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Eckmann CA, Bachy C, Wittmers F, Strauss J, Blanco-Bercial L, Vergin KL, Parsons RJ, Kudela RM, Johnson R, Bolaños LM, Giovannoni SJ, Carlson CA, Worden AZ. Recurring seasonality exposes dominant species and niche partitioning strategies of open ocean picoeukaryotic algae. COMMUNICATIONS EARTH & ENVIRONMENT 2024; 5:266. [PMID: 38779128 PMCID: PMC11106004 DOI: 10.1038/s43247-024-01395-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 04/16/2024] [Indexed: 05/25/2024]
Abstract
Ocean spring phytoplankton blooms are dynamic periods important to global primary production. We document vertical patterns of a diverse suite of eukaryotic algae, the prasinophytes, in the North Atlantic Subtropical Gyre with monthly sampling over four years at the Bermuda Atlantic Time-series Study site. Water column structure was used to delineate seasonal stability periods more ecologically relevant than seasons defined by calendar dates. During winter mixing, tiny prasinophytes dominated by Class II comprise 46 ± 24% of eukaryotic algal (plastid-derived) 16S rRNA V1-V2 amplicons, specifically Ostreococcus Clade OII, Micromonas commoda, and Bathycoccus calidus. In contrast, Class VII are rare and Classes I and VI peak during warm stratified periods when surface eukaryotic phytoplankton abundances are low. Seasonality underpins a reservoir of genetic diversity from multiple prasinophyte classes during warm periods that harbor ephemeral taxa. Persistent Class II sub-species dominating the winter/spring bloom period retreat to the deep chlorophyll maximum in summer, poised to seed the mixed layer upon winter convection, exposing a mechanism for initiating high abundances at bloom onset. Comparisons to tropical oceans reveal broad distributions of the dominant sub-species herein. This unparalleled window into temporal and spatial niche partitioning of picoeukaryotic primary producers demonstrates how key prasinophytes prevail in warm oceans.
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Affiliation(s)
- Charlotte A. Eckmann
- Marine Biological Laboratory, Woods Hole, MA 02543 USA
- Ocean Sciences Department, University of California, Santa Cruz, CA 95064 USA
| | - Charles Bachy
- Ocean EcoSystems Biology Research Unit, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, 24148 Germany
- Station Biologique de Roscoff, Sorbonne Université, CNRS, FR2424, Roscoff, 29680 France
| | - Fabian Wittmers
- Marine Biological Laboratory, Woods Hole, MA 02543 USA
- Ocean EcoSystems Biology Research Unit, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, 24148 Germany
| | - Jan Strauss
- Ocean EcoSystems Biology Research Unit, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, 24148 Germany
| | | | | | - Rachel J. Parsons
- Bermuda Institute of Ocean Sciences—Arizona State University, St. George’s, GE 01 Bermuda
| | - Raphael M. Kudela
- Ocean Sciences Department, University of California, Santa Cruz, CA 95064 USA
| | - Rod Johnson
- Bermuda Institute of Ocean Sciences—Arizona State University, St. George’s, GE 01 Bermuda
| | - Luis M. Bolaños
- Department of Microbiology, Oregon State University, Corvallis, OR 97331 USA
| | | | - Craig A. Carlson
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, CA 93106 USA
| | - Alexandra Z. Worden
- Marine Biological Laboratory, Woods Hole, MA 02543 USA
- Ocean Sciences Department, University of California, Santa Cruz, CA 95064 USA
- Ocean EcoSystems Biology Research Unit, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, 24148 Germany
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2
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Rey Redondo E, Xu Y, Yung CCM. Genomic characterisation and ecological distribution of Mantoniella tinhauana: a novel Mamiellophycean green alga from the Western Pacific. Front Microbiol 2024; 15:1358574. [PMID: 38774501 PMCID: PMC11106453 DOI: 10.3389/fmicb.2024.1358574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 04/12/2024] [Indexed: 05/24/2024] Open
Abstract
Mamiellophyceae are dominant marine algae in much of the ocean, the most prevalent genera belonging to the order Mamiellales: Micromonas, Ostreococcus and Bathycoccus, whose genetics and global distributions have been extensively studied. Conversely, the genus Mantoniella, despite its potential ecological importance, remains relatively under-characterised. In this study, we isolated and characterised a novel species of Mamiellophyceae, Mantoniella tinhauana, from subtropical coastal waters in the South China Sea. Morphologically, it resembles other Mantoniella species; however, a comparative analysis of the 18S and ITS2 marker genes revealed its genetic distinctiveness. Furthermore, we sequenced and assembled the first genome of Mantoniella tinhauana, uncovering significant differences from previously studied Mamiellophyceae species. Notably, the genome lacked any detectable outlier chromosomes and exhibited numerous unique orthogroups. We explored gene groups associated with meiosis, scale and flagella formation, shedding light on species divergence, yet further investigation is warranted. To elucidate the biogeography of Mantoniella tinhauana, we conducted a comprehensive analysis using global metagenomic read mapping to the newly sequenced genome. Our findings indicate this species exhibits a cosmopolitan distribution with a low-level prevalence worldwide. Understanding the intricate dynamics between Mamiellophyceae and the environment is crucial for comprehending their impact on the ocean ecosystem and accurately predicting their response to forthcoming environmental changes.
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Affiliation(s)
| | | | - Charmaine Cheuk Man Yung
- Department of Ocean Science, The Hong Kong University of Science and Technology, Kowloon, Hong Kong SAR, China
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3
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Tang WW, Foo SC. Microalgae for freshwater arsenic bioremediation: examining cellular toxicity, bioconcentration factor and eluding an alternative arsenic detoxification pathway. 3 Biotech 2024; 14:130. [PMID: 38605865 PMCID: PMC11006648 DOI: 10.1007/s13205-024-03977-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 03/13/2024] [Indexed: 04/13/2024] Open
Abstract
Microalgae are photoautotrophic organisms in freshwater systems known to uptake and bioremediate arsenic, a heavy metal. In this study, we compared the growth and arsenic uptake of two microalgae strains, Nostoc and Chlorella, to determine their suitability for arsenic bioremediation. As compared to the control, our results showed that treatment with As (III) enhanced the Nostoc growth by approximately 15% when grown in the absence of phosphate. The highest bioconcentration factor of Nostoc at this treatment was 1463.6, whereas 0.10 mg L-1 As (V) treatment improved the Chlorella growth by 25%, in the presence of phosphate. However, arsenic uptake reduced from 175.7 to 32.3 throughout the cultivation period for Chlorella. This suggests that Nostoc has an upper advantage in the bioremediation of arsenic as compared to the Chlorella strain. To gain insights into the potential of Nostoc in arsenic bioremediation, we further conducted SEM analysis on the vegetative cell surface. The SEM results showed that As (III) disrupted the Nostoc vegetative cell surface and structure. Further to this, pathway analysis and polymerase chain reaction (PCR) were conducted to identify the potential arsenic pathway regulated by Nostoc. The primary As (III)-related pathways elucidated include the arsA transporter and arsD complex that require ATP and As (III) methylation to S-adenosylmethionine. The phosphate deficiency condition resulting in the inability to generate ATP caused As (III) could not be excreted from the Nostoc cells, potentially contributing to the high arsenic concentration accumulated under phosphate-depleted conditions. These insights contribute to understanding the efficacy of microalgae strains in freshwater arsenic bioremediation.
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Affiliation(s)
- Wenn Wenn Tang
- School of Science, Monash University Malaysia, Jalan Lagoon Selatan, 47500 Bandar Sunway, Selangor Darul Ehsan Malaysia
| | - Su Chern Foo
- School of Science, Monash University Malaysia, Jalan Lagoon Selatan, 47500 Bandar Sunway, Selangor Darul Ehsan Malaysia
- Monash University Malaysia, Tropical Medicine and Biology Multidisciplinary Platform, Jalan Lagoon Selatan, 47500 Bandar Sunway, Selangor Darul Ehsan Malaysia
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4
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Harbeitner RC, Wittmers F, Yung CCM, Eckmann CA, Hehenberger E, Blum M, Needham DM, Worden AZ. Gradients of bacteria in the oceanic water column reveal finely-resolved vertical distributions. PLoS One 2024; 19:e0298139. [PMID: 38564528 PMCID: PMC10986988 DOI: 10.1371/journal.pone.0298139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 01/16/2024] [Indexed: 04/04/2024] Open
Abstract
Bacterial communities directly influence ecological processes in the ocean, and depth has a major influence due to the changeover in primary energy sources between the sunlit photic zone and dark ocean. Here, we examine the abundance and diversity of bacteria in Monterey Bay depth profiles collected from the surface to just above the sediments (e.g., 2000 m). Bacterial abundance in these Pacific Ocean samples decreased by >1 order of magnitude, from 1.22 ±0.69 ×106 cells ml-1 in the variable photic zone to 1.44 ± 0.25 ×105 and 6.71 ± 1.23 ×104 cells ml-1 in the mesopelagic and bathypelagic, respectively. V1-V2 16S rRNA gene profiling showed diversity increased sharply between the photic and mesopelagic zones. Weighted Gene Correlation Network Analysis clustered co-occurring bacterial amplicon sequence variants (ASVs) into seven subnetwork modules, of which five strongly correlated with depth-related factors. Within surface-associated modules there was a clear distinction between a 'copiotrophic' module, correlating with chlorophyll and dominated by e.g., Flavobacteriales and Rhodobacteraceae, and an 'oligotrophic' module dominated by diverse Oceanospirillales (such as uncultured JL-ETNP-Y6, SAR86) and Pelagibacterales. Phylogenetic reconstructions of Pelagibacterales and SAR324 using full-length 16S rRNA gene data revealed several additional subclades, expanding known microdiversity within these abundant lineages, including new Pelagibacterales subclades Ia.B, Id, and IIc, which comprised 4-10% of amplicons depending on the subclade and depth zone. SAR324 and Oceanospirillales dominated in the mesopelagic, with SAR324 clade II exhibiting its highest relative abundances (17±4%) in the lower mesopelagic (300-750 m). The two newly-identified SAR324 clades showed highest relative abundances in the photic zone (clade III), while clade IV was extremely low in relative abundance, but present across dark ocean depths. Hierarchical clustering placed microbial communities from 900 m samples with those from the bathypelagic, where Marinimicrobia was distinctively relatively abundant. The patterns resolved herein, through high resolution and statistical replication, establish baselines for marine bacterial abundance and taxonomic distributions across the Monterey Bay water column, against which future change can be assessed.
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Affiliation(s)
- Rachel C. Harbeitner
- Department of Ocean Sciences, University of California Santa Cruz, Santa Cruz, CA, United States of America
- Ocean EcoSystems Biology Unit, RD3, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, DE, Germany
| | - Fabian Wittmers
- Ocean EcoSystems Biology Unit, RD3, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, DE, Germany
- Marine Biological Laboratory, Woods Hole, MA, United States of America
| | - Charmaine C. M. Yung
- Ocean EcoSystems Biology Unit, RD3, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, DE, Germany
| | - Charlotte A. Eckmann
- Department of Ocean Sciences, University of California Santa Cruz, Santa Cruz, CA, United States of America
- Marine Biological Laboratory, Woods Hole, MA, United States of America
| | - Elisabeth Hehenberger
- Ocean EcoSystems Biology Unit, RD3, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, DE, Germany
| | - Marguerite Blum
- Monterey Bay Aquarium Research Institute, Moss Landing, CA, United States of America
| | - David M. Needham
- Ocean EcoSystems Biology Unit, RD3, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, DE, Germany
| | - Alexandra Z. Worden
- Department of Ocean Sciences, University of California Santa Cruz, Santa Cruz, CA, United States of America
- Ocean EcoSystems Biology Unit, RD3, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, DE, Germany
- Marine Biological Laboratory, Woods Hole, MA, United States of America
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5
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Ren CG, Zhong ZH, Liu ZY, Lin S, Luo YK, Qin S. The ever-lasting green tides: What can we do?. Heliyon 2024; 10:e25220. [PMID: 38333800 PMCID: PMC10850537 DOI: 10.1016/j.heliyon.2024.e25220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 12/20/2023] [Accepted: 01/23/2024] [Indexed: 02/10/2024] Open
Abstract
Macroalgal blooms (Green tides) are occurring more frequently in many regions of the world because of the combined effects of increasingly intense human activity and climate change. In the last decade, the world's largest Ulva prolifera green tide has become a recurrent phenomenon, appearing every summer in the southern Yellow Sea, China. Green tides can hurt coastal tourism and eradicate aquaculture and artisanal fishing. Eutrophication in nearshore waters is the ultimate explanation for the explosive growth of the macroalgal biomass, but the specific course of each nearshore green tide is often complex and requires in-depth and extensive research to develop effective mitigation strategies. Researchers have undertaken extensive studies on the prevention, control and mitigation of large-scale green algal blooms, and felicitated the utilization of green tide harmful biomass through bio-refining, bioconversion and other measures. However, due to the large-scale and trans-regional nature of the green tide, the government's administrative coordination measures are also essential for effective control. Nevertheless, it is becoming increasingly urgent to prevent and control the bloom at the early stage, and efficiently salvage and use these valuable raw materials.
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Affiliation(s)
- Cheng-Gang Ren
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, 17 Chun-hui Road, Lai-shan District, Yantai, China
| | - Zhi-Hai Zhong
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, 17 Chun-hui Road, Lai-shan District, Yantai, China
| | - Zhi-Yi Liu
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, 17 Chun-hui Road, Lai-shan District, Yantai, China
| | - Shuang Lin
- Academician Workstation of Agricultural High-tech Industrial Area of the Yellow River Delta, National Center of Technology Innovation for Comprehensive Utilization of Saline-Alkali Land, Dongying, Shandong, China
| | - Yong-Kai Luo
- Academician Workstation of Agricultural High-tech Industrial Area of the Yellow River Delta, National Center of Technology Innovation for Comprehensive Utilization of Saline-Alkali Land, Dongying, Shandong, China
| | - Song Qin
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, 17 Chun-hui Road, Lai-shan District, Yantai, China
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6
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Cerfonteyn M, Groben R, Vaulot D, Guðmundsson K, Vannier P, Pérez-Hernández MD, Marteinsson VÞ. The distribution and diversity of eukaryotic phytoplankton in the Icelandic marine environment. Sci Rep 2023; 13:8519. [PMID: 37231140 DOI: 10.1038/s41598-023-35537-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 05/19/2023] [Indexed: 05/27/2023] Open
Abstract
Phytoplankton play a crucial role in the marine food web and are sensitive indicators of environmental change. Iceland is at the center of a contrasting hydrography, with cold Arctic water coming in from the north and warmer Atlantic water from the south, making this geographical location very sensitive to climate change. We used DNA metabarcoding to determine the biogeography of phytoplankton in this area of accelerating change. Seawater samples were collected in spring (2012-2018), summer (2017) and winter (2018) together with corresponding physico-chemical metadata around Iceland. Amplicon sequencing of the V4 region of the 18S rRNA gene indicates that eukaryotic phytoplankton community composition is different between the northern and southern water masses, with some genera completely absent from Polar Water masses. Emiliania was more dominant in the Atlantic-influenced waters and in summer, and Phaeocystis was more dominant in the colder, northern waters and in winter. The Chlorophyta picophytoplankton genus, Micromonas, was similarly dominant to the dominant diatom genus, Chaetoceros. This study presents an extensive dataset which can be linked with other 18s rRNA datasets for further investigation into the diversity and biogeography of marine protists in the North Atlantic.
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Affiliation(s)
- Mia Cerfonteyn
- Matís, Vinlandsleið 12, 113, Reykjavík, Iceland.
- Faculty of Food Science and Nutrition, University of Iceland, Læknagarður, Vatnsmyrarvegur 16, 101, Reykjavík, Iceland.
- Marine and Freshwater Research Institute, Fornubúðir 5, 220, Hafnarfjörður, Iceland.
| | - René Groben
- Matís, Vinlandsleið 12, 113, Reykjavík, Iceland
| | - Daniel Vaulot
- Sorbonne Université, CNRS, UMR7144, Station Biologique de Roscoff, 29680, Roscoff, France
| | - Kristinn Guðmundsson
- Marine and Freshwater Research Institute, Fornubúðir 5, 220, Hafnarfjörður, Iceland
| | | | - María Dolores Pérez-Hernández
- Unidad Océano y Clima, Instituto de Oceanografía y Cambio Global, IOCAG, Universidad de Las Palmas de Gran Canaria, ULPGC, Unidad Asociada ULPGC-CSIC, Las Palmas de Gran Canaria, Spain
| | - Viggó Þór Marteinsson
- Matís, Vinlandsleið 12, 113, Reykjavík, Iceland
- Faculty of Food Science and Nutrition, University of Iceland, Læknagarður, Vatnsmyrarvegur 16, 101, Reykjavík, Iceland
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7
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Patin NV, Goodwin KD. Capturing marine microbiomes and environmental DNA: A field sampling guide. Front Microbiol 2023; 13:1026596. [PMID: 36713215 PMCID: PMC9877356 DOI: 10.3389/fmicb.2022.1026596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 11/22/2022] [Indexed: 01/15/2023] Open
Abstract
The expanding interest in marine microbiome and eDNA sequence data has led to a demand for sample collection and preservation standard practices to enable comparative assessments of results across studies and facilitate meta-analyses. We support this effort by providing guidelines based on a review of published methods and field sampling experiences. The major components considered here are environmental and resource considerations, sample processing strategies, sample storage options, and eDNA extraction protocols. It is impossible to provide universal recommendations considering the wide range of eDNA applications; rather, we provide information to design fit-for-purpose protocols. To manage scope, the focus here is on sampling collection and preservation of prokaryotic and microeukaryotic eDNA. Even with a focused view, the practical utility of any approach depends on multiple factors, including habitat type, available resources, and experimental goals. We broadly recommend enacting rigorous decontamination protocols, pilot studies to guide the filtration volume needed to characterize the target(s) of interest and minimize PCR inhibitor collection, and prioritizing sample freezing over (only) the addition of preservation buffer. An annotated list of studies that test these parameters is included for more detailed investigation on specific steps. To illustrate an approach that demonstrates fit-for-purpose methodologies, we provide a protocol for eDNA sampling aboard an oceanographic vessel. These guidelines can aid the decision-making process for scientists interested in sampling and sequencing marine microbiomes and/or eDNA.
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Affiliation(s)
- Nastassia Virginia Patin
- Atlantic Oceanographic and Meteorological Laboratory, Ocean Chemistry and Ecosystems Division, National Oceanic and Atmospheric Administration, Miami, FL, United States,Cooperative Institute for Marine and Atmospheric Studies, Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, Miami, FL, United States,Stationed at Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, La Jolla, CA, United States,*Correspondence: Nastassia Virginia Patin,
| | - Kelly D. Goodwin
- Atlantic Oceanographic and Meteorological Laboratory, Ocean Chemistry and Ecosystems Division, National Oceanic and Atmospheric Administration, Miami, FL, United States,Stationed at Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, La Jolla, CA, United States
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8
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Vaulot D, Sim CWH, Ong D, Teo B, Biwer C, Jamy M, Lopes dos Santos A. metaPR 2 : A database of eukaryotic 18S rRNA metabarcodes with an emphasis on protists. Mol Ecol Resour 2022; 22:3188-3201. [PMID: 35762265 PMCID: PMC9796713 DOI: 10.1111/1755-0998.13674] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 05/26/2022] [Accepted: 06/20/2022] [Indexed: 01/07/2023]
Abstract
In recent years, metabarcoding has become the method of choice for investigating the composition and assembly of microbial eukaryotic communities. The number of environmental data sets published has increased very rapidly. Although unprocessed sequence files are often publicly available, processed data, in particular clustered sequences, are rarely available in a usable format. Clustered sequences are reported as operational taxonomic units (OTUs) with different similarity levels or more recently as amplicon sequence variants (ASVs). This hampers comparative studies between different environments and data sets, for example examining the biogeographical patterns of specific groups/species, as well analysing the genetic microdiversity within these groups. Here, we present a newly-assembled database of processed 18S rRNA metabarcodes that are annotated with the PR2 reference sequence database. This database, called metaPR2 , contains 41 data sets corresponding to more than 4000 samples and 90,000 ASVs. The database, which is accessible through both a web-based interface (https://shiny.metapr2.org) and an R package, should prove very useful to all researchers working on protist diversity in a variety of systems.
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Affiliation(s)
- Daniel Vaulot
- UMR 7144, ECOMAP, CNRSSorbonne Université, Station Biologique de RoscoffRoscoffFrance
| | | | - Denise Ong
- Asian School of the EnvironmentNanyang Technological UniversitySingapore
| | - Bryan Teo
- Asian School of the EnvironmentNanyang Technological UniversitySingapore
| | - Charlie Biwer
- Department of Organismal Biology (Systematic Biology)Uppsala UniversityUppsalaSweden
| | - Mahwash Jamy
- Department of Organismal Biology (Systematic Biology)Uppsala UniversityUppsalaSweden
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9
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Ren CG, Liu ZY, Zhong ZH, Wang XL, Qin S. Integrated biotechnology to mitigate green tides. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 309:119764. [PMID: 35841985 DOI: 10.1016/j.envpol.2022.119764] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Revised: 06/10/2022] [Accepted: 07/09/2022] [Indexed: 06/15/2023]
Abstract
Around the world, green tides are happening with increasing frequency because of the dual effects of increasingly intense human activity and climate change; this leads to significant impacts on marine ecology and economies. In the last decade, the world's largest green tide, which is formed by Ulva/Enteromorpha porifera, has become a recurrent phenomenon every year in the southern Yellow Sea (China), and it has been getting worse. To alleviate the impacts of such green tide outbreaks, multiple measures need to be developed. Among these approaches, biotechnology plays important roles in revealing the outbreak mechanism (e.g., molecular identification technology for algal genotypes), controlling and preventing outbreaks at the origin sites (e.g., technology to inhibit propagation), and utilizing valuable algal biomass. This review focuses on the various previously used biotechnological approaches that may be applicable to worldwide seaweed blooms that result from global climate change and environmental degradation.
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Affiliation(s)
- Cheng-Gang Ren
- Key Laboratory of Biology and Utilization of Biological Resources of Coastal Zone, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, China; Center for Ocean Mag-Science, Chinese Academy of Sciences, Qingdao, China.
| | - Zheng-Yi Liu
- Key Laboratory of Biology and Utilization of Biological Resources of Coastal Zone, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, China; Center for Ocean Mag-Science, Chinese Academy of Sciences, Qingdao, China
| | - Zhi-Hai Zhong
- Key Laboratory of Biology and Utilization of Biological Resources of Coastal Zone, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, China; Center for Ocean Mag-Science, Chinese Academy of Sciences, Qingdao, China
| | | | - Song Qin
- Key Laboratory of Biology and Utilization of Biological Resources of Coastal Zone, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, China; Center for Ocean Mag-Science, Chinese Academy of Sciences, Qingdao, China.
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10
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Aalto NJ, Schweitzer HD, Krsmanovic S, Campbell K, Bernstein HC. Diversity and Selection of Surface Marine Microbiomes in the Atlantic-Influenced Arctic. Front Microbiol 2022; 13:892634. [PMID: 35910621 PMCID: PMC9329088 DOI: 10.3389/fmicb.2022.892634] [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: 03/09/2022] [Accepted: 06/14/2022] [Indexed: 11/13/2022] Open
Abstract
Arctic marine environments are experiencing rapid changes due to the polar amplification of global warming. These changes impact the habitat of the cold-adapted microbial communities, which underpin biogeochemical cycles and marine food webs. We comparatively investigated the differences in prokaryotic and microeukaryotic taxa between summer surface water microbiomes sampled along a latitudinal transect from the ice-free southern Barents Sea and into the sea-ice-covered Nansen Basin to disentangle the dominating community (ecological) selection processes driving phylogenetic diversity. The community structure and richness of each site-specific microbiome were assessed in relation to the physical and biogeochemical conditions of the environment. A strong homogeneous deterministic selection process was inferred across the entire sampling transect via a phylogenetic null modeling approach. The microbial species richness and diversity were not negatively influenced by northward decreasing temperature and salinity. The results also suggest that regional phytoplankton blooms are a major prevalent factor in governing the bacterial community structure. This study supports the consideration that strong homogeneous selection is imposed across these cold-water marine environments uniformly, regardless of geographic assignments within either the Nansen Basin or the Barents Sea.
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Affiliation(s)
- Nerea J. Aalto
- Faculty of Biosciences, Fisheries, and Economics, UiT—The Arctic University of Norway, Tromsø, Norway
- The Arctic Centre for Sustainable Energy, UiT—The Arctic University of Norway, Tromsø, Norway
| | - Hannah D. Schweitzer
- Faculty of Biosciences, Fisheries, and Economics, UiT—The Arctic University of Norway, Tromsø, Norway
- The Arctic Centre for Sustainable Energy, UiT—The Arctic University of Norway, Tromsø, Norway
| | - Stina Krsmanovic
- Faculty of Biosciences, Fisheries, and Economics, UiT—The Arctic University of Norway, Tromsø, Norway
| | - Karley Campbell
- Faculty of Biosciences, Fisheries, and Economics, UiT—The Arctic University of Norway, Tromsø, Norway
| | - Hans C. Bernstein
- Faculty of Biosciences, Fisheries, and Economics, UiT—The Arctic University of Norway, Tromsø, Norway
- The Arctic Centre for Sustainable Energy, UiT—The Arctic University of Norway, Tromsø, Norway
- *Correspondence: Hans C. Bernstein
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11
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Liu Q, Zhou L, Zhang W, Zhang L, Tan Y, Han T, Dai M, Liao X, Huang H. Rising temperature contributed to the outbreak of a macrozooplankton Creseis acicula by enhancing its feeding and assimilation for algal food nearby the coastal Daya Bay Nuclear Power Plant. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 238:113606. [PMID: 35533450 DOI: 10.1016/j.ecoenv.2022.113606] [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: 02/11/2022] [Revised: 04/30/2022] [Accepted: 05/02/2022] [Indexed: 06/14/2023]
Abstract
An outbreak of a macrozooplankton Creseis acicula occurred in the summer of 2020 nearby the Daya Bay Nuclear Power Plant located on the coast of the Daya Bay in the South China Sea. The outbreaks of C. acicula often threaten human health, the marine environment, and other human activities including the safe operation of coastal nuclear power plants. Seawater temperature has been suggested as an important factor influencing such outbreaks. However, the underlying mechanisms through which temperature influences C. acicula remains unknown. Here, we studied the effects of temperature on the ingestion and assimilation of algal food by feeding radiocarbon-labeled algae Chlorella sp. at simulated field temperatures (19-31 °C) to C. acicula collected during the outbreak in the Daya Bay. We also quantified the allocation of the food carbon to dissolved organic carbon (DOC), CO2, and fecal pellets. The results showed that the zooplankton during the same feeding time ingested doubled or tripled algal food at higher temperatures, and it produced and released significantly more DOC, CO2, and fecal pellets with more ingested food carbon. Meanwhile, the assimilation efficiency for the ingested food carbon slightly increased from 48% to 54% with rising temperature. As a result, higher assimilation rates indicating faster growth of C. acicula were observed at higher temperatures. In addition, the high activation energy of 0.908 eV indicated that the assimilation rate was very sensitive to temperature rising. Our results show that relatively rising temperature can enhance C. acicula's ingestion and assimilation rates for algal food, benefit its growth and metabolism, and contribute to its outbreak. This study provides a mechanistic interpretation for the relationship between rising temperature and the outbreaks of C. acicula and suggests that such outbreaks may occur more frequently and widely in the warming ocean.
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Affiliation(s)
- Qingxia Liu
- Guangdong Provincial Key Laboratory of Fishery Ecology and Environment, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China; CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Linbin Zhou
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China.
| | - Wanru Zhang
- Guangdong Provincial Key Laboratory of Fishery Ecology and Environment, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China
| | - Li Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Yehui Tan
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Tingting Han
- Guangdong Provincial Key Laboratory of Fishery Ecology and Environment, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Ming Dai
- Guangdong Provincial Key Laboratory of Fishery Ecology and Environment, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Xiuli Liao
- Guangdong Provincial Key Laboratory of Fishery Ecology and Environment, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Honghui Huang
- Guangdong Provincial Key Laboratory of Fishery Ecology and Environment, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China.
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12
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Poliner E, Busch AWU, Newton L, Kim YU, Clark R, Gonzalez-Martinez SC, Jeong BR, Montgomery BL, Farré EM. Aureochromes maintain polyunsaturated fatty acid content in Nannochloropsis oceanica. PLANT PHYSIOLOGY 2022; 189:906-921. [PMID: 35166829 PMCID: PMC9157131 DOI: 10.1093/plphys/kiac052] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 01/12/2022] [Indexed: 05/05/2023]
Abstract
Nannochloropsis oceanica, like other stramenopile microalgae, is rich in long-chain polyunsaturated fatty acids (LC-PUFAs) such as eicosapentaenoic acid (EPA). We observed that fatty acid desaturases (FADs) involved in LC-PUFA biosynthesis were among the strongest blue light-induced genes in N. oceanica CCMP1779. Blue light was also necessary for maintaining LC-PUFA levels in CCMP1779 cells, and growth under red light led to a reduction in EPA content. Aureochromes are stramenopile-specific proteins that contain a light-oxygen-voltage (LOV)-sensing domain that associates with a flavin mononucleotide and is able to sense blue light. These proteins also contain a basic leucine zipper DNA-binding motif and can act as blue light-regulated transcription factors by associating with an E-box like motif, which we found enriched in the promoters of blue light-induced genes. We demonstrated that, in vitro, two CCMP1779 aureochromes were able to absorb blue light. Moreover, the loss or reduction of the expression of any of the three aureochrome genes led to a decrease in the blue light-specific induction of several FADs in CCMP1779. EPA content was also significantly reduced in NoAUREO2 and NoAUREO4 mutants. Taken together, our results indicate that aureochromes mediate blue light-dependent regulation of LC-PUFA content in N. oceanica CCMP1779 cells.
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Affiliation(s)
- Eric Poliner
- Department of Plant Biology, Michigan State University, East Lansing, Michigan, USA
- Cell and Molecular Biology Program, Michigan State University, East Lansing, Michigan, USA
| | - Andrea W U Busch
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, Michigan, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, USA
| | - Linsey Newton
- Department of Plant Biology, Michigan State University, East Lansing, Michigan, USA
| | - Young Uk Kim
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
| | - Rachel Clark
- Department of Plant Biology, Michigan State University, East Lansing, Michigan, USA
| | | | - Byeong-Ryool Jeong
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandon Key Laboratory of Energy Genetics, Shandong Institute of Energy Research, Qingdao Institute of BioEnergy and Bioprocess Technology (QiBEBT), Chinese Academy of Sciences, Qingdao, Shandong 266101, China
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Korea
| | - Beronda L Montgomery
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, Michigan, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, USA
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
| | - Eva M Farré
- Department of Plant Biology, Michigan State University, East Lansing, Michigan, USA
- Author for correspondence: (E.M.F.)
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13
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Bachy C, Wittmers F, Muschiol J, Hamilton M, Henrissat B, Worden AZ. The Land-Sea Connection: Insights Into the Plant Lineage from a Green Algal Perspective. ANNUAL REVIEW OF PLANT BIOLOGY 2022; 73:585-616. [PMID: 35259927 DOI: 10.1146/annurev-arplant-071921-100530] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The colonization of land by plants generated opportunities for the rise of new heterotrophic life forms, including humankind. A unique event underpinned this massive change to earth ecosystems-the advent of eukaryotic green algae. Today, an abundant marine green algal group, the prasinophytes, alongside prasinodermophytes and nonmarine chlorophyte algae, is facilitating insights into plant developments. Genome-level data allow identification of conserved proteins and protein families with extensive modifications, losses, or gains and expansion patterns that connect to niche specialization and diversification. Here, we contextualize attributes according to Viridiplantae evolutionary relationships, starting with orthologous protein families, and then focusing on key elements with marked differentiation, resulting in patchy distributions across green algae and plants. We place attention on peptidoglycan biosynthesis, important for plastid division and walls; phytochrome photosensors that are master regulators in plants; and carbohydrate-active enzymes, essential to all manner of carbohydratebiotransformations. Together with advances in algal model systems, these areas are ripe for discovering molecular roles and innovations within and across plant and algal lineages.
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Affiliation(s)
- Charles Bachy
- Ocean EcoSystems Biology Unit, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Fabian Wittmers
- Ocean EcoSystems Biology Unit, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Jan Muschiol
- Ocean EcoSystems Biology Unit, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Maria Hamilton
- Ocean EcoSystems Biology Unit, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, CNRS UMR 7257, Aix-Marseille Université (AMU), Marseille, France
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
- DTU Bioengineering, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Alexandra Z Worden
- Ocean EcoSystems Biology Unit, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
- Marine Biological Laboratories, Woods Hole, Massachusetts, USA
- Max Planck Institute for Evolutionary Biology, Plön, Germany
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14
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Vacant S, Benites LF, Salmeron C, Intertaglia L, Norest M, Cadoudal A, Sanchez F, Caceres C, Piganeau G. Long-Term Stability of Bacterial Associations in a Microcosm of Ostreococcus tauri (Chlorophyta, Mamiellophyceae). FRONTIERS IN PLANT SCIENCE 2022; 13:814386. [PMID: 35463414 PMCID: PMC9024300 DOI: 10.3389/fpls.2022.814386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Accepted: 02/18/2022] [Indexed: 06/14/2023]
Abstract
Phytoplankton-bacteria interactions rule over carbon fixation in the sunlit ocean, yet only a handful of phytoplanktonic-bacteria interactions have been experimentally characterized. In this study, we investigated the effect of three bacterial strains isolated from a long-term microcosm experiment with one Ostreococcus strain (Chlorophyta, Mamiellophyceae). We provided evidence that two Roseovarius strains (Alphaproteobacteria) had a beneficial effect on the long-term survival of the microalgae whereas one Winogradskyella strain (Flavobacteriia) led to the collapse of the microalga culture. Co-cultivation of the beneficial and the antagonistic strains also led to the loss of the microalga cells. Metagenomic analysis of the microcosm is consistent with vitamin B12 synthesis by the Roseovarius strains and unveiled two additional species affiliated to Balneola (Balneolia) and Muricauda (Flavobacteriia), which represent less than 4% of the reads, whereas Roseovarius and Winogradskyella recruit 57 and 39% of the reads, respectively. These results suggest that the low-frequency bacterial species may antagonize the algicidal effect of Winogradskyella in the microbiome of Ostreococcus tauri and thus stabilize the microalga persistence in the microcosm. Altogether, these results open novel perspectives into long-term stability of phytoplankton cultures.
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Affiliation(s)
- Sophie Vacant
- Integrative Biology of Marine Organisms (BIOM), Sorbonne University, Centre National de la Recherche Scientifique, Oceanological Observatory of Banyuls, Banyuls-sur-Mer, France
| | - L. Felipe Benites
- Integrative Biology of Marine Organisms (BIOM), Sorbonne University, Centre National de la Recherche Scientifique, Oceanological Observatory of Banyuls, Banyuls-sur-Mer, France
| | - Christophe Salmeron
- Sorbonne Université, Centre National de la Recherche Scientifique, Observatoire Océanologique de Banyuls, FR3724, Banyuls-sur-Mer, France
| | - Laurent Intertaglia
- Sorbonne Université, Centre National de la Recherche Scientifique, Observatoire Océanologique de Banyuls, FR3724, Banyuls-sur-Mer, France
| | - Manon Norest
- Integrative Biology of Marine Organisms (BIOM), Sorbonne University, Centre National de la Recherche Scientifique, Oceanological Observatory of Banyuls, Banyuls-sur-Mer, France
| | - Adrien Cadoudal
- Integrative Biology of Marine Organisms (BIOM), Sorbonne University, Centre National de la Recherche Scientifique, Oceanological Observatory of Banyuls, Banyuls-sur-Mer, France
| | - Frederic Sanchez
- Integrative Biology of Marine Organisms (BIOM), Sorbonne University, Centre National de la Recherche Scientifique, Oceanological Observatory of Banyuls, Banyuls-sur-Mer, France
| | - Carlos Caceres
- Integrative Biology of Marine Organisms (BIOM), Sorbonne University, Centre National de la Recherche Scientifique, Oceanological Observatory of Banyuls, Banyuls-sur-Mer, France
| | - Gwenael Piganeau
- Integrative Biology of Marine Organisms (BIOM), Sorbonne University, Centre National de la Recherche Scientifique, Oceanological Observatory of Banyuls, Banyuls-sur-Mer, France
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15
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Pang M, Liu K, Liu H. Evidence for mixotrophy in pico-chlorophytes from a new Picochlorum (Trebouxiophyceae) strain. JOURNAL OF PHYCOLOGY 2022; 58:80-91. [PMID: 34676899 DOI: 10.1111/jpy.13218] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 09/02/2021] [Accepted: 09/03/2021] [Indexed: 06/13/2023]
Abstract
Mixotrophs are increasingly recognized for their wide distribution in aquatic ecosystems and significant contributions to biogeochemical cycling. Many taxa within the phyla Chrysophyta, Cryptophyta, and Haptophyta are capable of phago-mixotrophy, however, phagotrophy in the Chlorophyta remains controversial due to insufficient research and solid evidence. In this study, we identified a new strain, Picochlorum sp. GLMF1 (Trebouxiophyceae), using 18S rRNA gene analysis and morphological observations. It displayed multi-cell division through autosporulation (two- or four-cell daughters) and has two unequal flagella that have never been reported in the genus Picochlorum. By using multiple methods, including 3D bioimaging analysis, acidic food vacuole-like compartment staining, and prey reduction calculation, we discovered and confirmed bacterivory in Picochlorum, which provided strong evidence for phago-mixotrophy in this green alga. In addition, we found that Picochlorum sp. GLMF1 cannot grow under complete darkness or prey-depleted conditions, suggesting that both light and bacteria are indispensable for this strain, and its mixotrophic nutrition mode is obligate. Like other phago-phototrophs, Picochlorum sp. GLMF1 is capable of regulating their growth and ingestion rates according to light intensity and inorganic nutrient concentration. The confirmation of mixotrophy in this Picochlorum strain advances our understanding of the trophic roles of green algae, as well as the photosynthetic picoeukaryotes, in marine microbial food webs.
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Affiliation(s)
- Mengwen Pang
- Department of Ocean Science, Hong Kong University of Science and Technology, Clear Water Bay Road, Kowloon, Hong Kong, China
| | - Kailin Liu
- Department of Ocean Science, Hong Kong University of Science and Technology, Clear Water Bay Road, Kowloon, Hong Kong, China
| | - Hongbin Liu
- Department of Ocean Science, Hong Kong University of Science and Technology, Clear Water Bay Road, Kowloon, Hong Kong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
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16
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Zhang R, Liu Y, Zhao X, Zhang H, Zhao Z, Shang Z, Lan W. Eukaryotic communities in coastal water from Shenzhen in South China. ECOTOXICOLOGY (LONDON, ENGLAND) 2021; 30:1644-1651. [PMID: 33452970 DOI: 10.1007/s10646-020-02341-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 12/25/2020] [Indexed: 06/12/2023]
Abstract
Eukaryotic microorganisms are ubiquitous in the marine environment, and have a wide variety of ecosystem functions. Shenzhen is one of the most developed cities in South China, but the eukaryotic communities in the water along its coastlines remain poorly understood. The study applied 18S rRNA gene ITS (internal transcribed spacer) sequencing to identify the eukaryotic community from twenty sites of Shenzhen coast water. The alpha-diversity of the samples between these sites were significantly different, and the seawater of eastern coast had higher alpha-diversity compared to that of the western coast. The abundance of Chlorophyta was notably higher in the seawater of western coast, but Picozoa was relatively depleted. Specifically, Cryptocaryon, Pseudovorticella, and Cyclotella were significantly higher in the water of western coast, while Guinardia, Minutocellus, and Amoebophrya were increased in eastern samples. The spatially variations of eukaryotic microorganism community in the seawater of Shenzhen coast were associated with the water quality. The results have important significance for the understanding of coastal eukaryotic community, their interaction network, and build a foundation for future management and protection of coastal water quality.
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Affiliation(s)
- Rui Zhang
- Shenzhen Institute of Guangdong Ocean University, Shenzhen, 518108, Guangdong, PR China.
- College of Food Science and Technology, Modern Biochemistry Experimental Center, Guangdong Ocean University, Zhanjiang, 518088, Guangdong, PR China.
| | - Yu Liu
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, Guangdong, PR China
| | - Xianfeng Zhao
- R&D Key Laboratory of Alien Pest Detection Technology, the Shenzhen Academy of Science and Technology for Inspection and Quarantine. Technology Center for Animal and plant Inspection and Quarantine, Shenzhen Customs, Shenzhen, 518045, Guangdong, PR China
| | - Honglian Zhang
- College of Food Science and Technology, Modern Biochemistry Experimental Center, Guangdong Ocean University, Zhanjiang, 518088, Guangdong, PR China
| | - Zhihui Zhao
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, Guangdong, PR China
| | - Zhuangzhuang Shang
- Shenzhen Institute of Guangdong Ocean University, Shenzhen, 518108, Guangdong, PR China
- College of Food Science and Technology, Modern Biochemistry Experimental Center, Guangdong Ocean University, Zhanjiang, 518088, Guangdong, PR China
| | - Wensheng Lan
- R&D Key Laboratory of Alien Pest Detection Technology, the Shenzhen Academy of Science and Technology for Inspection and Quarantine. Technology Center for Animal and plant Inspection and Quarantine, Shenzhen Customs, Shenzhen, 518045, Guangdong, PR China.
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17
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Fais G, Malavasi V, Scano P, Soru S, Caboni P, Cao G. Metabolomics and lipid profile analysis of Coccomyxa melkonianii SCCA 048. Extremophiles 2021; 25:357-368. [PMID: 34057605 PMCID: PMC8254698 DOI: 10.1007/s00792-021-01234-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 05/20/2021] [Indexed: 01/05/2023]
Abstract
With an unsupervised GC-MS metabolomics approach, polar metabolite changes of the microalgae Coccomyxa melkonianii SCCA 048 grown under standard conditions for seven weeks were studied. C. melkonianii was sampled at the Rio Irvi River, in the mining site of Montevecchio-Ingurtosu (Sardinia, Italy), which is severely contaminated by heavy metals and shows high concentrations of sulfates. The partial-least-square (PLS) analysis of the GC-MS data indicated that growth of C. melkonianii was characterized by an increase of the levels of threonic acid, myo-inositol, malic acid, and fumaric acid. Furthermore, at the sixth week of exponential phase the lipid fingerprint of C. melkonianii was studied by LC-QTOF-MS. C. melkonianii lipid extract characterized through an iterative MS/MS analysis showed the following percent levels: 61.34 ± 0.60% for triacylglycerols (TAG); 11.55 ± 0.09% for diacylglyceryltrimethyl homoserines (DGTS), 11.34 ± 0.10% for sulfoquinovosyldiacylglycerols (SQDG) and, 5.29 ± 0.04% for lysodiacylglyceryltrimethyl homoserines (LDGTS). Noteworthy, we were able to annotate different fatty acid ester of hydroxyl fatty acid, such as FAHFA (18:1_20:3), FAHFA (18:2_20:4), FAHFA (18:0_20:2), and FAHFA (18:1_18:0), with relevant biological activity. These approaches can be useful to study the biochemistry of this extremophile algae in the view of its potential exploitation in the phycoremediation of polluted mining areas.
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Affiliation(s)
- Giacomo Fais
- Interdepartmental Centre of Environmental Science and Engineering (CINSA), University of Cagliari, via San Giorgio 12, 09124, Cagliari, Italy
| | - Veronica Malavasi
- Interdepartmental Centre of Environmental Science and Engineering (CINSA), University of Cagliari, via San Giorgio 12, 09124, Cagliari, Italy
| | - Paola Scano
- Department of Life and Environmental Sciences, University of Cagliari, 09124, Cagliari, Italy
| | - Santina Soru
- Interdepartmental Centre of Environmental Science and Engineering (CINSA), University of Cagliari, via San Giorgio 12, 09124, Cagliari, Italy
| | - Pierluigi Caboni
- Department of Life and Environmental Sciences, University of Cagliari, 09124, Cagliari, Italy.
| | - Giacomo Cao
- Interdepartmental Centre of Environmental Science and Engineering (CINSA), University of Cagliari, via San Giorgio 12, 09124, Cagliari, Italy.,Department of Mechanical, Chemical and Materials Engineering, University of Cagliari, piazza d'Armi, 09123, Cagliari, Italy
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18
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Kumar V, Al Momin S, Kumar VV, Ahmed J, Al-Musallam L, Shajan AB, Al-Aqeel H, Al-Mansour H, Al-Zakri WM. Distribution and diversity of eukaryotic microalgae in Kuwait waters assessed using 18S rRNA gene sequencing. PLoS One 2021; 16:e0250645. [PMID: 33901235 PMCID: PMC8075240 DOI: 10.1371/journal.pone.0250645] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Accepted: 04/08/2021] [Indexed: 11/18/2022] Open
Abstract
The microbial communities play a crucial role in ecosystem functioning through interactions among individuals and taxonomic groups in a highly dynamic marine ecosystem. The structure and functioning of the microbial communities are often influenced by the changes in the surrounding environment. Monitoring the microbial diversity of the marine ecosystem helps to understand spatial patterns of microbial community and changes due to season, climate, and various drivers of biological diversity. Kuwait is characterized by an arid environment with a high degree of temperature variation during summer and winter. Our understanding of spatial distribution patterns of microbial communities, their diversity, and the influence of human activities on the degree of changes in the diversity of the microbial community in Kuwait territorial waters remain unclear. In this study, we employed 18S rRNA sequencing to explore marine microalgal community composition and dynamics in seawater samples collected from Kuwait waters over two seasonal cycles across six locations. A total of 448,184 sequences across 36 replicates corresponding to 12 samples from six stations were obtained. The quality-filtered sequences were clustered into 1,293 representative sequences, which were then classified into different eukaryotic taxa. This study reveals that the phytoplankton community in Kuwait waters is diverse and shows significant variations among different taxa during summer and winter. Dinoflagellates and diatoms were the most abundant season-dependent microalgae taxa in Kuwait waters. Alexandrium and Pyrophacus were abundant in summer, whereas Gonyaulax was abundant during the winter. The abundance of Coscinodiscus and Navicula, of the diatom genera, were also dependent upon both seasonal and possible anthropogenic factors. Our results demonstrate the effectiveness of a sequencing-based approach, which could be used to improve the accuracy of quantitative eukaryotic microbial community profiles.
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Affiliation(s)
- Vinod Kumar
- Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Kuwait, Kuwait
- * E-mail:
| | - Sabah Al Momin
- Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Kuwait, Kuwait
| | - Vanitha V. Kumar
- Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Kuwait, Kuwait
| | - Jasim Ahmed
- Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Kuwait, Kuwait
| | - Lamya Al-Musallam
- Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Kuwait, Kuwait
| | - Anisha B. Shajan
- Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Kuwait, Kuwait
| | - Hamed Al-Aqeel
- Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Kuwait, Kuwait
| | - Hamad Al-Mansour
- Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Kuwait, Kuwait
| | - Walid M. Al-Zakri
- Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Kuwait, Kuwait
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García-Gómez C, Yebra L, Cortés D, Sánchez A, Alonso A, Valcárcel-Pérez N, Gómez-Jakobsen F, Herrera I, Johnstone C, Mercado JM. Shifts in the protist community associated with an anticyclonic gyre in the Alboran Sea (Mediterranean Sea). FEMS Microbiol Ecol 2021; 96:5911576. [PMID: 32975560 DOI: 10.1093/femsec/fiaa197] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 09/23/2020] [Indexed: 02/06/2023] Open
Abstract
The diversity of protists was researched in the Alboran Sea (SW Mediterranean Sea) by means of high-throughput sequencing technologies based on the amplification of the V9 region of 18S rRNA. Samples were collected at different depths in seven stations following an environmental gradient from a coastal upwelling zone to the core of an oligotrophic anticyclonic gyre (AG). Sampling was performed during summer, when the water column was stratified. The superphyla Alveolata, Stramenopila and Rhizaria accounted for 84% of the total operational taxonomic units (OTUs). The most diverse groups were Dinophyceae (21% of OTUs), Marine Alveolates-II (MALV-II; 20%), Ciliophora (9%) and MALV-I (6%). In terms of read abundance, the predominant groups were Dinophyceae (29%), Bacillariophyta (14%), MALV-II (11%) and Ciliophora (11%). Samples were clustered into three groups according to the sampling depth and position. The shallow community in coastal stations presented distinguishable patterns of diatoms and ciliates compared with AG stations. These results indicate that there was a strong horizontal coupling between phytoplankton and ciliate communities. Abundance of Radiolaria and Syndiniales increased with depth. Our analyses demonstrate that the stratification disruption produced by the AG caused shifts in the trophic ecology of the plankton assemblages inducing a transition from bottom-up to top-down control.
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Affiliation(s)
- Candela García-Gómez
- Centro Oceanográfico de Málaga, Instituto Español de Oceanografía, Puerto Pesquero s/n, 29640 Fuengirola, Spain
| | - Lidia Yebra
- Centro Oceanográfico de Málaga, Instituto Español de Oceanografía, Puerto Pesquero s/n, 29640 Fuengirola, Spain
| | - Dolores Cortés
- Centro Oceanográfico de Málaga, Instituto Español de Oceanografía, Puerto Pesquero s/n, 29640 Fuengirola, Spain
| | - Antonio Sánchez
- Centro Oceanográfico de Málaga, Instituto Español de Oceanografía, Puerto Pesquero s/n, 29640 Fuengirola, Spain
| | - Aitor Alonso
- Centro Oceanográfico de Málaga, Instituto Español de Oceanografía, Puerto Pesquero s/n, 29640 Fuengirola, Spain
| | - Nerea Valcárcel-Pérez
- Centro Oceanográfico de Málaga, Instituto Español de Oceanografía, Puerto Pesquero s/n, 29640 Fuengirola, Spain
| | - Francisco Gómez-Jakobsen
- Centro Oceanográfico de Málaga, Instituto Español de Oceanografía, Puerto Pesquero s/n, 29640 Fuengirola, Spain
| | - Inma Herrera
- Centro Oceanográfico de Málaga, Instituto Español de Oceanografía, Puerto Pesquero s/n, 29640 Fuengirola, Spain
| | - Carolina Johnstone
- Centro Oceanográfico de Málaga, Instituto Español de Oceanografía, Puerto Pesquero s/n, 29640 Fuengirola, Spain
| | - Jesús M Mercado
- Centro Oceanográfico de Málaga, Instituto Español de Oceanografía, Puerto Pesquero s/n, 29640 Fuengirola, Spain
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20
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Jimenez V, Burns JA, Le Gall F, Not F, Vaulot D. No evidence of Phago-mixotropy in Micromonas polaris (Mamiellophyceae), the Dominant Picophytoplankton Species in the Arctic. JOURNAL OF PHYCOLOGY 2021; 57:435-446. [PMID: 33394518 DOI: 10.1111/jpy.13125] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 11/28/2020] [Accepted: 12/06/2020] [Indexed: 06/12/2023]
Abstract
In the Arctic Ocean, the small green alga Micromonas polaris dominates picophytoplankton during the summer months but is also present in winter. It has been previously hypothesized to be phago-mixotrophic (capable of bacteria ingestion) based on laboratory and field experiments. Prey uptake was analyzed in several M. polaris strains isolated from different regions and depths of the Arctic Ocean and in Ochromonas triangulata, a known phago-mixotroph used as a control. Measuring ingestion of either fluorescent beads or fluorescently labeled bacteria by flow cytometry, we found no evidence of phago-mixotrophy in any M. polaris strain while O. triangulata was ingesting both beads and bacteria. In addition, in silico predictions revealed that members of the genus Micromonas lack a genetic signature of phagocytotic capacity.
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Affiliation(s)
- Valeria Jimenez
- Ecology of Marine Plankton, Sorbonne Université, CNRS, UMR7144, Station Biologique de Roscoff, Roscoff, 29680, France
| | - John A Burns
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, USA
| | - Florence Le Gall
- Ecology of Marine Plankton, Sorbonne Université, CNRS, UMR7144, Station Biologique de Roscoff, Roscoff, 29680, France
| | - Fabrice Not
- Ecology of Marine Plankton, Sorbonne Université, CNRS, UMR7144, Station Biologique de Roscoff, Roscoff, 29680, France
| | - Daniel Vaulot
- Ecology of Marine Plankton, Sorbonne Université, CNRS, UMR7144, Station Biologique de Roscoff, Roscoff, 29680, France
- Asian School of the Environment, Nanyang Technological University, 50 Nanyang Avenue, Singapore, 639798, Singapore
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21
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Thomy J, Sanchez F, Gut M, Cruz F, Alioto T, Piganeau G, Grimsley N, Yau S. Combining Nanopore and Illumina Sequencing Permits Detailed Analysis of Insertion Mutations and Structural Variations Produced by PEG-Mediated Transformation in Ostreococcus tauri. Cells 2021; 10:cells10030664. [PMID: 33802698 PMCID: PMC8002553 DOI: 10.3390/cells10030664] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 03/09/2021] [Accepted: 03/15/2021] [Indexed: 12/13/2022] Open
Abstract
Ostreococcus tauri is a simple unicellular green alga representing an ecologically important group of phytoplankton in oceans worldwide. Modern molecular techniques must be developed in order to understand the mechanisms that permit adaptation of microalgae to their environment. We present for the first time in O. tauri a detailed characterization of individual genomic integration events of foreign DNA of plasmid origin after PEG-mediated transformation. Vector integration occurred randomly at a single locus in the genome and mainly as a single copy. Thus, we confirmed the utility of this technique for insertional mutagenesis. While the mechanism of double-stranded DNA repair in the O. tauri model remains to be elucidated, we clearly demonstrate by genome resequencing that the integration of the vector leads to frequent structural variations (deletions/insertions and duplications) and some chromosomal rearrangements in the genome at the insertion loci. Furthermore, we often observed variations in the vector sequence itself. From these observations, we speculate that a nonhomologous end-joining-like mechanism is employed during random insertion events, as described in plants and other freshwater algal models. PEG-mediated transformation is therefore a promising molecular biology tool, not only for functional genomic studies, but also for biotechnological research in this ecologically important marine alga.
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Affiliation(s)
- Julie Thomy
- Sorbonne Université, CNRS, UMR 7232 Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, F-66650 Banyuls-sur-Mer, France; (J.T.); (F.S.); (G.P.)
| | - Frederic Sanchez
- Sorbonne Université, CNRS, UMR 7232 Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, F-66650 Banyuls-sur-Mer, France; (J.T.); (F.S.); (G.P.)
| | - Marta Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain; (M.G.); (F.C.); (T.A.)
- Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Fernando Cruz
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain; (M.G.); (F.C.); (T.A.)
| | - Tyler Alioto
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain; (M.G.); (F.C.); (T.A.)
- Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Gwenael Piganeau
- Sorbonne Université, CNRS, UMR 7232 Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, F-66650 Banyuls-sur-Mer, France; (J.T.); (F.S.); (G.P.)
| | - Nigel Grimsley
- Sorbonne Université, CNRS, UMR 7232 Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, F-66650 Banyuls-sur-Mer, France; (J.T.); (F.S.); (G.P.)
- Correspondence: (N.G.); (S.Y.)
| | - Sheree Yau
- Sorbonne Université, CNRS, UMR 7232 Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, F-66650 Banyuls-sur-Mer, France; (J.T.); (F.S.); (G.P.)
- Correspondence: (N.G.); (S.Y.)
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22
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Lloyd C, Tan KH, Lim KL, Valu VG, Fun SMY, Chye TR, Mak HM, Sim WX, Musa SL, Ng JJQ, Bte Nordin NS, Bte Md Aidzil N, Eng ZYW, Manickavasagam P, New JY. Identification of microalgae cultured in Bold's Basal medium from freshwater samples, from a high-rise city. Sci Rep 2021; 11:4474. [PMID: 33627771 PMCID: PMC7904821 DOI: 10.1038/s41598-021-84112-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 02/12/2021] [Indexed: 11/30/2022] Open
Abstract
This study aimed at exploring microalgal heterogeneity from fresh water samples collected from inland water bodies in the heavily built city of Singapore. Culturable pure isolates (n = 94) were subject to an in-house microalgal DNA extraction method and LSU rDNA sequencing. Isolates were analysed for their predominance and distribution. A total of 17 different algal genera were identified (H = 2.8, EH = 0.6), of which Scenedesmus spp. and Chlorella spp. constituted 27.5% and 21.3% of isolates respectively, followed by Micractinium spp. (18.8%) and Chlamydomonas spp. (12.5%). We also report 16 new microalgal strains from this region. The data is important from an ecological and biotechnological perspective.
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Affiliation(s)
- Charmaine Lloyd
- School of Life Sciences and Chemical Technology - Microalgal Research Group, Ngee Ann Polytechnic, Clementi, Singapore. .,School of Health and Medical Sciences, Swinburne University of Technology, Melbourne, VIC, 3122, Australia.
| | - Kai Heng Tan
- School of Life Sciences and Chemical Technology - Microalgal Research Group, Ngee Ann Polytechnic, Clementi, Singapore
| | - Kar Leong Lim
- School of Life Sciences and Chemical Technology - Microalgal Research Group, Ngee Ann Polytechnic, Clementi, Singapore
| | - Vimala Gana Valu
- School of Life Sciences and Chemical Technology - Microalgal Research Group, Ngee Ann Polytechnic, Clementi, Singapore
| | - Sarah Mei Ying Fun
- School of Life Sciences and Chemical Technology - Microalgal Research Group, Ngee Ann Polytechnic, Clementi, Singapore
| | - Teng Rong Chye
- School of Life Sciences and Chemical Technology - Microalgal Research Group, Ngee Ann Polytechnic, Clementi, Singapore
| | - Hui Min Mak
- School of Life Sciences and Chemical Technology - Microalgal Research Group, Ngee Ann Polytechnic, Clementi, Singapore
| | - Wei Xiong Sim
- School of Life Sciences and Chemical Technology - Microalgal Research Group, Ngee Ann Polytechnic, Clementi, Singapore
| | - Sarah Liyana Musa
- School of Life Sciences and Chemical Technology - Microalgal Research Group, Ngee Ann Polytechnic, Clementi, Singapore
| | - Joscelyn Jun Quan Ng
- School of Life Sciences and Chemical Technology - Microalgal Research Group, Ngee Ann Polytechnic, Clementi, Singapore
| | - Nazurah Syazana Bte Nordin
- School of Life Sciences and Chemical Technology - Microalgal Research Group, Ngee Ann Polytechnic, Clementi, Singapore
| | - Nurhazlyn Bte Md Aidzil
- School of Life Sciences and Chemical Technology - Microalgal Research Group, Ngee Ann Polytechnic, Clementi, Singapore
| | - Zephyr Yu Wen Eng
- School of Life Sciences and Chemical Technology - Microalgal Research Group, Ngee Ann Polytechnic, Clementi, Singapore
| | - Punithavathy Manickavasagam
- School of Life Sciences and Chemical Technology - Microalgal Research Group, Ngee Ann Polytechnic, Clementi, Singapore
| | - Jen Yan New
- School of Life Sciences and Chemical Technology - Microalgal Research Group, Ngee Ann Polytechnic, Clementi, Singapore
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23
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Cyanobacteria and Algae in Clouds and Rain in the Area of puy de Dôme, Central France. Appl Environ Microbiol 2020; 87:AEM.01850-20. [PMID: 33097513 DOI: 10.1128/aem.01850-20] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 10/10/2020] [Indexed: 01/04/2023] Open
Abstract
The atmosphere contains diverse living microbes, of which the heterotrophic community has been the best studied. Microbes with other trophic modes, such as photoautotrophy, have received much less attention. In this study, culture-independent and dependent methods were used to examine the presence and diversity of oxygenic photoautotrophic microbes in clouds and rain collected at or around puy de Dôme Mountain, central France. Cloud water was collected from the summit of puy de Dôme (1,465 m above sea level [a.s.l.]) for cultivation and metagenomic analysis. Cyanobacteria, diatoms, green algae, and other oxygenic photoautotrophs were found to be recurrent members of clouds, while green algae affiliated with the Chlorellaceae were successfully cultured from three different clouds. Additionally, rain samples were collected below the mountain from Opme meteorological station (680 m a.s.l.). The abundance of chlorophyll a-containing cells and the diversity of cyanobacteria and green algae in rain were assessed by flow cytometry and amplicon sequencing. The corresponding downward flux of chlorophyll a-containing organisms to the ground, entering surface ecosystems with rain, varied with time and was estimated to be between ∼1 and >300 cells cm-2 day-1 during the sampling period. Besides abundant pollen from Pinales and Rosales, cyanobacteria of the Chroococcidiopsidales and green algae of the Trebouxiales were dominant in rain samples. Certain members of these taxa are known to be ubiquitous and stress tolerant and could use the atmosphere for dispersal. Overall, our results indicate that the atmosphere carries diverse, viable oxygenic photoautotrophic microbes and acts as a dispersal vector for this microbial guild.IMPORTANCE Information regarding the diversity and abundance of oxygenic photoautotrophs in the atmosphere is limited. More information from diverse locations is needed. These airborne organisms could have important impacts upon atmospheric processes and on the ecosystems they enter after deposition. Oxygenic photoautotrophic microbes are integral to ecosystem functioning, and some have the potential to affect human health. A better understanding of the diversity and the movements of these aeolian dispersed organisms is needed to understand their ecology, as well as how they could affect ecosystems and human health.
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24
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Ferrera I, Reñé A, Funosas D, Camp J, Massana R, Gasol JM, Garcés E. Assessment of microbial plankton diversity as an ecological indicator in the NW Mediterranean coast. MARINE POLLUTION BULLETIN 2020; 160:111691. [PMID: 33181960 DOI: 10.1016/j.marpolbul.2020.111691] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 09/15/2020] [Accepted: 09/15/2020] [Indexed: 06/11/2023]
Abstract
High-throughput sequencing of microbial assemblages has been proposed as an alternative methodology to the traditional ones used in marine monitoring and environmental assessment. Here, we evaluated pico- and nanoplankton diversity as ecological indicators in NW Mediterranean coastal waters by comparing their diversity in samples subjected to varying degrees of continental pressures. Using metabarcoding of the 16S and 18S rRNA genes, we explored whether alphadiversity indices, abundance of Operational Taxonomic Units and taxonomic groups (and their ratios) provide information on the ecological quality of coastal waters. Our results revealed that only eukaryotic diversity metrics and a limited number of prokaryotic and eukaryotic taxa displayed potential in assessing continental influences in our surveyed area, resulting thus in a restrained potential of microbial plankton diversity as an ecological indicator. Therefore, incorporating microbial plankton diversity in environmental assessment could not always result in a significant improvement of current marine monitoring strategies.
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Affiliation(s)
- Isabel Ferrera
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, CSIC, Barcelona, Catalunya, Spain; Centro Oceanográfico de Málaga, Instituto Español de Oceanografía, Fuengirola, Málaga, Spain.
| | - Albert Reñé
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, CSIC, Barcelona, Catalunya, Spain
| | - David Funosas
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, CSIC, Barcelona, Catalunya, Spain
| | - Jordi Camp
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, CSIC, Barcelona, Catalunya, Spain
| | - Ramon Massana
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, CSIC, Barcelona, Catalunya, Spain
| | - Josep M Gasol
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, CSIC, Barcelona, Catalunya, Spain
| | - Esther Garcés
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, CSIC, Barcelona, Catalunya, Spain.
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25
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Yau S, Krasovec M, Benites LF, Rombauts S, Groussin M, Vancaester E, Aury JM, Derelle E, Desdevises Y, Escande ML, Grimsley N, Guy J, Moreau H, Sanchez-Brosseau S, van de Peer Y, Vandepoele K, Gourbiere S, Piganeau G. Virus-host coexistence in phytoplankton through the genomic lens. SCIENCE ADVANCES 2020; 6:eaay2587. [PMID: 32270031 PMCID: PMC7112755 DOI: 10.1126/sciadv.aay2587] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 01/09/2020] [Indexed: 05/02/2023]
Abstract
Virus-microbe interactions in the ocean are commonly described by "boom and bust" dynamics, whereby a numerically dominant microorganism is lysed and replaced by a virus-resistant one. Here, we isolated a microalga strain and its infective dsDNA virus whose dynamics are characterized instead by parallel growth of both the microalga and the virus. Experimental evolution of clonal lines revealed that this viral production originates from the lysis of a minority of virus-susceptible cells, which are regenerated from resistant cells. Whole-genome sequencing demonstrated that this resistant-susceptible switch involved a large deletion on one chromosome. Mathematical modeling explained how the switch maintains stable microalga-virus population dynamics consistent with their observed growth pattern. Comparative genomics confirmed an ancient origin of this "accordion" chromosome despite a lack of sequence conservation. Together, our results show how dynamic genomic rearrangements may account for a previously overlooked coexistence mechanism in microalgae-virus interactions.
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Affiliation(s)
- Sheree Yau
- Sorbonne Université, CNRS, UMR 7232 Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, F-66650 Banyuls-sur-Mer, France
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM), CSIC, Barcelona, Spain
- Corresponding author. (G.P.); (S.Y.)
| | - Marc Krasovec
- Sorbonne Université, CNRS, UMR 7232 Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, F-66650 Banyuls-sur-Mer, France
| | - L. Felipe Benites
- Sorbonne Université, CNRS, UMR 7232 Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, F-66650 Banyuls-sur-Mer, France
| | - Stephane Rombauts
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark-Zwijnaarde 71, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark-Zwijnaarde 71, 9052 Ghent, Belgium
| | - Mathieu Groussin
- Department of Biological Engineering, Massachusetts Institute of Technology, 500 Technology Square NE47-378, Cambridge, MA 02139, USA
| | - Emmelien Vancaester
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark-Zwijnaarde 71, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark-Zwijnaarde 71, 9052 Ghent, Belgium
| | - Jean-Marc Aury
- Genoscope, Institut de biologie François Jacob, Commissariat à l’Energie Atomique (CEA), Université Paris-Saclay, Evry, France
| | - Evelyne Derelle
- Sorbonne Université, CNRS, UMR 7232 Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, F-66650 Banyuls-sur-Mer, France
- Univ. Brest, CNRS, IRD, Ifremer, LEMAR, F-29280 Plouzane, France
| | - Yves Desdevises
- Sorbonne Université, CNRS, UMR 7232 Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, F-66650 Banyuls-sur-Mer, France
| | - Marie-Line Escande
- Sorbonne Université, CNRS, UMR 7232 Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, F-66650 Banyuls-sur-Mer, France
| | - Nigel Grimsley
- Sorbonne Université, CNRS, UMR 7232 Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, F-66650 Banyuls-sur-Mer, France
| | - Julie Guy
- Genoscope, Institut de biologie François Jacob, Commissariat à l’Energie Atomique (CEA), Université Paris-Saclay, Evry, France
| | - Hervé Moreau
- Sorbonne Université, CNRS, UMR 7232 Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, F-66650 Banyuls-sur-Mer, France
| | - Sophie Sanchez-Brosseau
- Sorbonne Université, CNRS, UMR 7232 Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, F-66650 Banyuls-sur-Mer, France
| | - Yves van de Peer
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark-Zwijnaarde 71, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark-Zwijnaarde 71, 9052 Ghent, Belgium
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0028, South Africa
| | - Klaas Vandepoele
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark-Zwijnaarde 71, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark-Zwijnaarde 71, 9052 Ghent, Belgium
| | - Sebastien Gourbiere
- Laboratoire Génome et Développement des Plantes, Université de Perpignan Via Domitia, UMR 5096, 52 Avenue Paul Alduy, 66860 Perpignan, France
| | - Gwenael Piganeau
- Sorbonne Université, CNRS, UMR 7232 Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, F-66650 Banyuls-sur-Mer, France
- Corresponding author. (G.P.); (S.Y.)
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26
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Yau S, Lopes Dos Santos A, Eikrem W, Gérikas Ribeiro C, Gourvil P, Balzano S, Escande ML, Moreau H, Vaulot D. Mantoniella beaufortii and Mantoniella baffinensis sp. nov. (Mamiellales, Mamiellophyceae), two new green algal species from the high arctic 1. JOURNAL OF PHYCOLOGY 2020; 56:37-51. [PMID: 31608987 DOI: 10.1111/jpy.12932] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Accepted: 07/22/2019] [Indexed: 06/10/2023]
Abstract
Members of the class Mamiellophyceae comprise species that can dominate picophytoplankton diversity in polar waters. Yet, polar species are often morphologically indistinguishable from temperate species, although clearly separated by molecular features. Here we examine four Mamiellophyceae strains from the Canadian Arctic. The 18S rRNA and Internal Transcribed Spacer 2 (ITS2) gene phylogeny place these strains within the family Mamiellaceae (Mamiellales, Mamiellophyceae) in two separate clades of the genus Mantoniella. ITS2 synapomorphies support their placement as two new species, Mantoniella beaufortii and Mantoniella baffinensis. Both species have round green cells with diameter between 3 and 5 μm, one long flagellum and a short flagellum (~1 μm) and are covered by spiderweb-like scales, making both species similar to other Mantoniella species. Morphologically, M. beaufortii and M. baffinensis are most similar to the cosmopolitan M. squamata with only minor differences in scale structure distinguishing them. Screening of global marine metabarcoding data sets indicates M. beaufortii has only been recorded in seawater and sea ice samples from the Arctic, while no environmental barcode matches M. baffinensis. Like other Mamiellophyceae genera that have distinct polar and temperate species, the polar distribution of these new species suggests they are cold or ice-adapted Mantoniella species.
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Affiliation(s)
- Sheree Yau
- Integrative Marine Biology Laboratory (BIOM), CNRS, UMR7232, Sorbonne Université, Banyuls sur Mer, France
| | - Adriana Lopes Dos Santos
- Asian School of the Environment, Nanyang Technological University, 50 Nanyang Avenue, Singapore, Singapore
- Centro de Genómica, Ecología y Medio Ambiente, Facultad de Ciencias, Universidad Mayor, Camino La Pirámide 5750, Huechuraba, Santiago, Chile
| | - Wenche Eikrem
- Norwegian Institute for Water Research, Gaustadallèen 21, 0349, Oslo, Norway
- Department of Biosciences, University of Oslo, P.O. box 1066, Blindern, Oslo, 0316, Norway
- Natural History Museum, University of Oslo, P.O. box 1172 Blindern, 0318, Oslo, Norway
| | | | - Priscillia Gourvil
- Sorbonne Université, CNRS, UMR7144, Station Biologique de Roscoff, Roscoff, France
| | - Sergio Balzano
- Stazione Zoologica Anton Dohrn, Istituto Nazionale di Biologia, Ecologia e Biotecnologie Marine, Naples, Italy
| | - Marie-Line Escande
- Integrative Marine Biology Laboratory (BIOM), CNRS, UMR7232, Sorbonne Université, Banyuls sur Mer, France
| | - Hervé Moreau
- Integrative Marine Biology Laboratory (BIOM), CNRS, UMR7232, Sorbonne Université, Banyuls sur Mer, France
| | - Daniel Vaulot
- Sorbonne Université, CNRS, UMR7144, Station Biologique de Roscoff, Roscoff, France
- Asian School of the Environment, Nanyang Technological University, 50 Nanyang Avenue, Singapore, Singapore
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27
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Lukešová S, Karlicki M, Tomečková Hadariová L, Szabová J, Karnkowska A, Hampl V. Analyses of environmental sequences and two regions of chloroplast genomes revealed the presence of new clades of photosynthetic euglenids in marine environments. ENVIRONMENTAL MICROBIOLOGY REPORTS 2020; 12:78-91. [PMID: 31845515 DOI: 10.1111/1758-2229.12817] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 11/23/2019] [Accepted: 11/30/2019] [Indexed: 06/10/2023]
Abstract
Euglenophyceae are unicellular algae with the majority of their diversity known from small freshwater reservoirs. Only two dozen species have been described to occur in marine habitats, but their abundance and diversity remain unexplored. Phylogenetic studies revealed marine prasinophyte green alga, Pyramimonas parkeae, as the closest extant relative of the euglenophytes' plastid, but similarly to euglenophytes, our knowledge about the diversity of Pyramimonadales is limited. Here we explored Euglenophyceae and Pyramimonadales phylogenetic diversity in marine environmental samples. We yielded 18S rDNA and plastid 16S rDNA sequences deposited in public repositories and reconstructed Euglenophyceae reference trees. We searched high-throughput environmental sequences from the TARA Oceans expedition and Ocean Sampling Day initiative for 18S rDNA and 16S rDNA, placed them in the phylogenetic context and estimated their relative abundances. To avoid polymerase chain reaction (PCR) bias, we also exploited metagenomic data from the TARA Oceans expedition for the presence of rRNA sequences from these groups. Finally, we targeted these protists in coastal samples by specific PCR amplification of two parts of the plastid genome uniquely shared between euglenids and Pyramimonadales. All approaches revealed previously undetected, but relatively low-abundant lineages of marine Euglenophyceae. Surprisingly, some of those lineages are branching within the freshwater or brackish genera.
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Affiliation(s)
- Soňa Lukešová
- Faculty of Science, Department of Parasitology, BIOCEV, Charles University, Průmyslová, 595, Vestec, 25250, Czech Republic
| | - Michał Karlicki
- Faculty of Biology, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, Warsaw, 02 089, Poland
| | - Lucia Tomečková Hadariová
- Faculty of Science, Department of Parasitology, BIOCEV, Charles University, Průmyslová, 595, Vestec, 25250, Czech Republic
| | - Jana Szabová
- Faculty of Science, Department of Parasitology, BIOCEV, Charles University, Průmyslová, 595, Vestec, 25250, Czech Republic
| | - Anna Karnkowska
- Faculty of Biology, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, Warsaw, 02 089, Poland
| | - Vladimír Hampl
- Faculty of Science, Department of Parasitology, BIOCEV, Charles University, Průmyslová, 595, Vestec, 25250, Czech Republic
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28
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Abstract
Nitrous oxide (N2O), the third most important greenhouse gas in the atmosphere, is produced in great quantities by microalgae, but molecular mechanisms remain elusive. Here we show that the green microalga Chlamydomonas reinhardtii produces N2O in the light by a reduction of NO driven by photosynthesis and catalyzed by flavodiiron proteins, the dark N2O production being catalyzed by a cytochrome p450. Both mechanisms of N2O production are present in chlorophytes, but absent from diatoms. Our study provides an unprecedented mechanistic understanding of N2O production by microalgae, allowing a better assessment of N2O-producing hot spots in aquatic environments. Nitrous oxide (N2O), a potent greenhouse gas in the atmosphere, is produced mostly from aquatic ecosystems, to which algae substantially contribute. However, mechanisms of N2O production by photosynthetic organisms are poorly described. Here we show that the green microalga Chlamydomonas reinhardtii reduces NO into N2O using the photosynthetic electron transport. Through the study of C. reinhardtii mutants deficient in flavodiiron proteins (FLVs) or in a cytochrome p450 (CYP55), we show that FLVs contribute to NO reduction in the light, while CYP55 operates in the dark. Both pathways are active when NO is produced in vivo during the reduction of nitrites and participate in NO homeostasis. Furthermore, NO reduction by both pathways is restricted to chlorophytes, organisms particularly abundant in ocean N2O-producing hot spots. Our results provide a mechanistic understanding of N2O production in eukaryotic phototrophs and represent an important step toward a comprehensive assessment of greenhouse gas emission by aquatic ecosystems.
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Chambouvet A, Monier A, Maguire F, Itoïz S, del Campo J, Elies P, Edvardsen B, Eikreim W, Richards TA. Intracellular Infection of Diverse Diatoms by an Evolutionary Distinct Relative of the Fungi. Curr Biol 2019; 29:4093-4101.e4. [DOI: 10.1016/j.cub.2019.09.074] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 07/12/2019] [Accepted: 09/30/2019] [Indexed: 11/29/2022]
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Wetherbee R, Rossetto Marcelino V, Costa JF, Grant B, Crawford S, Waller RF, Andersen RA, Berry D, McFadden GI, Verbruggen H. A new marine prasinophyte genus alternates between a flagellate and a dominant benthic stage with microrhizoids for adhesion. JOURNAL OF PHYCOLOGY 2019; 55:1210-1225. [PMID: 31393007 DOI: 10.1111/jpy.12909] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 06/13/2019] [Indexed: 06/10/2023]
Abstract
Prasinophytes (Chlorophyta) are a diverse, paraphyletic group of planktonic microalgae for which benthic species are largely unknown. Here, we report a sand-dwelling, marine prasinophyte with several novel features observed in clonal cultures established from numerous locations around Australia. The new genus and species, which we name Microrhizoidea pickettheapsiorum (Mamiellophyceae), alternates between a benthic palmelloid colony, where cell division occurs, and a planktonic flagellate. Flagellates are short lived, settle and quickly resorb their flagella, the basal bodies then nucleate novel tubular appendages, termed "microrhizoids", that lack an axoneme and function to anchor benthic cells to the substratum. To our knowledge, microrhizoids have not been observed in any other green alga or protist, are slightly smaller in diameter than flagella, generally contain nine microtubules, are long (3-5 times the length of flagella) and are not encased in scales. Following settlement, cell divisions result in a loose, palmelloid colony, each cell connected to the substratum by two microrhizoids. Flagellates are round to bean-shaped with two long, slightly uneven flagella. Both benthic cells and flagellates, along with their flagella, are encased in thin scales. Phylogenies based on the complete chloroplast genome of Microrhizoidea show that it is clearly a member of the Mamiellophyceae, most closely related to Dolichomastix tenuilepsis. More taxon-rich phylogenetic analyses of the 18S rRNA gene, including metabarcodes from the Tara Oceans and Ocean Sampling Day projects, confidently show the distinctive nature of Microrhizoidea, and that the described biodiversity of the Mamiellophyceae is a fraction of its real biodiversity. The discovery of a largely benthic prasinophyte changes our perspective on this group of algae and, along with the observation of other potential benthic lineages in environmental sequences, illustrates that benthic habitats can be a rich ground for algal biodiscovery.
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Affiliation(s)
- Richard Wetherbee
- School of BioSciences, University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Vanessa Rossetto Marcelino
- Westmead Institute for Medical Research, The University of Sydney, Westmead, New South Wales, 2145, Australia
| | - Joana F Costa
- School of BioSciences, University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Brenna Grant
- School of BioSciences, University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Simon Crawford
- School of BioSciences, University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Ross F Waller
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Robert A Andersen
- Friday Harbor Laboratories, University of Washington, Seattle, Washington, USA
| | - Drew Berry
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia
| | - Geoffrey I McFadden
- School of BioSciences, University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Heroen Verbruggen
- School of BioSciences, University of Melbourne, Parkville, Victoria, 3010, Australia
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31
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Benites LF, Poulton N, Labadie K, Sieracki ME, Grimsley N, Piganeau G. Single cell ecogenomics reveals mating types of individual cells and ssDNA viral infections in the smallest photosynthetic eukaryotes. Philos Trans R Soc Lond B Biol Sci 2019; 374:20190089. [PMID: 31587637 DOI: 10.1098/rstb.2019.0089] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Planktonic photosynthetic organisms of the class Mamiellophyceae include the smallest eukaryotes (less than 2 µm), are globally distributed and form the basis of coastal marine ecosystems. Eight complete fully annotated 13-22 Mb genomes from three genera, Ostreococcus, Bathycoccus and Micromonas, are available from previously isolated clonal cultured strains and provide an ideal resource to explore the scope and challenges of analysing single cell amplified genomes (SAGs) isolated from a natural environment. We assembled data from 12 SAGs sampled during the Tara Oceans expedition to gain biological insights about their in situ ecology, which might be lost by isolation and strain culture. Although the assembled nuclear genomes were incomplete, they were large enough to infer the mating types of four Ostreococcus SAGs. The systematic occurrence of sequences from the mitochondria and chloroplast, representing less than 3% of the total cell's DNA, intimates that SAGs provide suitable substrates for detection of non-target sequences, such as those of virions. Analysis of the non-Mamiellophyceae assemblies, following filtering out cross-contaminations during the sequencing process, revealed two novel 1.6 and 1.8 kb circular DNA viruses, and the presence of specific Bacterial and Oomycete sequences suggests that these organisms might co-occur with the Mamiellales. This article is part of a discussion meeting issue 'Single cell ecology'.
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Affiliation(s)
- L Felipe Benites
- Integrative Biology of Marine Organisms (BIOM), Sorbonne University, CNRS, Oceanological Observatory of Banyuls, 66650 Banyuls-sur-Mer, France
| | - Nicole Poulton
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME 04544, USA
| | - Karine Labadie
- Genoscope, Institut de Biologie François-Jacob, Commissariat à l'Energie Atomique, université Paris Saclay, 9105 Evry, France
| | | | - Nigel Grimsley
- Integrative Biology of Marine Organisms (BIOM), Sorbonne University, CNRS, Oceanological Observatory of Banyuls, 66650 Banyuls-sur-Mer, France
| | - Gwenael Piganeau
- Integrative Biology of Marine Organisms (BIOM), Sorbonne University, CNRS, Oceanological Observatory of Banyuls, 66650 Banyuls-sur-Mer, France
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32
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Strategies among phytoplankton in response to alleviation of nutrient stress in a subtropical gyre. ISME JOURNAL 2019; 13:2984-2997. [PMID: 31439897 DOI: 10.1038/s41396-019-0489-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 07/07/2019] [Accepted: 08/02/2019] [Indexed: 11/08/2022]
Abstract
Despite generally low primary productivity and diatom abundances in oligotrophic subtropical gyres, the North Atlantic Subtropical Gyre (NASG) exhibits significant diatom-driven carbon export on an annual basis. Subsurface pulses of nutrients likely fuel brief episodes of diatom growth, but the exact mechanisms utilized by diatoms in response to these nutrient injections remain understudied within near-natural settings. Here we simulated delivery of subsurface nutrients and compare the response among eukaryotic phytoplankton using a combination of physiological techniques and metatranscriptomics. We show that eukaryotic phytoplankton groups exhibit differing levels of transcriptional responsiveness and expression of orthologous genes in response to release from nutrient limitation. In particular, strategies for use of newly delivered nutrients are distinct among phytoplankton groups. Diatoms channel new nitrate to growth-related strategies while physiological measurements and gene expression patterns of other groups suggest alternative strategies. The gene expression patterns displayed here provide insights into the cellular mechanisms that underlie diatom subsistence during chronic nitrogen-depleted conditions and growth upon nutrient delivery that can enhance carbon export from the surface ocean.
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33
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De Luca D, Kooistra WHCF, Sarno D, Gaonkar CC, Piredda R. Global distribution and diversity of Chaetoceros (Bacillariophyta, Mediophyceae): integration of classical and novel strategies. PeerJ 2019; 7:e7410. [PMID: 31489261 PMCID: PMC6705385 DOI: 10.7717/peerj.7410] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Accepted: 07/04/2019] [Indexed: 11/20/2022] Open
Abstract
Information on taxa distribution is a prerequisite for many research fields, and biological records are a major source of data contributing to biogeographic studies. The Global Biodiversity Information Facility (GBIF) and the Ocean Biogeographic Information System (OBIS) are important infrastructures facilitating free and open access to classical biological data from several sources in both temporal and spatial scales. Over the last ten years, high throughput sequencing (HTS) metabarcoding data have become available, which constitute a great source of detailed occurrence data. Among the global sampling projects that have contributed to such data are Tara Oceans and the Ocean Sampling Day (OSD). Integration of classical and metabarcoding data may aid a more comprehensive assessment of the geographic range of species, especially of microscopic ones such as protists. Rare, small and cryptic species are often ignored in surveys or mis-assigned with the classical approaches. Here we show how integration of data from various sources can contribute to insight in the biogeography and diversity at the genus- and species-level using Chaetoceros as study system, one of the most diverse and abundant genera among marine planktonic diatoms. Chaetoceros records were extracted from GBIF and OBIS and literature data were collected by means of a Google Scholar search. Chaetoceros references barcodes where mapped against the metabarcode datasets of Tara Oceans (210 sites) and OSD (144 sites). We compared the resolution of different data sources in determining the global distribution of the genus and provided examples, at the species level, of detection of cryptic species, endemism and cosmopolitan or restricted distributions. Our results highlighted at genus level a comparable picture from the different sources but a more complete assessment when data were integrated. Both the importance of the integration but also the challenges related to it were illustrated. Chaetoceros data collected in this study are organised and available in the form of tables and maps, providing a powerful tool and a baseline for further research in e.g., ecology, conservation and evolutionary biology.
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Affiliation(s)
- Daniele De Luca
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Napoli, Italy
| | - Wiebe H C F Kooistra
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Napoli, Italy
| | - Diana Sarno
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Napoli, Italy
| | - Chetan C Gaonkar
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Napoli, Italy.,Department of Oceanography, Texas A&M University, College Station, TX, United States of America
| | - Roberta Piredda
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Napoli, Italy
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34
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Metz S, Singer D, Domaizon I, Unrein F, Lara E. Global distribution of Trebouxiophyceae diversity explored by high-throughput sequencing and phylogenetic approaches. Environ Microbiol 2019; 21:3885-3895. [PMID: 31299138 DOI: 10.1111/1462-2920.14738] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 06/22/2019] [Accepted: 07/10/2019] [Indexed: 11/30/2022]
Abstract
Trebouxiophyceae are a ubiquitous class of Chlorophyta encountered in aquatic and terrestrial environments. Most taxa are photosynthetic, and many acts as photobionts in symbiotic relationships, while others are free-living. Trebouxiophyceae have also been widely investigated for their use for biotechnological applications. In this work, we aimed at obtaining a comprehensive image of their diversity by compiling the information of 435 freshwater, soil and marine environmental DNA samples surveyed with Illumina sequencing technology in order to search for the most relevant environments for bioprospecting. Freshwater and soil were most diverse and shared more than half of all operational taxonomic units (OTUs), however, their communities were significantly distinct. Oceans hosted the highest genetic novelty, and did not share any OTUs with the other environments; also, marine samples host more diversity in warm waters. Symbiotic genera usually found in lichens such as Trebouxia, Myrmecia and Symbiochloris were also abundantly detected in the ocean, suggesting either free-living lifestyles or unknown symbiotic relationships with marine planktonic organisms. Altogether, our study opens the way to new prospection for trebouxiophycean strains, especially in understudied environments like the ocean.
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Affiliation(s)
- Sebastian Metz
- Instituto Tecnológico de Chascomús (INTECH), UNSAM-CONICET, Chascomús, Buenos Aires, Argentina
| | - David Singer
- Laboratory of Soil Biodiversity, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland.,Department of Zoology, Institute of Biosciences, University of São Paulo, Butantã, São Paulo, Brazil
| | | | - Fernando Unrein
- Instituto Tecnológico de Chascomús (INTECH), UNSAM-CONICET, Chascomús, Buenos Aires, Argentina
| | - Enrique Lara
- Real Jardín Botánico de Madrid, CSIC, Madrid, Spain
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35
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Turmel M, Lopes Dos Santos A, Otis C, Sergerie R, Lemieux C. Tracing the Evolution of the Plastome and Mitogenome in the Chloropicophyceae Uncovered Convergent tRNA Gene Losses and a Variant Plastid Genetic Code. Genome Biol Evol 2019; 11:1275-1292. [PMID: 30937436 PMCID: PMC6486808 DOI: 10.1093/gbe/evz074] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/30/2019] [Indexed: 01/06/2023] Open
Abstract
The tiny green algae belonging to the Chloropicophyceae play a key role in marine phytoplankton communities; this newly erected class of prasinophytes comprises two genera (Chloropicon and Chloroparvula) containing each several species. We sequenced the plastomes and mitogenomes of eight Chloropicon and five Chloroparvula species to better delineate the phylogenetic affinities of these taxa and to infer the suite of changes that their organelle genomes sustained during evolution. The relationships resolved in organelle-based phylogenomic trees were essentially congruent with previously reported rRNA trees, and similar evolutionary trends but distinct dynamics were identified for the plastome and mitogenome. Although the plastome sustained considerable changes in gene content and order at the time the two genera split, subsequently it remained stable and maintained a very small size. The mitogenome, however, was remodeled more gradually and showed more fluctuation in size, mainly as a result of expansions/contractions of intergenic regions. Remarkably, the plastome and mitogenome lost a common set of three tRNA genes, with the trnI(cau) and trnL(uaa) losses being accompanied with important variations in codon usage. Unexpectedly, despite the disappearance of trnI(cau) from the plastome in the Chloroparvula lineage, AUA codons (the codons recognized by this gene product) were detected in certain plastid genes. By comparing the sequences of plastid protein-coding genes from chloropicophycean and phylogenetically diverse chlorophyte algae with those of the corresponding predicted proteins, we discovered that the AUA codon was reassigned from isoleucine to methionine in Chloroparvula. This noncanonical genetic code has not previously been uncovered in plastids.
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Affiliation(s)
- Monique Turmel
- Département de biochimie, de microbiologie et de bio-informatique, Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec City, Québec, Canada
| | - Adriana Lopes Dos Santos
- Asian School of the Environment, Nanyang Technological University, Singapore.,CNRS, Sorbonne Université, UMR 7144 Station Biologique de Roscoff, Roscoff, France
| | - Christian Otis
- Département de biochimie, de microbiologie et de bio-informatique, Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec City, Québec, Canada
| | - Roxanne Sergerie
- Département de biochimie, de microbiologie et de bio-informatique, Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec City, Québec, Canada
| | - Claude Lemieux
- Département de biochimie, de microbiologie et de bio-informatique, Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec City, Québec, Canada
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36
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Sanchez F, Geffroy S, Norest M, Yau S, Moreau H, Grimsley N. Simplified Transformation of Ostreococcus tauri Using Polyethylene Glycol. Genes (Basel) 2019; 10:E399. [PMID: 31130696 PMCID: PMC6562926 DOI: 10.3390/genes10050399] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 05/16/2019] [Accepted: 05/21/2019] [Indexed: 12/21/2022] Open
Abstract
Ostreococcustauri is an easily cultured representative of unicellular algae (class Mamiellophyceae) that abound in oceans worldwide. Eight complete 13-22 Mb genomes of phylogenetically divergent species within this class are available, and their DNA sequences are nearly always present in metagenomic data produced from marine samples. Here we describe a simplified and robust transformation protocol for the smallest of these algae (O. tauri). Polyethylene glycol (PEG) treatment was much more efficient than the previously described electroporation protocol. Short (2 min or less) incubation times in PEG gave >104 transformants per microgram DNA. The time of cell recovery after transformation could be reduced to a few hours, permitting the experiment to be done in a day rather than overnight as used in previous protocols. DNA was randomly inserted in the O. tauri genome. In our hands PEG was 20-40-fold more efficient than electroporation for the transformation of O. tauri, and this improvement will facilitate mutagenesis of all of the dispensable genes present in the tiny O. tauri genome.
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Affiliation(s)
- Frédéric Sanchez
- CNRS UMR7232 BIOM (Biologie Intégrative des Organismes Marin) Sorbonne University, 66650 Banyuls sur Mer, France.
| | - Solène Geffroy
- IFREMER, Centre Atlantique, 44331 Nantes CEDEX 03, France.
| | - Manon Norest
- CNRS UMR7232 BIOM (Biologie Intégrative des Organismes Marin) Sorbonne University, 66650 Banyuls sur Mer, France.
| | - Sheree Yau
- CNRS UMR7232 BIOM (Biologie Intégrative des Organismes Marin) Sorbonne University, 66650 Banyuls sur Mer, France.
| | - Hervé Moreau
- CNRS UMR7232 BIOM (Biologie Intégrative des Organismes Marin) Sorbonne University, 66650 Banyuls sur Mer, France.
| | - Nigel Grimsley
- CNRS UMR7232 BIOM (Biologie Intégrative des Organismes Marin) Sorbonne University, 66650 Banyuls sur Mer, France.
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37
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Tragin M, Vaulot D. Novel diversity within marine Mamiellophyceae (Chlorophyta) unveiled by metabarcoding. Sci Rep 2019; 9:5190. [PMID: 30914730 PMCID: PMC6435750 DOI: 10.1038/s41598-019-41680-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 03/13/2019] [Indexed: 11/21/2022] Open
Abstract
Mamiellophyceae (unicellular green algae) are a key phytoplankton group in coastal waters. Although extensively studied over the last 20 years, the overall oceanic distribution of the major species/clades is still poorly known. To address this problem, we analyzed the 2014 Ocean Sampling Day (OSD) metabarcoding dataset providing sequences from the V4 hypervariable region of the 18S rRNA gene for 157 samples collected at 143 mostly coastal stations. Mamiellophyceae were found at nearly all OSD stations and represented 55% of the green microalgae (Chlorophyta) reads. We performed phylogenetic analyses of unique OSD metabarcodes (amplicon single variants, ASVs) and GenBank reference sequences from cultures and from the environment, focusing on the four most represented genera: Ostreococcus (45% of the Mamiellophyceae reads), Micromonas (34%), Bathycoccus (10%) and Mantoniella (8.7%). These analyses uncovered novel diversity within each genus except Bathycoccus. In Ostreococcus, a new clade (E) was the second most represented clade after Ostreococcus "lucimarinus". Micromonas could be separated into nine clades, exceeding the six species and candidate species already described. Finally, we found two new environmental clades within Mantoniella. Each Mamiellophyceae clade had a specific distribution in the OSD dataset suggesting that they are adapted to different ecological niches.
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Affiliation(s)
- Margot Tragin
- Sorbonne Université, CNRS, UMR 7144, Station Biologique, Place Georges Teissier, 29680, Roscoff, France
| | - Daniel Vaulot
- Sorbonne Université, CNRS, UMR 7144, Station Biologique, Place Georges Teissier, 29680, Roscoff, France.
- Asian School of the Environment, Nanyang Technological University, Singapore, Singapore.
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38
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Nelson DR, Chaiboonchoe A, Fu W, Hazzouri KM, Huang Z, Jaiswal A, Daakour S, Mystikou A, Arnoux M, Sultana M, Salehi-Ashtiani K. Potential for Heightened Sulfur-Metabolic Capacity in Coastal Subtropical Microalgae. iScience 2019; 11:450-465. [PMID: 30684492 PMCID: PMC6348204 DOI: 10.1016/j.isci.2018.12.035] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 11/07/2018] [Accepted: 12/28/2018] [Indexed: 12/05/2022] Open
Abstract
The activities of microalgae support nutrient cycling that helps to sustain aquatic and terrestrial ecosystems. Most microalgal species, especially those from the subtropics, are genomically uncharacterized. Here we report the isolation and genomic characterization of 22 microalgal species from subtropical coastal regions belonging to multiple clades and three from temperate areas. Halotolerant strains including Halamphora, Dunaliella, Nannochloris, and Chloroidium comprised the majority of these isolates. The subtropical-based microalgae contained arrays of methyltransferase, pyridine nucleotide-disulfide oxidoreductase, abhydrolase, cystathionine synthase, and small-molecule transporter domains present at high relative abundance. We found that genes for sulfate transport, sulfotransferase, and glutathione S-transferase activities were especially abundant in subtropical, coastal microalgal species and halophytic species in general. Our metabolomics analyses indicate lineage- and habitat-specific sets of biomolecules implicated in niche-specific biological processes. This work effectively expands the collection of available microalgal genomes by ∼50%, and the generated resources provide perspectives for studying halophyte adaptive traits. We have sequenced 20+ microallgal genomes from the subtropics This new collection increases the available microalgal genomes by ∼50% Metabolomics indicates lineage- and habitat-specificity of biomolecules Coastal, subtropical species of microalgae show expansion of sulfur-metabolic genes
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Affiliation(s)
- David R Nelson
- Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, UAE
| | | | - Weiqi Fu
- Division of Science and Math, New York University Abu Dhabi, Abu Dhabi, UAE
| | - Khaled M Hazzouri
- Khalifa Center for Genetic Engineering and Biotechnology (KCGEB), United Arab Emirates University, Al-Ain, UAE
| | - Ziyuan Huang
- Department of Computer Science, New York University Shanghai, Shanghai, China
| | - Ashish Jaiswal
- Division of Science and Math, New York University Abu Dhabi, Abu Dhabi, UAE
| | - Sarah Daakour
- Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, UAE
| | - Alexandra Mystikou
- Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, UAE
| | - Marc Arnoux
- Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, UAE
| | - Mehar Sultana
- Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, UAE
| | - Kourosh Salehi-Ashtiani
- Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, UAE; Division of Science and Math, New York University Abu Dhabi, Abu Dhabi, UAE.
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