natural communities sampled from the surface layer were exposed to a concentration gradient of a mixture of 16 priority PAHs at in situ conditions for 48 h. The populations of the dominant picocyanobacteria Synechococcus sp., picophytoeukaryotes, and low nucleic acid (LNA) bacteria decreased upon exposure to PAHs in a strong dose-dependent manner. Chlorophyll-a, which was measured as an indicator of the total autotrophic community response, also decreased substantially. High nucleic acid (HNA) bacteria, however, exhibited lower growth inhibition (<50%). The lethal concentration (LC10) thresholds to the 16-PAH mixture demonstrated contrasting sensitivities among the microbial communities studied increasing from picoeukaryotes (5.98 ± 2.08 μg L-1) < chlorophyll-a (19.51 ± 8.11 μg L-1) < LNA bacteria (23.63 ± 10.64 μg L-1) < Synechococcus sp. (26.77 ± 13.34 μg L-1) < HNA bacteria (97.13 ± 17.28 μg L-1). The sensitivity of Red Sea Synechococcus and picophytoeukaryotes to the 16-PAH mixture was between 2 and 6.5 times higher compared to single PAH compounds tested previously. However, some populations of HNA bacteria and Synechococcus sp., were highly tolerant, suggesting an adaptation to chronic pollution. Concerningly, the LC10 toxicity thresholds approached the ambient PAH concentrations in the Red Sea, suggesting that environmental oil pollution actively shapes the microbial community structures in the region.
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Affiliation(s)
- Ananya Ashok
- Red Sea Research Center, King Abdullah University of Science and Technology, Saudi Arabia.
| | - Susana Agusti
- Red Sea Research Center, King Abdullah University of Science and Technology, Saudi Arabia
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A Review of Cyanophage–Host Relationships: Highlighting Cyanophages as a Potential Cyanobacteria Control Strategy. Toxins (Basel) 2022; 14:toxins14060385. [PMID: 35737046 PMCID: PMC9229316 DOI: 10.3390/toxins14060385] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 05/20/2022] [Accepted: 05/23/2022] [Indexed: 11/16/2022] Open
Abstract
Harmful algal blooms (HABs) are naturally occurring phenomena, and cyanobacteria are the most commonly occurring HABs in freshwater systems. Cyanobacteria HABs (cyanoHABs) negatively affect ecosystems and drinking water resources through the production of potent toxins. Furthermore, the frequency, duration, and distribution of cyanoHABs are increasing, and conditions that favor cyanobacteria growth are predicted to increase in the coming years. Current methods for mitigating cyanoHABs are generally short-lived and resource-intensive, and have negative impacts on non-target species. Cyanophages (viruses that specifically target cyanobacteria) have the potential to provide a highly specific control strategy with minimal impacts on non-target species and propagation in the environment. A detailed review (primarily up to 2020) of cyanophage lifecycle, diversity, and factors influencing infectivity is provided in this paper, along with a discussion of cyanophage and host cyanobacteria relationships for seven prominent cyanoHAB-forming genera in North America, including: Synechococcus, Microcystis, Dolichospermum, Aphanizomenon, Cylindrospermopsis, Planktothrix, and Lyngbya. Lastly, factors affecting the potential application of cyanophages as a cyanoHAB control strategy are discussed, including efficacy considerations, optimization, and scalability for large-scale applications.
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Pearman JK, Casas L, Michell C, Aldanondo N, Mojib N, Holtermann K, Georgakakis I, Curdia J, Carvalho S, Gusti A, Irigoien X. Comparative metagenomics of phytoplankton blooms after nutrient enrichment of oligotrophic marine waters. METABARCODING AND METAGENOMICS 2022. [DOI: 10.3897/mbmg.6.79208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Increasing anthropogenic pressures on the coastal marine environments impact these ecosystems via a variety of mechanisms including nutrient loading, leading to eutrophication and increases in algal blooms. Here, we use a metagenomics approach to assess the taxonomic and functional changes of the microbial community throughout a nutrient enriched mesocosm phytoplankton bloom. We tested four different nutrient treatments consisting of either nitrate and phosphate or nitrate, phosphate and silicate, administered on the first day or continuously for the first two weeks of the experiment. Our results show a shift in the taxonomic composition of the community over time that is dependent on the nutrient addition regime. Significant differences in the functional potential of the communities were detected, with an interaction between bloom period (pre-bloom, bloom and post-bloom) and nutrient treatment (p = 0.004). A sharp drop in functional similarity was observed in the first week in all treatments and after 20 days had not returned to pre-bloom levels. Changes within energy metabolism pathways showed a remarkable enrichment of the dissimilatory nitrate reduction pathway in the post-bloom period. Eukaryotic oxidative phosphorylation and photosynthetic antenna proteins were more abundant during the bloom, especially in the continuous treatment with silicate. Our results suggest that continuous (i.e. chronic) nutrient enrichment has a larger effect on the functioning of marine systems compared to a single (i.e acute) addition. A deep understanding of the functional and taxonomic shifts in the community during blooms is essential to reverse or mitigate human impacts on coastal environments.
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Voigt E, Rall BC, Chatzinotas A, Brose U, Rosenbaum B. Phage strategies facilitate bacterial coexistence under environmental variability. PeerJ 2021; 9:e12194. [PMID: 34760346 PMCID: PMC8572521 DOI: 10.7717/peerj.12194] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 08/31/2021] [Indexed: 12/14/2022] Open
Abstract
Bacterial communities are often exposed to temporal variations in resource availability, which exceed bacterial generation times and thereby affect bacterial coexistence. Bacterial population dynamics are also shaped by bacteriophages, which are a main cause of bacterial mortality. Several strategies are proposed in the literature to describe infections by phages, such as "Killing the Winner", "Piggyback the loser" (PtL) or "Piggyback the Winner" (PtW). The two temperate phage strategies PtL and PtW are defined by a change from lytic to lysogenic infection when the host density changes, from high to low or from low to high, respectively. To date, the occurrence of different phage strategies and their response to environmental variability is poorly understood. In our study, we developed a microbial trophic network model using ordinary differential equations (ODEs) and performed 'in silico' experiments. To model the switch from the lysogenic to the lytic cycle, we modified the lysis rate of infected bacteria and their growth was turned on or off using a density-dependent switching point. We addressed whether and how the different phage strategies facilitate bacteria coexistence competing for limiting resources. We also studied the impact of a fluctuating resource inflow to evaluate the response of the different phage strategies to environmental variability. Our results show that the viral shunt (i.e. nutrient release after bacterial lysis) leads to an enrichment of the system. This enrichment enables bacterial coexistence at lower resource concentrations. We were able to show that an established, purely lytic model leads to stable bacterial coexistence despite fluctuating resources. Both temperate phage models differ in their coexistence patterns. The model of PtW yields stable bacterial coexistence at a limited range of resource supply and is most sensitive to resource fluctuations. Interestingly, the purely lytic phage strategy and PtW both result in stable bacteria coexistence at oligotrophic conditions. The PtL model facilitates stable bacterial coexistence over a large range of stable and fluctuating resource inflow. An increase in bacterial growth rate results in a higher resilience to resource variability for the PtL and the lytic infection model. We propose that both temperate phage strategies represent different mechanisms of phages coping with environmental variability. Our study demonstrates how phage strategies can maintain bacterial coexistence in constant and fluctuating environments.
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Affiliation(s)
- Esther Voigt
- German Centre for Integrative Biodiversity Research (iDiv), Leipzig, Germany.,Institute of Biodiversity, Friedrich Schiller University Jena, Jena, Germany
| | - Björn C Rall
- German Centre for Integrative Biodiversity Research (iDiv), Leipzig, Germany.,Institute of Biodiversity, Friedrich Schiller University Jena, Jena, Germany
| | - Antonis Chatzinotas
- German Centre for Integrative Biodiversity Research (iDiv), Leipzig, Germany.,Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany.,Institute of Biology, Leipzig University, Leipzig, Germany
| | - Ulrich Brose
- German Centre for Integrative Biodiversity Research (iDiv), Leipzig, Germany.,Institute of Biodiversity, Friedrich Schiller University Jena, Jena, Germany
| | - Benjamin Rosenbaum
- German Centre for Integrative Biodiversity Research (iDiv), Leipzig, Germany.,Institute of Biodiversity, Friedrich Schiller University Jena, Jena, Germany
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Estimating maximal microbial growth rates from cultures, metagenomes, and single cells via codon usage patterns. Proc Natl Acad Sci U S A 2021; 118:2016810118. [PMID: 33723043 PMCID: PMC8000110 DOI: 10.1073/pnas.2016810118] [Citation(s) in RCA: 91] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Despite the wide perception that microbes have rapid growth rates, many environments like seawater and soil are often dominated by microorganisms that can only grow very slowly. Our knowledge about growth is necessarily biased toward easily culturable organisms, which tend to be those that grow fast, because microbial growth rates have traditionally been measured using laboratory growth experiments. However, how are potential growth rates distributed in nature? Using genomic data, we predicted the growth rates of over 200,000 organisms, including many as yet uncultivated species. These data reveal how current culture collections are strongly biased toward fast-growing organisms. Finally, we noticed a bimodal distribution of maximal growth rates, suggesting a natural division of microbial growth strategies into two classes. Maximal growth rate is a basic parameter of microbial lifestyle that varies over several orders of magnitude, with doubling times ranging from a matter of minutes to multiple days. Growth rates are typically measured using laboratory culture experiments. Yet, we lack sufficient understanding of the physiology of most microbes to design appropriate culture conditions for them, severely limiting our ability to assess the global diversity of microbial growth rates. Genomic estimators of maximal growth rate provide a practical solution to survey the distribution of microbial growth potential, regardless of cultivation status. We developed an improved maximal growth rate estimator and predicted maximal growth rates from over 200,000 genomes, metagenome-assembled genomes, and single-cell amplified genomes to survey growth potential across the range of prokaryotic diversity; extensions allow estimates from 16S rRNA sequences alone as well as weighted community estimates from metagenomes. We compared the growth rates of cultivated and uncultivated organisms to illustrate how culture collections are strongly biased toward organisms capable of rapid growth. Finally, we found that organisms naturally group into two growth classes and observed a bias in growth predictions for extremely slow-growing organisms. These observations ultimately led us to suggest evolutionary definitions of oligotrophy and copiotrophy based on the selective regime an organism occupies. We found that these growth classes are associated with distinct selective regimes and genomic functional potentials.
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Labban A, Palacio AS, García FC, Hadaidi G, Ansari MI, López-Urrutia Á, Alonso-Sáez L, Hong PY, Morán XAG. Temperature Responses of Heterotrophic Bacteria in Co-culture With a Red Sea Synechococcus Strain. Front Microbiol 2021; 12:612732. [PMID: 34040590 PMCID: PMC8141594 DOI: 10.3389/fmicb.2021.612732] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 03/29/2021] [Indexed: 11/29/2022] Open
Abstract
Interactions between autotrophic and heterotrophic bacteria are fundamental for marine biogeochemical cycling. How global warming will affect the dynamics of these essential microbial players is not fully understood. The aims of this study were to identify the major groups of heterotrophic bacteria present in a Synechococcus culture originally isolated from the Red Sea and assess their joint responses to experimental warming within the metabolic ecology framework. A co-culture of Synechococcus sp. RS9907 and their associated heterotrophic bacteria, after determining their taxonomic affiliation by 16S rRNA gene sequencing, was acclimated and maintained in the lab at different temperatures (24-34°C). The abundance and cellular properties of Synechococcus and the three dominant heterotrophic bacterial groups (pertaining to the genera Paracoccus, Marinobacter, and Muricauda) were monitored by flow cytometry. The activation energy of Synechococcus, which grew at 0.94-1.38 d-1, was very similar (0.34 ± 0.02 eV) to the value hypothesized by the metabolic theory of ecology (MTE) for autotrophs (0.32 eV), while the values of the three heterotrophic bacteria ranged from 0.16 to 1.15 eV and were negatively correlated with their corresponding specific growth rates (2.38-24.4 d-1). The corresponding carrying capacities did not always follow the inverse relationship with temperature predicted by MTE, nor did we observe a consistent response of bacterial cell size and temperature. Our results show that the responses to future ocean warming of autotrophic and heterotrophic bacteria in microbial consortia might not be well described by theoretical universal rules.
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Affiliation(s)
- Abbrar Labban
- Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Water Desalination and Reuse Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Antonio S. Palacio
- AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), Sukarrieta, Spain
| | - Francisca C. García
- Environment and Sustainability Institute, University of Exeter, Penryn, United Kingdom
| | - Ghaida Hadaidi
- Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Mohd I. Ansari
- Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Ángel López-Urrutia
- Centro Oceanográfico de Gijón/Xixón, Instituto Español de Oceanografía, Gijón, Spain
| | - Laura Alonso-Sáez
- AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), Sukarrieta, Spain
| | - Pei-Ying Hong
- Water Desalination and Reuse Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Xosé Anxelu G. Morán
- Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Centro Oceanográfico de Gijón/Xixón, Instituto Español de Oceanografía, Gijón, Spain
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