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Zarcero J, Antich A, Rius M, Wangensteen OS, Turon X. A new sampling device for metabarcoding surveillance of port communities and detection of non-indigenous species. iScience 2024; 27:108588. [PMID: 38111684 PMCID: PMC10726295 DOI: 10.1016/j.isci.2023.108588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 10/04/2023] [Accepted: 11/23/2023] [Indexed: 12/20/2023] Open
Abstract
Metabarcoding techniques are revolutionizing studies of marine biodiversity. They can be used for monitoring non-indigenous species (NIS) in ports and harbors. However, they are often biased by inconsistent sampling methods and incomplete reference databases. Logistic constraints in ports prompt the development of simple, easy-to-deploy samplers. We tested a new device called polyamide mesh for ports organismal monitoring (POMPOM) with a high surface-to-volume ratio. POMPOMS were deployed inside a fishing and recreational port in the Mediterranean alongside conventional settlement plates. We also compiled a curated database with cytochrome oxidase (COI) sequences of Mediterranean NIS. COI metabarcoding of the communities settled in the POMPOMs captured a similar biodiversity than settlement plates, with shared molecular operational units (MOTUs) representing ca. 99% of reads. 38 NIS were detected in the port accounting for ca. 26% of reads. POMPOMs were easy to deploy and handle and provide an efficient method for NIS surveillance.
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Affiliation(s)
- Jesús Zarcero
- Department of Marine Ecology, Centre for Advanced Studies of Blanes (CEAB), CSIC, 17300 Blanes, Catalonia, Spain
- Department of Evolutionary Biology, Ecology and Environmental Sciences and Biodiversity Research Institute (IRBio), University of Barcelona, 08028 Barcelona, Catalonia, Spain
| | - Adrià Antich
- Department of Marine Ecology, Centre for Advanced Studies of Blanes (CEAB), CSIC, 17300 Blanes, Catalonia, Spain
| | - Marc Rius
- Department of Marine Ecology, Centre for Advanced Studies of Blanes (CEAB), CSIC, 17300 Blanes, Catalonia, Spain
- Department of Zoology, Centre for Ecological Genomics and Wildlife Conservation, University of Johannesburg, Auckland Park Johannesburg 2006, South Africa
| | - Owen S. Wangensteen
- Department of Evolutionary Biology, Ecology and Environmental Sciences and Biodiversity Research Institute (IRBio), University of Barcelona, 08028 Barcelona, Catalonia, Spain
| | - Xavier Turon
- Department of Marine Ecology, Centre for Advanced Studies of Blanes (CEAB), CSIC, 17300 Blanes, Catalonia, Spain
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2
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Justel-Díez M, Delgadillo-Nuño E, Gutiérrez-Barral A, García-Otero P, Alonso-Barciela I, Pereira-Villanueva P, Álvarez-Salgado XA, Velando A, Teira E, Fernández E. Inputs of seabird guano alter microbial growth, community composition and the phytoplankton-bacterial interactions in a coastal system. Environ Microbiol 2023. [PMID: 36752021 DOI: 10.1111/1462-2920.16349] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 02/06/2023] [Indexed: 02/09/2023]
Abstract
Seabird guano enters coastal waters providing bioavailable substrates for microbial plankton, but their role in marine ecosystem functioning remains poorly understood. Two concentrations of the water soluble fraction (WSF) of gull guano were added to different natural microbial communities collected in surface waters from the Ría de Vigo (NW Spain) in spring, summer, and winter. Samples were incubated with or without antibiotics (to block bacterial activity) to test whether gull guano stimulated phytoplankton and bacterial growth, caused changes in taxonomic composition, and altered phytoplankton-bacteria interactions. Alteromonadales, Sphingobacteriales, Verrucomicrobia and diatoms were generally stimulated by guano. Chlorophyll a (Chl a) concentration and bacterial abundance significantly increased after additions independently of the initial ambient nutrient concentrations. Our study demonstrates, for the first time, that the addition of guano altered the phytoplankton-bacteria interaction index from neutral (i.e. phytoplankton growth was not affected by bacterial activity) to positive (i.e. phytoplankton growth was stimulated by bacterial activity) in the low-nutrient environment occurring in spring. In contrast, when environmental nutrient concentrations were high, the interaction index changed from positive to neutral after guano additions, suggesting the presence of some secondary metabolite in the guano that is needed for phytoplankton growth, which would otherwise be supplied by bacteria.
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Affiliation(s)
- Maider Justel-Díez
- Centro de Investigación Marina, Departamento de Ecología e Biología Animal, Universidad de Vigo, Vigo, Spain
| | - Erick Delgadillo-Nuño
- Centro de Investigación Marina, Departamento de Ecología e Biología Animal, Universidad de Vigo, Vigo, Spain
| | - Alberto Gutiérrez-Barral
- Centro de Investigación Marina, Departamento de Ecología e Biología Animal, Universidad de Vigo, Vigo, Spain
| | - Paula García-Otero
- Centro de Investigación Marina, Departamento de Ecología e Biología Animal, Universidad de Vigo, Vigo, Spain
| | - Isaac Alonso-Barciela
- Centro de Investigación Marina, Departamento de Ecología e Biología Animal, Universidad de Vigo, Vigo, Spain
| | - Pablo Pereira-Villanueva
- Centro de Investigación Marina, Departamento de Ecología e Biología Animal, Universidad de Vigo, Vigo, Spain
| | | | - Alberto Velando
- Centro de Investigación Marina, Departamento de Ecología e Biología Animal, Universidad de Vigo, Vigo, Spain
| | - Eva Teira
- Centro de Investigación Marina, Departamento de Ecología e Biología Animal, Universidad de Vigo, Vigo, Spain
| | - Emilio Fernández
- Centro de Investigación Marina, Departamento de Ecología e Biología Animal, Universidad de Vigo, Vigo, Spain
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Sehein TR, Gast RJ, Pachiadaki M, Guillou L, Edgcomb VP. Parasitic infections by Group II Syndiniales target selected dinoflagellate host populations within diverse protist assemblages in a model coastal pond. Environ Microbiol 2022; 24:1818-1834. [PMID: 35315564 DOI: 10.1111/1462-2920.15977] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 03/13/2022] [Indexed: 11/29/2022]
Abstract
Protists are integral to marine food webs and biogeochemical cycles; however, there is a paucity of data describing specific ecological niches for some of the most abundant taxa in marker gene libraries. Syndiniales are one such group, often representing the majority of sequence reads recovered from picoplankton samples across the global ocean. However, the prevalence and impacts of syndinian parasitism in marine environments remains unclear. We began to address these critical knowledge gaps by generating a high-resolution time series (March-October 2018) in a productive coastal pond. Seasonal shifts in protist populations, including parasitic Syndiniales, were documented during periods of higher primary productivity and increased summer temperature-driven stratification. Elevated concentrations of infected hosts and free-living parasite spores occurred at nearly monthly intervals in July, August, and September. We suggest intensifying stratification during this period correlated with the increased prevalence of dinoflagellates that were parasitized by Group II Syndiniales. Infections in some protist populations were comparable to previously reported large single-taxon dinoflagellate blooms. Infection dynamics in Salt Pond demonstrated the propagation of syndinian parasites through mixed protist assemblages and highlighted patterns of host/parasite interactions that better reflect many other marine environments where single taxon blooms are uncommon.
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Affiliation(s)
- Taylor R Sehein
- MIT-WHOI Joint Program in Biological Oceanography, Cambridge and Woods Hole, MA, United States
| | - Rebecca J Gast
- Department of Biology, Woods Hole Oceanographic Institution, Woods Hole, MA, United States
| | - Maria Pachiadaki
- Department of Biology, Woods Hole Oceanographic Institution, Woods Hole, MA, United States
| | - Laure Guillou
- Sorbonne Université & Centre National pour la Recherche Scientifique, Station Biologique de Roscoff, UMR7144, Roscoff, France
| | - Virginia P Edgcomb
- Department of Geology and Geophysics, Woods Hole Oceanographic Institution, Woods Hole, MA, United States
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Burki F, Sandin MM, Jamy M. Diversity and ecology of protists revealed by metabarcoding. Curr Biol 2021; 31:R1267-R1280. [PMID: 34637739 DOI: 10.1016/j.cub.2021.07.066] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Protists are the dominant eukaryotes in the biosphere where they play key functional roles. While protists have been studied for over a century, it is the high-throughput sequencing of molecular markers from environmental samples - the approach of metabarcoding - that has revealed just how diverse, and abundant, these small organisms are. Metabarcoding is now routine to survey environmental diversity, so data have rapidly accumulated from a multitude of environments and at different sampling scales. This mass of data has provided unprecedented opportunities to study the taxonomic and functional diversity of protists, and how this diversity is organised in space and time. Here, we use metabarcoding as a common thread to discuss the state of knowledge in protist diversity research, from technical considerations of the approach to important insights gained on diversity patterns and the processes that might have structured this diversity. In addition to these insights, we conclude that metabarcoding is on the verge of an exciting added dimension thanks to the maturation of high-throughput long-read sequencing, so that a robust eco-evolutionary framework of protist diversity is within reach.
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Affiliation(s)
- Fabien Burki
- Department of Organismal Biology (Systematic Biology), Uppsala University, Norbyv. 18D, 75236 Uppsala, Sweden; Science For Life Laboratory, Uppsala University, 75236 Uppsala, Sweden.
| | - Miguel M Sandin
- Department of Organismal Biology (Systematic Biology), Uppsala University, Norbyv. 18D, 75236 Uppsala, Sweden
| | - Mahwash Jamy
- Department of Organismal Biology (Systematic Biology), Uppsala University, Norbyv. 18D, 75236 Uppsala, Sweden
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Ballesteros I, Terán P, Guamán-Burneo C, González N, Cruz A, Castillejo P. DNA barcoding approach to characterize microalgae isolated from freshwater systems in Ecuador. NEOTROPICAL BIODIVERSITY 2021. [DOI: 10.1080/23766808.2021.1920296] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Affiliation(s)
- Isabel Ballesteros
- AgroScience & Food Research Group, Universidad de las Américas, Quito, Ecuador
| | - Paulina Terán
- AgroScience & Food Research Group, Universidad de las Américas, Quito, Ecuador
| | | | - Nory González
- AgroScience & Food Research Group, Universidad de las Américas, Quito, Ecuador
| | - Alejandra Cruz
- Ingeniería en Biotecnología. Facultad de Ingenierías y Ciencias Aplicadas, Universidad de las Américas, Quito, Ecuador
| | - Pablo Castillejo
- Grupo de Investigación en Biodiversidad, Medio Ambiente y Salud (BIOMAS), Universidad de las Américas, Quito, Ecuador
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Yu RC, Zhang QC, Liu Y, Chen ZF, Geng HX, Dai L, Lin ZR, Tang WJ, Kong FZ, Yan T, Zhou MJ. The dinoflagellate Alexandrium catenella producing only carbamate toxins may account for the seafood poisonings in Qinhuangdao, China. HARMFUL ALGAE 2021; 103:101980. [PMID: 33980430 DOI: 10.1016/j.hal.2021.101980] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 12/25/2020] [Accepted: 01/21/2021] [Indexed: 06/12/2023]
Abstract
An outbreak of paralytic shellfish poisoning, recorded in April 2016 in Qinhuangdao China, was suspected to be caused by a toxic species in genus Alexandrium. Shortly after the poisoning outbreak, shellfish and net-concentrated phytoplankton samples were collected from the Bohai Sea, and analysed using high performance liquid chromatography coupled with fluorescence detection. Paralytic shellfish toxins (PSTs) were detected in both phytoplankton and shellfish samples, with similar toxin profiles dominated by carbamate toxins. High throughput sequencing data for phytoplankton samples collected previously in the coastal waters of Qinhuangdao were then analysed, and 8 operational taxonomic units (OTUs) were assigned to Alexandrium affine, A. andersonii/A. ostenfeldii, A. catenella, A. fraterculus, A. hiranoi/A. pseudogonyaulax, A. margalefii, A. pacificum and A. pohangense, among which A. catenella, A. pacificum and A. ostenfeldii could be potential producers of PSTs. During a cruise in 2019, three isolates of Alexandrium were established by cyst germination, and identified as A. catenella based on the sequences of the 28S ribosomal RNA gene (28S rDNA) D1-D2 region. Interestingly, all the three strains had the same toxin profile consisting of gonyautoxins 1, 3, 4 (GTX1, 3, 4) and neosaxitoxin (NEO). The toxin profile is similar to those of phytoplankton samples collected previously in the coastal waters of Qinhuangdao, but remarkably different from the general toxin profile of A. catenella dominated by N-sulfocarbamoyl toxins C1-2 in the Bohai Sea and the Yellow Sea. The results suggest that A. catenella is most likely to be the causative species of the poisoning outbreak in Qinhuangdao. As far as we know, this is the first report of A. catenella in the Bohai Sea producing PSTs dominated by high potent gonyautoxins GTX1-4. Occurrence of the highly toxic A. catenella will increase the risk of paralytic shellfish poisoning, which necessitates in-depth mechanism studies and increasing monitoring efforts.
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Affiliation(s)
- Ren-Cheng Yu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Key Laboratory for Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266071, China; University of Chinese Academy of Sciences, Beijing 100049, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China.
| | - Qing-Chun Zhang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Key Laboratory for Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266071, China
| | - Yang Liu
- 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
| | - Zhen-Fan Chen
- College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Hui-Xia Geng
- Changjiang River Estuary Ecosystem Research Station, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Li Dai
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhuo-Ru Lin
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wen-Jiao Tang
- College of Marine Life Science, Ocean University of China, Qingdao 266003, China
| | - Fan-Zhou Kong
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Key Laboratory for Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266071, China
| | - Tian Yan
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Key Laboratory for Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266071, China
| | - Ming-Jiang Zhou
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
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Logares R, Deutschmann IM, Junger PC, Giner CR, Krabberød AK, Schmidt TSB, Rubinat-Ripoll L, Mestre M, Salazar G, Ruiz-González C, Sebastián M, de Vargas C, Acinas SG, Duarte CM, Gasol JM, Massana R. Disentangling the mechanisms shaping the surface ocean microbiota. MICROBIOME 2020; 8:55. [PMID: 32312331 PMCID: PMC7171866 DOI: 10.1186/s40168-020-00827-8] [Citation(s) in RCA: 107] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2019] [Accepted: 03/13/2020] [Indexed: 05/19/2023]
Abstract
BACKGROUND The ocean microbiota modulates global biogeochemical cycles and changes in its configuration may have large-scale consequences. Yet, the underlying ecological mechanisms structuring it are unclear. Here, we investigate how fundamental ecological mechanisms (selection, dispersal and ecological drift) shape the smallest members of the tropical and subtropical surface-ocean microbiota: prokaryotes and minute eukaryotes (picoeukaryotes). Furthermore, we investigate the agents exerting abiotic selection on this assemblage as well as the spatial patterns emerging from the action of ecological mechanisms. To explore this, we analysed the composition of surface-ocean prokaryotic and picoeukaryotic communities using DNA-sequence data (16S- and 18S-rRNA genes) collected during the circumglobal expeditions Malaspina-2010 and TARA-Oceans. RESULTS We found that the two main components of the tropical and subtropical surface-ocean microbiota, prokaryotes and picoeukaryotes, appear to be structured by different ecological mechanisms. Picoeukaryotic communities were predominantly structured by dispersal-limitation, while prokaryotic counterparts appeared to be shaped by the combined action of dispersal-limitation, selection and drift. Temperature-driven selection appeared as a major factor, out of a few selected factors, influencing species co-occurrence networks in prokaryotes but not in picoeukaryotes, indicating that association patterns may contribute to understand ocean microbiota structure and response to selection. Other measured abiotic variables seemed to have limited selective effects on community structure in the tropical and subtropical ocean. Picoeukaryotes displayed a higher spatial differentiation between communities and a higher distance decay when compared to prokaryotes, consistent with a scenario of higher dispersal limitation in the former after considering environmental heterogeneity. Lastly, random dynamics or drift seemed to have a more important role in structuring prokaryotic communities than picoeukaryotic counterparts. CONCLUSIONS The differential action of ecological mechanisms seems to cause contrasting biogeography, in the tropical and subtropical ocean, among the smallest surface plankton, prokaryotes and picoeukaryotes. This suggests that the idiosyncrasy of the main constituents of the ocean microbiota should be considered in order to understand its current and future configuration, which is especially relevant in a context of global change, where the reaction of surface ocean plankton to temperature increase is still unclear. Video Abstract.
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Affiliation(s)
- Ramiro Logares
- Institute of Marine Sciences (ICM), CSIC, 08003 Barcelona, Catalonia Spain
- Department of Biosciences, Section for Genetics and Evolutionary Biology, University of Oslo, 0316 Oslo, Norway
| | - Ina M. Deutschmann
- Institute of Marine Sciences (ICM), CSIC, 08003 Barcelona, Catalonia Spain
| | - Pedro C. Junger
- Laboratory of Microbial Processes & Biodiversity (LMPB), Department of Hydrobiology (DHB), Universidade Federal de São Carlos (UFSCar), São Carlos, 13565-905 SP Brazil
| | - Caterina R. Giner
- Institute of Marine Sciences (ICM), CSIC, 08003 Barcelona, Catalonia Spain
- Institute for the Oceans and Fisheries, University of British Columbia, 2202 Main Mall, Vancouver, BC V6T 1Z4 Canada
| | - Anders K. Krabberød
- Department of Biosciences, Section for Genetics and Evolutionary Biology, University of Oslo, 0316 Oslo, Norway
| | - Thomas S. B. Schmidt
- European Molecular Biology Laboratory, Meyerhofstr. 1, 69117 Heidelberg, Germany
| | - Laura Rubinat-Ripoll
- Sorbonne Universités, UPMC Univ Paris 06, CNRS UMR 7144, Adaptation et Diversité en Milieu Marin, Equipe EPEP, Station Biologique de Roscoff, 29680 Roscoff, France
| | - Mireia Mestre
- Institute of Marine Sciences (ICM), CSIC, 08003 Barcelona, Catalonia Spain
- Centro de Investigación Oceanográfica COPAS Sur-Austral, Departamento de Oceanografía, Universidad de Concepción, Concepción, Chile
- Centro FONDAP de Investigación Dinámica de Ecosistemas Marinos de Altas Latitudes (IDEAL), Universidad Austral de Chile, Valdivia, Chile
| | - Guillem Salazar
- Institute of Marine Sciences (ICM), CSIC, 08003 Barcelona, Catalonia Spain
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, 8093 Zürich, Switzerland
| | | | - Marta Sebastián
- Institute of Marine Sciences (ICM), CSIC, 08003 Barcelona, Catalonia Spain
- Oceanography and Global Change Institute, IOCAG, University of Las Palmas de Gran Canaria, ULPGC, 35214 Gran Canaria, Spain
| | - Colomban de Vargas
- Sorbonne Universités, UPMC Univ Paris 06, CNRS UMR 7144, Adaptation et Diversité en Milieu Marin, Equipe EPEP, Station Biologique de Roscoff, 29680 Roscoff, France
| | - Silvia G. Acinas
- Institute of Marine Sciences (ICM), CSIC, 08003 Barcelona, Catalonia Spain
| | - Carlos M. Duarte
- King Abdullah University of Science and Technology (KAUST), Red Sea Research Center (RSRC), Thuwal, Saudi Arabia
| | - Josep M. Gasol
- Institute of Marine Sciences (ICM), CSIC, 08003 Barcelona, Catalonia Spain
- Centre for Marine Ecosystems Research, School of Science, Edith Cowan University, Joondalup, WA Australia
| | - Ramon Massana
- Institute of Marine Sciences (ICM), CSIC, 08003 Barcelona, Catalonia Spain
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Annenkova NV, Giner CR, Logares R. Tracing the Origin of Planktonic Protists in an Ancient Lake. Microorganisms 2020; 8:microorganisms8040543. [PMID: 32283732 PMCID: PMC7232311 DOI: 10.3390/microorganisms8040543] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 04/05/2020] [Accepted: 04/07/2020] [Indexed: 11/28/2022] Open
Abstract
Ancient lakes are among the most interesting models for evolution studies because their biodiversity is the result of a complex combination of migration and speciation. Here, we investigate the origin of single celled planktonic eukaryotes from the oldest lake in the world—Lake Baikal (Russia). By using 18S rDNA metabarcoding, we recovered 1414 Operational Taxonomic Units (OTUs) belonging to protists populating surface waters (1–50 m) and representing pico/nano-sized cells. The recovered communities resembled other lacustrine freshwater assemblages found elsewhere, especially the taxonomically unclassified protists. However, our results suggest that a fraction of Baikal protists could belong to glacial relicts and have close relationships with marine/brackish species. Moreover, our results suggest that rapid radiation may have occurred among some protist taxa, partially mirroring what was already shown for multicellular organisms in Lake Baikal. We found 16% of the OTUs belonging to potential species flocks in Stramenopiles, Alveolata, Opisthokonta, Archaeplastida, Rhizaria, and Hacrobia. Putative flocks predominated in Chrysophytes, which are highly diverse in Lake Baikal. Also, the 18S rDNA of a number of species (7% of the total) differed >10% from other known sequences. These taxa as well as those belonging to the flocks may be endemic to Lake Baikal. Overall, our study points to novel diversity of planktonic protists in Lake Baikal, some of which may have emerged in situ after evolutionary diversification.
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Affiliation(s)
- Nataliia V. Annenkova
- Limnological Institute Siberian Branch of the Russian Academy of Sciences 3, Ulan-Batorskaya St., 664033 Irkutsk, Russia
- Correspondence: (N.V.A.); (R.L.)
| | - Caterina R. Giner
- Institute of Marine Sciences (ICM), CSIC, Passeig Marítim de la Barceloneta, 37-49, ES08003 Barcelona, Spain;
- Institute for the Oceans and Fisheries, University of British Columbia, 2202 Main Mall, Vancouver, BC V6T 1Z4, Canada
| | - Ramiro Logares
- Institute of Marine Sciences (ICM), CSIC, Passeig Marítim de la Barceloneta, 37-49, ES08003 Barcelona, Spain;
- Correspondence: (N.V.A.); (R.L.)
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Cai R, Kayal E, Alves-de-Souza C, Bigeard E, Corre E, Jeanthon C, Marie D, Porcel BM, Siano R, Szymczak J, Wolf M, Guillou L. Cryptic species in the parasitic Amoebophrya species complex revealed by a polyphasic approach. Sci Rep 2020; 10:2531. [PMID: 32054950 PMCID: PMC7018713 DOI: 10.1038/s41598-020-59524-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 01/27/2020] [Indexed: 12/02/2022] Open
Abstract
As critical primary producers and recyclers of organic matter, the diversity of marine protists has been extensively explored by high-throughput barcode sequencing. However, classification of short metabarcoding sequences into traditional taxonomic units is not trivial, especially for lineages mainly known by their genetic fingerprints. This is the case for the widespread Amoebophrya ceratii species complex, parasites of their dinoflagellate congeners. We used genetic and phenotypic characters, applied to 119 Amoebophrya individuals sampled from the same geographic area, to construct practical guidelines for species delineation that could be applied in DNA/RNA based diversity analyses. Based on the internal transcribed spacer (ITS) regions, ITS2 compensatory base changes (CBC) and genome k-mer comparisons, we unambiguously defined eight cryptic species among closely related ribotypes that differed by less than 97% sequence identity in their SSU rDNA. We then followed the genetic signatures of these parasitic species during a three-year survey of Alexandrium minutum blooms. We showed that these cryptic Amoebophrya species co-occurred and shared the same ecological niche. We also observed a maximal ecological fitness for parasites having narrow to intermediate host ranges, reflecting a high cost for infecting a broader host range. This study suggests that a complete taxonomic revision of these parasitic dinoflagellates is long overdue to understand their diversity and ecological role in the marine plankton.
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Affiliation(s)
- Ruibo Cai
- Sorbonne Université, CNRS, UMR7144 Adaptation et Diversité en Milieu Marin, Ecology of Marine Plankton (ECOMAP), Station Biologique de Roscoff SBR, 29680, Roscoff, France
| | - Ehsan Kayal
- Sorbonne Université, CNRS, FR2424 ABIMS, Station Biologique de Roscoff SBR, 29680, Roscoff, France
| | - Catharina Alves-de-Souza
- Algal Resources Collection, MARBIONC, Center for Marine Sciences, University of North Carolina Wilmington, 5600 Marvin K. Moss Lane, Wilmington, NC, 28409, US
| | - Estelle Bigeard
- Sorbonne Université, CNRS, UMR7144 Adaptation et Diversité en Milieu Marin, Ecology of Marine Plankton (ECOMAP), Station Biologique de Roscoff SBR, 29680, Roscoff, France
| | - Erwan Corre
- Sorbonne Université, CNRS, FR2424 ABIMS, Station Biologique de Roscoff SBR, 29680, Roscoff, France
| | - Christian Jeanthon
- Sorbonne Université, CNRS, UMR7144 Adaptation et Diversité en Milieu Marin, Ecology of Marine Plankton (ECOMAP), Station Biologique de Roscoff SBR, 29680, Roscoff, France
| | - Dominique Marie
- Sorbonne Université, CNRS, UMR7144 Adaptation et Diversité en Milieu Marin, Ecology of Marine Plankton (ECOMAP), Station Biologique de Roscoff SBR, 29680, Roscoff, France
| | - Betina M Porcel
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, University Evry, Université Paris-Saclay, 91057, Evry, France
| | - Raffaele Siano
- Ifremer-Centre de Bretagne, Département/Unité/Laboratoire ODE/DYNECO/Pelagos, Z.I. Technopôle Brest-Iroise, Pointe du Diable BP70, 29280, Plouzané, France
| | - Jeremy Szymczak
- Sorbonne Université, CNRS, UMR7144 Adaptation et Diversité en Milieu Marin, Ecology of Marine Plankton (ECOMAP), Station Biologique de Roscoff SBR, 29680, Roscoff, France
| | - Matthias Wolf
- Department of Bioinformatics, Biocenter, University of Würzburg, Am Hubland, 97074, Würzburg, Germany
| | - Laure Guillou
- Sorbonne Université, CNRS, UMR7144 Adaptation et Diversité en Milieu Marin, Ecology of Marine Plankton (ECOMAP), Station Biologique de Roscoff SBR, 29680, Roscoff, France.
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10
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Marked changes in diversity and relative activity of picoeukaryotes with depth in the world ocean. ISME JOURNAL 2019; 14:437-449. [PMID: 31645670 PMCID: PMC6976695 DOI: 10.1038/s41396-019-0506-9] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Revised: 06/10/2019] [Accepted: 08/02/2019] [Indexed: 12/20/2022]
Abstract
Microbial eukaryotes are key components of the ocean plankton. Yet, our understanding of their community composition and activity in different water layers of the ocean is limited, particularly for picoeukaryotes (0.2–3 µm cell size). Here, we examined the picoeukaryotic communities inhabiting different vertical zones of the tropical and subtropical global ocean: surface, deep chlorophyll maximum, mesopelagic (including the deep scattering layer and oxygen minimum zones), and bathypelagic. Communities were analysed by high-tthroughput sequencing of the 18S rRNA gene (V4 region) as represented by DNA (community structure) and RNA (metabolism), followed by delineation of Operational Taxonomic Units (OTUs) at 99% similarity. We found a stratification of the picoeukaryotic communities along the water column, with assemblages corresponding to the sunlit and dark ocean. Specific taxonomic groups either increased (e.g., Chrysophyceae or Bicosoecida) or decreased (e.g., Dinoflagellata or MAST-3) in abundance with depth. We used the rRNA:rDNA ratio of each OTU as a proxy of metabolic activity. The highest relative activity was found in the mesopelagic layer for most taxonomic groups, and the lowest in the bathypelagic. Altogether, we characterize the change in community structure and metabolic activity of picoeukaryotes with depth in the global ocean, suggesting a hotspot of activity in the mesopelagic.
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11
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Giner CR, Balagué V, Krabberød AK, Ferrera I, Reñé A, Garcés E, Gasol JM, Logares R, Massana R. Quantifying long‐term recurrence in planktonic microbial eukaryotes. Mol Ecol 2019; 28:923-935. [DOI: 10.1111/mec.14929] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 10/08/2018] [Accepted: 10/30/2018] [Indexed: 01/20/2023]
Affiliation(s)
- Caterina R. Giner
- Department of Marine Biology and OceanographyInstitut de Ciències del Mar (ICM‐CSIC) Barcelona Spain
| | - Vanessa Balagué
- Department of Marine Biology and OceanographyInstitut de Ciències del Mar (ICM‐CSIC) Barcelona Spain
| | - Anders K. Krabberød
- Department of Biosciences, Section for Genetics and Evolutionary Biology (Evogene) University of Oslo Oslo Norway
| | - Isabel Ferrera
- Department of Marine Biology and OceanographyInstitut de Ciències del Mar (ICM‐CSIC) Barcelona Spain
| | - Albert Reñé
- Department of Marine Biology and OceanographyInstitut de Ciències del Mar (ICM‐CSIC) Barcelona Spain
| | - Esther Garcés
- Department of Marine Biology and OceanographyInstitut de Ciències del Mar (ICM‐CSIC) Barcelona Spain
| | - Josep M. Gasol
- Department of Marine Biology and OceanographyInstitut de Ciències del Mar (ICM‐CSIC) Barcelona Spain
| | - Ramiro Logares
- Department of Marine Biology and OceanographyInstitut de Ciències del Mar (ICM‐CSIC) Barcelona Spain
- Department of Biosciences, Section for Genetics and Evolutionary Biology (Evogene) University of Oslo Oslo Norway
| | - Ramon Massana
- Department of Marine Biology and OceanographyInstitut de Ciències del Mar (ICM‐CSIC) Barcelona Spain
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12
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Corcoll N, Yang J, Backhaus T, Zhang X, Eriksson KM. Copper Affects Composition and Functioning of Microbial Communities in Marine Biofilms at Environmentally Relevant Concentrations. Front Microbiol 2019; 9:3248. [PMID: 30671047 PMCID: PMC6331542 DOI: 10.3389/fmicb.2018.03248] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 12/14/2018] [Indexed: 02/01/2023] Open
Abstract
Copper (Cu) pollution in coastal areas is a worldwide threat for aquatic communities. This study aims to demonstrate the usefulness of the DNA metabarcoding analysis in order to describe the ecotoxicological effect of Cu at environmental concentrations on marine periphyton. Additionally, the study investigates if Cu-induced changes in community structure co-occurs with changes in community functioning (i.e., photosynthesis and community tolerance to Cu). Periphyton was exposed for 18 days to five Cu concentrations, between 0.01 and 10 μM, in a semi-static test. Diversity and community structure of prokaryotic and eukaryotic organisms were assessed by 16S and 18S amplicon sequencing, respectively. Community function was studied as impacts on algal biomass and photosynthetic activity. Additionally, we studied Pollution-Induced Community Tolerance (PICT) using photosynthesis as the endpoint. Sequencing results detected an average of 9,504 and 1,242 OTUs for 16S and 18S, respectively, reflecting the high biodiversity of marine periphytic biofilms. Eukaryotes represent the most Cu-sensitive kingdom, where effects were seen already at concentrations as low as 0.01 μM. The structure of the prokaryotic part of the community was impacted at slightly higher concentrations (0.06 μM), which is still in the range of the Cu concentrations observed in the area (0.08 μM). The current environmental quality standard for Cu of 0.07 μM therefore does not seem to be sufficiently protective for periphyton. Cu exposure resulted in a more Cu-tolerant community, which was accompanied by a reduced total algal biomass, increased relative abundance of diatoms and a reduction of photosynthetic activity. Cu exposure changed the network of associations between taxa in the communities. A total of 23 taxa, including taxa within Proteobacteria, Bacteroidetes, Stramenopiles, and Hacrobia, were identified as being particularly sensitive to Cu. DNA metabarcoding is presented as a sensitive tool for community-level ecotoxicological studies that allows to observe impacts simultaneously on a multitude of pro- and eukaryotic taxa, and therefore to identify particularly sensitive, non-cultivable taxa.
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Affiliation(s)
- Natàlia Corcoll
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Jianghua Yang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, China
| | - Thomas Backhaus
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Xiaowei Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, China
| | - Karl Martin Eriksson
- Department of Mechanics and Maritime Sciences, Chalmers University of Technology, Gothenburg, Sweden
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13
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Hernández-Ruiz M, Barber-Lluch E, Prieto A, Álvarez-Salgado XA, Logares R, Teira E. Seasonal succession of small planktonic eukaryotes inhabiting surface waters of a coastal upwelling system. Environ Microbiol 2018; 20:2955-2973. [DOI: 10.1111/1462-2920.14313] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 06/12/2018] [Indexed: 11/27/2022]
Affiliation(s)
- Marta Hernández-Ruiz
- Biological Oceanography Group, Department of Ecology and Animal Biology; University of Vigo; Vigo, 36310 Spain
- Oceanography, Marine Science Station of Toralla (ECIMAT); University of Vigo; Vigo, 36331 Spain
| | - Esther Barber-Lluch
- Biological Oceanography Group, Department of Ecology and Animal Biology; University of Vigo; Vigo, 36310 Spain
- Oceanography, Marine Science Station of Toralla (ECIMAT); University of Vigo; Vigo, 36331 Spain
| | - Antero Prieto
- Biological Oceanography Group, Department of Ecology and Animal Biology; University of Vigo; Vigo, 36310 Spain
- Oceanography, Marine Science Station of Toralla (ECIMAT); University of Vigo; Vigo, 36331 Spain
| | | | - Ramiro Logares
- Marine Biology and Oceanography, Institute of Marine Sciences (ICM-CSIC); Barcelona, 08003 Spain
| | - Eva Teira
- Biological Oceanography Group, Department of Ecology and Animal Biology; University of Vigo; Vigo, 36310 Spain
- Oceanography, Marine Science Station of Toralla (ECIMAT); University of Vigo; Vigo, 36331 Spain
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14
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Logares R, Tesson SVM, Canbäck B, Pontarp M, Hedlund K, Rengefors K. Contrasting prevalence of selection and drift in the community structuring of bacteria and microbial eukaryotes. Environ Microbiol 2018; 20:2231-2240. [PMID: 29727053 DOI: 10.1111/1462-2920.14265] [Citation(s) in RCA: 102] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2017] [Revised: 04/30/2018] [Accepted: 04/30/2018] [Indexed: 11/30/2022]
Abstract
Whether or not communities of microbial eukaryotes are structured in the same way as bacteria is a general and poorly explored question in ecology. Here, we investigated this question in a set of planktonic lake microbiotas in Eastern Antarctica that represent a natural community ecology experiment. Most of the analysed lakes emerged from the sea during the last 6000 years, giving rise to waterbodies that originally contained marine microbiotas and that subsequently evolved into habitats ranging from freshwater to hypersaline. We show that habitat diversification has promoted selection driven by the salinity gradient in bacterial communities (explaining ∼ 72% of taxa turnover), while microeukaryotic counterparts were predominantly structured by ecological drift (∼72% of the turnover). Nevertheless, we also detected a number of microeukaryotes with specific responses to salinity, indicating that albeit minor, selection has had a role in the structuring of specific members of their communities. In sum, we conclude that microeukaryotes and bacteria inhabiting the same communities can be structured predominantly by different processes. This should be considered in future studies aiming to understand the mechanisms that shape microbial assemblages.
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Affiliation(s)
- Ramiro Logares
- Institute of Marine Sciences (ICM), CSIC, Barcelona, Spain
| | - Sylvie V M Tesson
- Department of Chemistry and Molecular Biology, University of Gothenburg, Göteborg, Sweden.,Department of Biology, Lund University, Lund, Sweden
| | - Björn Canbäck
- Department of Biology, Lund University, Lund, Sweden
| | - Mikael Pontarp
- Department of Biology, Lund University, Lund, Sweden.,Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland.,Department of Ecology and Environmental Science, Umeå University, Umeå, Sweden
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15
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Lentendu G, Mahé F, Bass D, Rueckert S, Stoeck T, Dunthorn M. Consistent patterns of high alpha and low beta diversity in tropical parasitic and free-living protists. Mol Ecol 2018; 27:2846-2857. [PMID: 29851187 DOI: 10.1111/mec.14731] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 04/27/2018] [Accepted: 05/18/2018] [Indexed: 01/11/2023]
Abstract
Tropical animals and plants are known to have high alpha diversity within forests, but low beta diversity between forests. By contrast, it is unknown whether microbes inhabiting the same ecosystems exhibit similar biogeographic patterns. To evaluate the biogeographies of tropical protists, we used metabarcoding data of species sampled in the soils of three lowland Neotropical rainforests. Taxa-area and distance-decay relationships for three of the dominant protist taxa and their subtaxa were estimated at both the OTU and phylogenetic levels, with presence-absence and abundance-based measures. These estimates were compared to null models. High local alpha and low regional beta diversity patterns were consistently found for both the parasitic Apicomplexa and the largely free-living Cercozoa and Ciliophora. Similar to animals and plants, the protists showed spatial structures between forests at the OTU and phylogenetic levels, and only at the phylogenetic level within forests. These results suggest that the biogeographies of macro- and micro-organismal eukaryotes in lowland Neotropical rainforests are partially structured by the same general processes. However, and unlike the animals and plants, the protist OTUs did not exhibit spatial structures within forests, which hinders our ability to estimate the local and regional diversity of protists in tropical forests.
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Affiliation(s)
- Guillaume Lentendu
- Department of Ecology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Frédéric Mahé
- Department of Ecology, University of Kaiserslautern, Kaiserslautern, Germany.,CIRAD, UMR LSTM, Montpellier, France
| | - David Bass
- Department of Life Sciences, The Natural History Museum London, London, UK.,Centre for Environment, Fisheries & Aquaculture Science (Cefas), Weymouth, Dorset, UK
| | - Sonja Rueckert
- School of Applied Sciences, Edinburgh Napier University, Edinburgh, UK
| | - Thorsten Stoeck
- Department of Ecology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Micah Dunthorn
- Department of Ecology, University of Kaiserslautern, Kaiserslautern, Germany
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16
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Surface ocean metabarcoding confirms limited diversity in planktonic foraminifera but reveals unknown hyper-abundant lineages. Sci Rep 2018; 8:2539. [PMID: 29416071 PMCID: PMC5803224 DOI: 10.1038/s41598-018-20833-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 01/24/2018] [Indexed: 12/20/2022] Open
Abstract
Since the advent of DNA metabarcoding surveys, the planktonic realm is considered a treasure trove of diversity, inhabited by a small number of abundant taxa, and a hugely diverse and taxonomically uncharacterized consortium of rare species. Here we assess if the apparent underestimation of plankton diversity applies universally. We target planktonic foraminifera, a group of protists whose known morphological diversity is limited, taxonomically resolved and linked to ribosomal DNA barcodes. We generated a pyrosequencing dataset of ~100,000 partial 18S rRNA foraminiferal sequences from 32 size fractioned photic-zone plankton samples collected at 8 stations in the Indian and Atlantic Oceans during the Tara Oceans expedition (2009–2012). We identified 69 genetic types belonging to 41 morphotaxa in our metabarcoding dataset. The diversity saturated at local and regional scale as well as in the three size fractions and the two depths sampled indicating that the diversity of foraminifera is modest and finite. The large majority of the newly discovered lineages occur in the small size fraction, neglected by classical taxonomy. These unknown lineages dominate the bulk [>0.8 µm] size fraction, implying that a considerable part of the planktonic foraminifera community biomass has its origin in unknown lineages.
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17
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Abstract
Global patterns of planktonic diversity are mainly determined by the dispersal of propagules with ocean currents. However, the role that abundance and body size play in determining spatial patterns of diversity remains unclear. Here we analyse spatial community structure - β-diversity - for several planktonic and nektonic organisms from prokaryotes to small mesopelagic fishes collected during the Malaspina 2010 Expedition. β-diversity was compared to surface ocean transit times derived from a global circulation model, revealing a significant negative relationship that is stronger than environmental differences. Estimated dispersal scales for different groups show a negative correlation with body size, where less abundant large-bodied communities have significantly shorter dispersal scales and larger species spatial turnover rates than more abundant small-bodied plankton. Our results confirm that the dispersal scale of planktonic and micro-nektonic organisms is determined by local abundance, which scales with body size, ultimately setting global spatial patterns of diversity. Body size is hypothesised to be a major determinant of β-diversity in passively-dispersing marine organisms. Here, Villarino et al. show that plankton body size determines rates of dispersal along marine currents, with shorter dispersal and higher species spatial turnover in larger organisms.
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18
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Zhang W, Pan Y, Yang J, Chen H, Holohan B, Vaudrey J, Lin S, McManus GB. The diversity and biogeography of abundant and rare intertidal marine microeukaryotes explained by environment and dispersal limitation. Environ Microbiol 2017; 20:462-476. [PMID: 28881067 DOI: 10.1111/1462-2920.13916] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Revised: 08/15/2017] [Accepted: 08/26/2017] [Indexed: 02/03/2023]
Abstract
Benthic microeukaryotes are key ecosystem drivers in marine sandy beaches, an important and dynamic environment; however, little is known about their diversity and biogeography on a large spatial scale. Here, we investigated the community composition and geographical distributions of benthic microeukaryotes using high-throughput sequencing of the 18S rRNA gene and quantified the contributions of environmental factors and spatial separation on the distribution patterns of both rare and abundant taxa. We collected 36 intertidal samples at 12 sandy beaches from four regions that spanned distances from 0.001 to 12,000 km. We found 12,890 operational taxonomic units (OTUs; 97% sequence identity level) including members of all eukaryotic super-groups and several phyla of uncertain position. Arthropoda and Diatomeae dominated the sequence reads in abundance, but Ciliophora and Discoba were the most diverse groups across all samples. About one-third of the OTUs could not be definitively classified at a similarity level of 80%, supporting the view that a large number of rare and minute marine species may have escaped previous characterization. We found generally similar geographical patterns for abundant and rare microeukaryotic sub-communities, and both showed a significant distance-decay similarity trend. Variation partitioning showed that both rare and abundant sub-communities exhibited a slightly stronger response to environmental factors than spatial (distance) factors. However, the abundant sub-community was strongly correlated with variations in spatial, environmental and sediment grain size factors (66% of variance explained), but the rare assemblage was not (16%). This suggests that different or more complex mechanisms generate and maintain diversity in the rare biosphere in this habitat.
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Affiliation(s)
- Wenjing Zhang
- State Key Laboratory of Marine Environmental Science, Marine Biodiversity and Global Change Research Center, Xiamen University, Xiamen 361005, People's Republic of China.,Department of Marine Sciences, University of Connecticut, Groton, CT 06340, USA
| | - Yongbo Pan
- State Key Laboratory of Marine Environmental Science, Marine Biodiversity and Global Change Research Center, Xiamen University, Xiamen 361005, People's Republic of China
| | - Jun Yang
- Aquatic EcoHealth Group, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, People's Republic of China
| | - Huihuang Chen
- Aquatic EcoHealth Group, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, People's Republic of China
| | - Bridget Holohan
- Department of Marine Sciences, University of Connecticut, Groton, CT 06340, USA
| | - Jamie Vaudrey
- Department of Marine Sciences, University of Connecticut, Groton, CT 06340, USA
| | - Senjie Lin
- State Key Laboratory of Marine Environmental Science, Marine Biodiversity and Global Change Research Center, Xiamen University, Xiamen 361005, People's Republic of China.,Department of Marine Sciences, University of Connecticut, Groton, CT 06340, USA
| | - George B McManus
- Department of Marine Sciences, University of Connecticut, Groton, CT 06340, USA
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19
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Tragin M, Zingone A, Vaulot D. Comparison of coastal phytoplankton composition estimated from the V4 and V9 regions of the 18S rRNA gene with a focus on photosynthetic groups and especially Chlorophyta. Environ Microbiol 2017; 20:506-520. [DOI: 10.1111/1462-2920.13952] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 09/30/2017] [Indexed: 11/30/2022]
Affiliation(s)
- Margot Tragin
- Sorbonne Universités, UPMC Univ Paris 06, UMR 7144, CNRS, Station Biologique, Place Georges Teissier; 29680 Roscoff France
| | - Adriana Zingone
- Department of Integrative Marine Ecology; Stazione Zoologica Anton Dohrn, Villa Comunale; Naples Italy
| | - Daniel Vaulot
- Sorbonne Universités, UPMC Univ Paris 06, UMR 7144, CNRS, Station Biologique, Place Georges Teissier; 29680 Roscoff France
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20
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Cabello AM, Latasa M, Forn I, Morán XAG, Massana R. Vertical distribution of major photosynthetic picoeukaryotic groups in stratified marine waters. Environ Microbiol 2017; 18:1578-90. [PMID: 26971724 DOI: 10.1111/1462-2920.13285] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Revised: 02/26/2016] [Accepted: 02/28/2016] [Indexed: 02/01/2023]
Abstract
Photosynthetic picoeukaryotes (PPEs) are fundamental contributors to oceanic primary production and form diverse communities dominated by prymnesiophytes, chlorophytes, pelagophytes and chrysophytes. Here, we studied the vertical distribution of these major groups in two offshore regions of the northern Iberian Peninsula during summer stratification. We performed a fine-scale vertical sampling (every ∼2 m) across the DCM and used fluorescence in situ hybridization (FISH) to determine the PPE composition and to explore the possible segregation of target groups in the light, nutrient and temperature gradients. Chlorophytes, pelagophytes and prymnesiophytes, in this order of abundance, accounted for the total PPEs recorded by flow cytometry in the Avilés canyon, and for more than half in the Galicia Bank, whereas chrysophytes were undetected. Among the three detected groups, often the prymnesiophytes were dominant in biomass. In general, all groups were present throughout the water column with abundance peaks around the DCM, but their distributions differed: pelagophytes were located deeper than the other two groups, chlorophytes presented two peaks and prymnesiophytes exhibited surface abundances comparable to those at the DCM. This study offers first indications that the vertical distribution of different PPE groups is heterogeneous within the DCM.
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Affiliation(s)
- Ana M Cabello
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (CSIC), Barcelona, Catalonia, Spain
| | - Mikel Latasa
- Instituto Español de Oceanografía (IEO), Centro oceanográfico de Xixón, Xixón, Spain
| | - Irene Forn
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (CSIC), Barcelona, Catalonia, Spain
| | - Xosé Anxelu G Morán
- Instituto Español de Oceanografía (IEO), Centro oceanográfico de Xixón, Xixón, Spain.,Division of Biological and Environmental Sciences and Engineering, Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Ramon Massana
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (CSIC), Barcelona, Catalonia, Spain
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21
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Jeanbille M, Gury J, Duran R, Tronczynski J, Ghiglione JF, Agogué H, Saïd OB, Taïb N, Debroas D, Garnier C, Auguet JC. Chronic Polyaromatic Hydrocarbon (PAH) Contamination Is a Marginal Driver for Community Diversity and Prokaryotic Predicted Functioning in Coastal Sediments. Front Microbiol 2016; 7:1303. [PMID: 27594854 PMCID: PMC4990537 DOI: 10.3389/fmicb.2016.01303] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 08/08/2016] [Indexed: 01/11/2023] Open
Abstract
Benthic microorganisms are key players in the recycling of organic matter and recalcitrant compounds such as polyaromatic hydrocarbons (PAHs) in coastal sediments. Despite their ecological importance, the response of microbial communities to chronic PAH pollution, one of the major threats to coastal ecosystems, has received very little attention. In one of the largest surveys performed so far on coastal sediments, the diversity and composition of microbial communities inhabiting both chronically contaminated and non-contaminated coastal sediments were investigated using high-throughput sequencing on the 18S and 16S rRNA genes. Prokaryotic alpha-diversity showed significant association with salinity, temperature, and organic carbon content. The effect of particle size distribution was strong on eukaryotic diversity. Similarly to alpha-diversity, beta-diversity patterns were strongly influenced by the environmental filter, while PAHs had no influence on the prokaryotic community structure and a weak impact on the eukaryotic community structure at the continental scale. However, at the regional scale, PAHs became the main driver shaping the structure of bacterial and eukaryotic communities. These patterns were not found for PICRUSt predicted prokaryotic functions, thus indicating some degree of functional redundancy. Eukaryotes presented a greater potential for their use as PAH contamination biomarkers, owing to their stronger response at both regional and continental scales.
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Affiliation(s)
- Mathilde Jeanbille
- Equipe Environnement et Microbiologie, Institut Pluridisciplinaire de Recherche sur l'Environnement et les Matériaux, UMR 5254 CNRS - Université de Pau et des Pays de L'Adour Pau, France
| | - Jérôme Gury
- Equipe Environnement et Microbiologie, Institut Pluridisciplinaire de Recherche sur l'Environnement et les Matériaux, UMR 5254 CNRS - Université de Pau et des Pays de L'Adour Pau, France
| | - Robert Duran
- Equipe Environnement et Microbiologie, Institut Pluridisciplinaire de Recherche sur l'Environnement et les Matériaux, UMR 5254 CNRS - Université de Pau et des Pays de L'Adour Pau, France
| | - Jacek Tronczynski
- Laboratoire Biogéochimie des Contaminants Organiques, Unité Biogéochimie et Ecotoxicologie, Département Ressources Biologiques et Environnement, Ifremer Centre Atlantique Nantes, France
| | - Jean-François Ghiglione
- Laboratoire d'Océanographie Microbienne, Sorbonne Universités, CNRS, Université Pierre-et-Marie-Curie, UMR 7621, Observatoire Océanologique Banyuls-sur-mer, France
| | - Hélène Agogué
- Littoral, Environnement et Sociétés, UMR 7266 CNRS - Université de La Rochelle La Rochelle, France
| | - Olfa Ben Saïd
- Laboratoire de Bio-surveillance de l'Environnement, Faculté des Sciences de Bizerte Zarzouna, Tunisia
| | - Najwa Taïb
- Laboratoire Microorganismes: Génome et Environnement, UMR 6023 CNRS - Université Blaise Pascal Aubière, France
| | - Didier Debroas
- Laboratoire Microorganismes: Génome et Environnement, UMR 6023 CNRS - Université Blaise Pascal Aubière, France
| | - Cédric Garnier
- Processus de Transferts et d'Echanges dans l'Environnement, EA 3819, Université de Toulon La Garde, France
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22
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Protist metabarcoding and environmental biomonitoring: Time for change. Eur J Protistol 2016; 55:12-25. [DOI: 10.1016/j.ejop.2016.02.003] [Citation(s) in RCA: 99] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Revised: 01/29/2016] [Accepted: 02/12/2016] [Indexed: 01/06/2023]
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23
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Giner CR, Forn I, Romac S, Logares R, de Vargas C, Massana R. Environmental Sequencing Provides Reasonable Estimates of the Relative Abundance of Specific Picoeukaryotes. Appl Environ Microbiol 2016; 82:4757-4766. [PMID: 27235440 PMCID: PMC4984273 DOI: 10.1128/aem.00560-16] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Accepted: 05/23/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED High-throughput sequencing (HTS) is revolutionizing environmental surveys of microbial diversity in the three domains of life by providing detailed information on which taxa are present in microbial assemblages. However, it is still unclear how the relative abundance of specific taxa gathered by HTS correlates with cell abundances. Here, we quantified the relative cell abundance of 6 picoeukaryotic taxa in 13 planktonic samples from 6 European coastal sites using epifluorescence microscopy on tyramide signal amplification-fluorescence in situ hybridization preparations. These relative abundance values were then compared with HTS data obtained in three separate molecular surveys: 454 sequencing of the V4 region of the 18S ribosomal DNA (rDNA) using DNA and RNA extracts (DNA-V4 and cDNA-V4) and Illumina sequencing of the V9 region (cDNA-V9). The microscopic and molecular signals were generally correlated, indicating that a relative increase in specific 18S rDNA was the result of a large proportion of cells in the given taxa. Despite these positive correlations, the slopes often deviated from 1, precluding a direct translation of sequences to cells. Our data highlighted clear differences depending on the nucleic acid template or the 18S rDNA region targeted. Thus, the molecular signal obtained using cDNA templates was always closer to relative cell abundances, while the V4 and V9 regions gave better results depending on the taxa. Our data support the quantitative use of HTS data but warn about considering it as a direct proxy of cell abundances. IMPORTANCE Direct studies on marine picoeukaryotes by epifluorescence microscopy are problematic due to the lack of morphological features and due to the limited number and poor resolution of specific phylogenetic probes used in fluorescence in situ hybridization (FISH) routines. As a consequence, there is an increasing use of molecular methods, including high-throughput sequencing (HTS), to study marine microbial diversity. HTS can provide a detailed picture of the taxa present in a community and can reveal diversity not evident using other methods, but it is still unclear what the meaning of the sequence abundance in a given taxon is. Our aim is to investigate the correspondence between the relative HTS signal and relative cell abundances in selected picoeukaryotic taxa. Environmental sequencing provides reasonable estimates of the relative abundance of specific taxa. Better results are obtained when using RNA extracts as the templates, while the region of 18S ribosomal DNA had different influences depending on the taxa assayed.
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Affiliation(s)
- Caterina R Giner
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (CSIC), Barcelona, Spain
| | - Irene Forn
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (CSIC), Barcelona, Spain
| | - Sarah Romac
- CNRS, UMR 7144, Station Biologique de Roscoff, Roscoff, France
- Université Pierre et Marie Curie Paris 06, UMR 7144, Station Biologique de Roscoff, Roscoff, France
| | - Ramiro Logares
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (CSIC), Barcelona, Spain
| | - Colomban de Vargas
- CNRS, UMR 7144, Station Biologique de Roscoff, Roscoff, France
- Université Pierre et Marie Curie Paris 06, UMR 7144, Station Biologique de Roscoff, Roscoff, France
| | - Ramon Massana
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (CSIC), Barcelona, Spain
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24
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Forster D, Dunthorn M, Stoeck T, Mahé F. Comparison of three clustering approaches for detecting novel environmental microbial diversity. PeerJ 2016; 4:e1692. [PMID: 26966652 PMCID: PMC4782723 DOI: 10.7717/peerj.1692] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 01/24/2016] [Indexed: 11/29/2022] Open
Abstract
Discovery of novel diversity in high-throughput sequencing studies is an important aspect in environmental microbial ecology. To evaluate the effects that amplicon clustering methods have on the discovery of novel diversity, we clustered an environmental marine high-throughput sequencing dataset of protist amplicons together with reference sequences from the taxonomically curated Protist Ribosomal Reference (PR2) database using three de novo approaches: sequence similarity networks, USEARCH, and Swarm. The potentially novel diversity uncovered by each clustering approach differed drastically in the number of operational taxonomic units (OTUs) and in the number of environmental amplicons in these novel diversity OTUs. Global pairwise alignment comparisons revealed that numerous amplicons classified as potentially novel by USEARCH and Swarm were more than 97% similar to references of PR2. Using shortest path analyses on sequence similarity network OTUs and Swarm OTUs we found additional novel diversity within OTUs that would have gone unnoticed without further exploiting their underlying network topologies. These results demonstrate that graph theory provides powerful tools for microbial ecology and the analysis of environmental high-throughput sequencing datasets. Furthermore, sequence similarity networks were most accurate in delineating novel diversity from previously discovered diversity.
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Affiliation(s)
- Dominik Forster
- Department of Ecology, Technische Universität Kaiserslautern , Kaiserslautern , Germany
| | - Micah Dunthorn
- Department of Ecology, Technische Universität Kaiserslautern , Kaiserslautern , Germany
| | - Thorsten Stoeck
- Department of Ecology, Technische Universität Kaiserslautern , Kaiserslautern , Germany
| | - Frédéric Mahé
- Department of Ecology, Technische Universität Kaiserslautern , Kaiserslautern , Germany
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25
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Pernice MC, Giner CR, Logares R, Perera-Bel J, Acinas SG, Duarte CM, Gasol JM, Massana R. Large variability of bathypelagic microbial eukaryotic communities across the world's oceans. ISME JOURNAL 2015; 10:945-58. [PMID: 26451501 DOI: 10.1038/ismej.2015.170] [Citation(s) in RCA: 95] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Revised: 07/30/2015] [Accepted: 08/13/2015] [Indexed: 01/26/2023]
Abstract
In this work, we study the diversity of bathypelagic microbial eukaryotes (0.8-20 μm) in the global ocean. Seawater samples from 3000 to 4000 m depth from 27 stations in the Atlantic, Pacific and Indian Oceans were analyzed by pyrosequencing the V4 region of the 18S ribosomal DNA. The relative abundance of the most abundant operational taxonomic units agreed with the results of a parallel metagenomic analysis, suggesting limited PCR biases in the tag approach. Although rarefaction curves for single stations were seldom saturated, the global analysis of all sequences together suggested an adequate recovery of bathypelagic diversity. Community composition presented a large variability among samples, which was poorly explained by linear geographic distance. In fact, the similarity between communities was better explained by water mass composition (26% of the variability) and the ratio in cell abundance between prokaryotes and microbial eukaryotes (21%). Deep diversity appeared dominated by four taxonomic groups (Collodaria, Chrysophytes, Basidiomycota and MALV-II) appearing in different proportions in each sample. Novel diversity amounted to 1% of the pyrotags and was lower than expected. Our study represents an essential step in the investigation of bathypelagic microbial eukaryotes, indicating dominating taxonomic groups and suggesting idiosyncratic assemblages in distinct oceanic regions.
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Affiliation(s)
- Massimo C Pernice
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (CSIC), Barcelona, Spain
| | - Caterina R Giner
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (CSIC), Barcelona, Spain
| | - Ramiro Logares
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (CSIC), Barcelona, Spain
| | - Júlia Perera-Bel
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (CSIC), Barcelona, Spain
| | - Silvia G Acinas
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (CSIC), Barcelona, Spain
| | - Carlos M Duarte
- Division of Biological and Environmental Science and Engineering, Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia.,IMEDEA (UiB-CSIC), Department of Global Change Research, Institut Mediterraneo de Estudios Avanzados, Esporles, Spain
| | - Josep M Gasol
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (CSIC), Barcelona, Spain
| | - Ramon Massana
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (CSIC), Barcelona, Spain
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26
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Tanabe AS, Nagai S, Hida K, Yasuike M, Fujiwara A, Nakamura Y, Takano Y, Katakura S. Comparative study of the validity of three regions of the 18S-rRNA gene for massively parallel sequencing-based monitoring of the planktonic eukaryote community. Mol Ecol Resour 2015; 16:402-14. [PMID: 26309223 DOI: 10.1111/1755-0998.12459] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2014] [Revised: 08/05/2015] [Accepted: 08/21/2015] [Indexed: 11/27/2022]
Abstract
The nuclear 18S-rRNA gene has been used as a metabarcoding marker in massively parallel sequencing (MPS)-based environmental surveys for plankton biodiversity research. However, different hypervariable regions have been used in different studies, and their utility has been debated among researchers. In this study, detailed investigations into 18S-rRNA were carried out; we investigated the effective number of sequences deposited in international nucleotide sequence databases (INSDs), the amplification bias, and the amplicon sequence variability among the three variable regions, V1-3, V4-5 and V7-9, using in silico polymerase chain reaction (PCR) amplification based on INSDs. We also examined the primer universality and the taxonomic identification power, using MPS-based environmental surveys in the Sea of Okhotsk, to determine which region is more useful for MPS-based monitoring. The primer universality was not significantly different among the three regions, but the number of sequences deposited in INSDs was markedly larger for the V4-5 region than for the other two regions. The sequence variability was significantly different, with the highest variability in the V1-3 region, followed by the V7-9 region, and the lowest variability in the V4-5 region. The results of the MPS-based environmental surveys showed significantly higher identification power in the V1-3 and V7-9 regions than in the V4-5 region, but no significant difference was detected between the V1-3 and V7-9 regions. We therefore conclude that the V1-3 region will be the most suitable for future MPS-based monitoring of natural eukaryote communities, as the number of sequences deposited in INSDs increases.
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Affiliation(s)
- Akifumi S Tanabe
- Research Center for Aquatic Genomics, National Research Institute of Fisheries Science, 2-12-4 Fukuura, Kanazawa-ku, Yokohama, Kanagawa, 236-8648, Japan
| | - Satoshi Nagai
- Research Center for Aquatic Genomics, National Research Institute of Fisheries Science, 2-12-4 Fukuura, Kanazawa-ku, Yokohama, Kanagawa, 236-8648, Japan
| | - Kohsuke Hida
- AXIOHELIX Co. Ltd., 5-11 Kakozaki, Nihonbashi, Chuouku, Tokyo, 103-0015, Japan
| | - Motoshige Yasuike
- Research Center for Aquatic Genomics, National Research Institute of Fisheries Science, 2-12-4 Fukuura, Kanazawa-ku, Yokohama, Kanagawa, 236-8648, Japan
| | - Atushi Fujiwara
- Research Center for Aquatic Genomics, National Research Institute of Fisheries Science, 2-12-4 Fukuura, Kanazawa-ku, Yokohama, Kanagawa, 236-8648, Japan
| | - Yoji Nakamura
- Research Center for Aquatic Genomics, National Research Institute of Fisheries Science, 2-12-4 Fukuura, Kanazawa-ku, Yokohama, Kanagawa, 236-8648, Japan
| | - Yoshihito Takano
- Research Center for Aquatic Genomics, National Research Institute of Fisheries Science, 2-12-4 Fukuura, Kanazawa-ku, Yokohama, Kanagawa, 236-8648, Japan
| | - Seiji Katakura
- City of Mombetsu, Kaiyo-koryukan, Kaiyo-koen, Mombetsu, Hokkaido, 094-0031, Japan
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27
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Massana R, Gobet A, Audic S, Bass D, Bittner L, Boutte C, Chambouvet A, Christen R, Claverie JM, Decelle J, Dolan JR, Dunthorn M, Edvardsen B, Forn I, Forster D, Guillou L, Jaillon O, Kooistra WHCF, Logares R, Mahé F, Not F, Ogata H, Pawlowski J, Pernice MC, Probert I, Romac S, Richards T, Santini S, Shalchian-Tabrizi K, Siano R, Simon N, Stoeck T, Vaulot D, Zingone A, de Vargas C. Marine protist diversity in European coastal waters and sediments as revealed by high-throughput sequencing. Environ Microbiol 2015; 17:4035-49. [PMID: 26119494 DOI: 10.1111/1462-2920.12955] [Citation(s) in RCA: 205] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Revised: 06/09/2015] [Accepted: 06/12/2015] [Indexed: 02/06/2023]
Abstract
Although protists are critical components of marine ecosystems, they are still poorly characterized. Here we analysed the taxonomic diversity of planktonic and benthic protist communities collected in six distant European coastal sites. Environmental deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) from three size fractions (pico-, nano- and micro/mesoplankton), as well as from dissolved DNA and surface sediments were used as templates for tag pyrosequencing of the V4 region of the 18S ribosomal DNA. Beta-diversity analyses split the protist community structure into three main clusters: picoplankton-nanoplankton-dissolved DNA, micro/mesoplankton and sediments. Within each cluster, protist communities from the same site and time clustered together, while communities from the same site but different seasons were unrelated. Both DNA and RNA-based surveys provided similar relative abundances for most class-level taxonomic groups. Yet, particular groups were overrepresented in one of the two templates, such as marine alveolates (MALV)-I and MALV-II that were much more abundant in DNA surveys. Overall, the groups displaying the highest relative contribution were Dinophyceae, Diatomea, Ciliophora and Acantharia. Also, well represented were Mamiellophyceae, Cryptomonadales, marine alveolates and marine stramenopiles in the picoplankton, and Monadofilosa and basal Fungi in sediments. Our extensive and systematic sequencing of geographically separated sites provides the most comprehensive molecular description of coastal marine protist diversity to date.
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Affiliation(s)
- Ramon Massana
- Institut de Ciències del Mar (CSIC), ES-08003, Barcelona, Catalonia, Spain
| | - Angélique Gobet
- Ecologie Systematique Evolution, CNRS, FR-29682, Roscoff, France.,UMR7144 - Equipe EPPO: Evolution du Plancton et PaléoOcéans, UPMC Université Paris 06, Roscoff, France
| | - Stéphane Audic
- Ecologie Systematique Evolution, CNRS, FR-29682, Roscoff, France.,UMR7144 - Equipe EPPO: Evolution du Plancton et PaléoOcéans, UPMC Université Paris 06, Roscoff, France
| | - David Bass
- The Natural History Museum, London, SW7 5BD, UK.,Cefas, Weymouth, Dorset, DT4 8UB, UK
| | - Lucie Bittner
- Ecologie Systematique Evolution, CNRS, FR-29682, Roscoff, France.,UMR7144 - Equipe EPPO: Evolution du Plancton et PaléoOcéans, UPMC Université Paris 06, Roscoff, France.,University of Kaiserslautern, D-67663, Kaiserslautern, Germany
| | - Christophe Boutte
- Ecologie Systematique Evolution, CNRS, FR-29682, Roscoff, France.,UMR7144 - Equipe EPPO: Evolution du Plancton et PaléoOcéans, UPMC Université Paris 06, Roscoff, France
| | | | - Richard Christen
- CNRS, UMR 7138, Université Nice Sophia Antipolis, FR-06108, Nice, France
| | | | - Johan Decelle
- Ecologie Systematique Evolution, CNRS, FR-29682, Roscoff, France.,UMR7144 - Equipe EPPO: Evolution du Plancton et PaléoOcéans, UPMC Université Paris 06, Roscoff, France
| | - John R Dolan
- CNRS, UMR 7093, UPMC Université Paris 06, Laboratoire d'Océanographie de Villefranche, FR-06230, Villefranche-sur-Mer, France
| | - Micah Dunthorn
- University of Kaiserslautern, D-67663, Kaiserslautern, Germany
| | - Bente Edvardsen
- Department Biosciences, University of Oslo, N-0316, Oslo, Norway
| | - Irene Forn
- Institut de Ciències del Mar (CSIC), ES-08003, Barcelona, Catalonia, Spain
| | - Dominik Forster
- University of Kaiserslautern, D-67663, Kaiserslautern, Germany
| | - Laure Guillou
- Ecologie Systematique Evolution, CNRS, FR-29682, Roscoff, France.,UMR7144 - Equipe EPPO: Evolution du Plancton et PaléoOcéans, UPMC Université Paris 06, Roscoff, France
| | - Olivier Jaillon
- CEA, Genoscope, 2 rue Gaston Crémieux, FR-91000, Evry, France
| | | | - Ramiro Logares
- Institut de Ciències del Mar (CSIC), ES-08003, Barcelona, Catalonia, Spain
| | - Frédéric Mahé
- University of Kaiserslautern, D-67663, Kaiserslautern, Germany
| | - Fabrice Not
- Ecologie Systematique Evolution, CNRS, FR-29682, Roscoff, France.,UMR7144 - Equipe EPPO: Evolution du Plancton et PaléoOcéans, UPMC Université Paris 06, Roscoff, France
| | - Hiroyuki Ogata
- Institute for Chemical Research, Kyoto University, Uji, Kyoto, 611-0011, Japan
| | | | - Massimo C Pernice
- Institut de Ciències del Mar (CSIC), ES-08003, Barcelona, Catalonia, Spain
| | - Ian Probert
- Ecologie Systematique Evolution, CNRS, FR-29682, Roscoff, France.,UMR7144 - Equipe EPPO: Evolution du Plancton et PaléoOcéans, UPMC Université Paris 06, Roscoff, France
| | - Sarah Romac
- Ecologie Systematique Evolution, CNRS, FR-29682, Roscoff, France.,UMR7144 - Equipe EPPO: Evolution du Plancton et PaléoOcéans, UPMC Université Paris 06, Roscoff, France
| | | | - Sébastien Santini
- CNRS, UMR 7256, Aix-Marseille Université, FR-13288, Marseille, France
| | | | | | - Nathalie Simon
- Ecologie Systematique Evolution, CNRS, FR-29682, Roscoff, France.,UMR7144 - Equipe EPPO: Evolution du Plancton et PaléoOcéans, UPMC Université Paris 06, Roscoff, France
| | - Thorsten Stoeck
- University of Kaiserslautern, D-67663, Kaiserslautern, Germany
| | - Daniel Vaulot
- Ecologie Systematique Evolution, CNRS, FR-29682, Roscoff, France.,UMR7144 - Equipe EPPO: Evolution du Plancton et PaléoOcéans, UPMC Université Paris 06, Roscoff, France
| | - Adriana Zingone
- Stazione Zoologica Anton Dohrn, Villa Comunale, I-80121, Naples, Italy
| | - Colomban de Vargas
- Ecologie Systematique Evolution, CNRS, FR-29682, Roscoff, France.,UMR7144 - Equipe EPPO: Evolution du Plancton et PaléoOcéans, UPMC Université Paris 06, Roscoff, France
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28
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Hu SK, Liu Z, Lie AAY, Countway PD, Kim DY, Jones AC, Gast RJ, Cary SC, Sherr EB, Sherr BF, Caron DA. Estimating Protistan Diversity Using High-Throughput Sequencing. J Eukaryot Microbiol 2015; 62:688-93. [PMID: 25851049 DOI: 10.1111/jeu.12217] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Revised: 01/17/2015] [Accepted: 01/26/2015] [Indexed: 11/28/2022]
Abstract
Sequencing hypervariable regions from the 18S rRNA gene is commonly employed to characterize protistan biodiversity, yet there are concerns that short reads do not provide the same taxonomic resolution as full-length sequences. A total of 7,432 full-length sequences were used to perform an in silico analysis of how sequences of various lengths and target regions impact downstream ecological interpretations. Sequences that were longer than 400 nucleotides and included the V4 hypervariable region generated results similar to those derived from full-length 18S rRNA gene sequences. Present high-throughput sequencing capabilities are approaching protistan diversity estimation comparable to whole gene sequences.
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Affiliation(s)
- Sarah K Hu
- Department of Biological Sciences, University of Southern California, Los Angeles, California, 90089, USA
| | - Zhenfeng Liu
- Department of Biological Sciences, University of Southern California, Los Angeles, California, 90089, USA
| | - Alle A Y Lie
- Department of Biological Sciences, University of Southern California, Los Angeles, California, 90089, USA
| | - Peter D Countway
- Bigelow Laboratory for Ocean Sciences, East Boothbay, Maine, 04544, USA
| | - Diane Y Kim
- Department of Biological Sciences, University of Southern California, Los Angeles, California, 90089, USA
| | - Adriane C Jones
- Mount St. Mary's College, Los Angeles, California, 90049, USA
| | - Rebecca J Gast
- Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, 02543, USA
| | - S Craig Cary
- Environmental Research Institute, School of Science, University of Waikato, Hamilton, 3240, New Zealand.,College of Earth and Ocean Science, University of Delaware, Newark, Delaware, 19716, USA
| | - Evelyn B Sherr
- College of Oceanic and Atmospheric Sciences, Oregon State University, Corvallis, Oregon, 97331, USA
| | - Barry F Sherr
- College of Oceanic and Atmospheric Sciences, Oregon State University, Corvallis, Oregon, 97331, USA
| | - David A Caron
- Department of Biological Sciences, University of Southern California, Los Angeles, California, 90089, USA
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29
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Del Campo J, Mallo D, Massana R, de Vargas C, Richards TA, Ruiz-Trillo I. Diversity and distribution of unicellular opisthokonts along the European coast analysed using high-throughput sequencing. Environ Microbiol 2015; 17:3195-207. [PMID: 25556908 DOI: 10.1111/1462-2920.12759] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Revised: 12/18/2014] [Accepted: 12/18/2014] [Indexed: 10/24/2022]
Abstract
The opisthokonts are one of the major super groups of eukaryotes. It comprises two major clades: (i) the Metazoa and their unicellular relatives and (ii) the Fungi and their unicellular relatives. There is, however, little knowledge of the role of opisthokont microbes in many natural environments, especially among non-metazoan and non-fungal opisthokonts. Here, we begin to address this gap by analysing high-throughput 18S rDNA and 18S rRNA sequencing data from different European coastal sites, sampled at different size fractions and depths. In particular, we analyse the diversity and abundance of choanoflagellates, filastereans, ichthyosporeans, nucleariids, corallochytreans and their related lineages. Our results show the great diversity of choanoflagellates in coastal waters as well as a relevant representation of the ichthyosporeans and the uncultured marine opisthokonts (MAOP). Furthermore, we describe a new lineage of marine fonticulids (MAFO) that appears to be abundant in sediments. Taken together, our work points to a greater potential ecological role for unicellular opisthokonts than previously appreciated in marine environments, both in water column and sediments, and also provides evidence of novel opisthokont phylogenetic lineages. This study highlights the importance of high-throughput sequencing approaches to unravel the diversity and distribution of both known and novel eukaryotic lineages.
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Affiliation(s)
- Javier Del Campo
- Institut de Biologia Evolutiva (CSIC-UPF), Passeig Marítim de la Barceloneta 37-49, 08003, Barcelona, Catalonia, Spain
| | - Diego Mallo
- Department of Biochemistry, Genetics and Immunology, University of Vigo, Vigo, Galicia, Spain
| | - Ramon Massana
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (CSIC), Passeig Marítim de la Barceloneta 37-49, 08003, Barcelona, Catalonia, Spain
| | - Colomban de Vargas
- CNRS, Adaptation et Diversité en Milieu Marin, Station Biologique de Roscoff, UMR 7144, Roscoff, France.,Station Biologique de Roscoff, UPMC University Paris 06, Roscoff, UMR 7144, France
| | - Thomas A Richards
- Geoffrey Pope Building, Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, UK.,Canadian Institute for Advanced Research, CIFAR Program in Integrated Microbial Biodiversity, Toronto, Canada
| | - Iñaki Ruiz-Trillo
- Institut de Biologia Evolutiva (CSIC-UPF), Passeig Marítim de la Barceloneta 37-49, 08003, Barcelona, Catalonia, Spain.,Departament de Genètica, Universitat de Barcelona, Barcelona, Catalonia, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain
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30
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Gong J, Shi F, Ma B, Dong J, Pachiadaki M, Zhang X, Edgcomb VP. Depth shapes α- and β-diversities of microbial eukaryotes in surficial sediments of coastal ecosystems. Environ Microbiol 2015; 17:3722-37. [DOI: 10.1111/1462-2920.12763] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Revised: 12/23/2014] [Accepted: 12/23/2014] [Indexed: 11/28/2022]
Affiliation(s)
- Jun Gong
- Laboratory of Microbial Ecology; Yantai Institute of Coastal Zone Research; Chinese Academy of Sciences; Yantai 264003 China
| | - Fei Shi
- Laboratory of Microbial Ecology; Yantai Institute of Coastal Zone Research; Chinese Academy of Sciences; Yantai 264003 China
- College of Resources and Environment; University of Chinese Academy of Sciences; Beijing 100049 China
| | - Bin Ma
- Laboratory of Microbial Ecology; Yantai Institute of Coastal Zone Research; Chinese Academy of Sciences; Yantai 264003 China
| | - Jun Dong
- Laboratory of Microbial Ecology; Yantai Institute of Coastal Zone Research; Chinese Academy of Sciences; Yantai 264003 China
| | - Maria Pachiadaki
- Department of Geology and Geophysics; Woods Hole Oceanographic Institution; Woods Hole MA 02543 USA
| | - Xiaoli Zhang
- Laboratory of Microbial Ecology; Yantai Institute of Coastal Zone Research; Chinese Academy of Sciences; Yantai 264003 China
| | - Virginia P. Edgcomb
- Department of Geology and Geophysics; Woods Hole Oceanographic Institution; Woods Hole MA 02543 USA
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31
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Mahé F, Mayor J, Bunge J, Chi J, Siemensmeyer T, Stoeck T, Wahl B, Paprotka T, Filker S, Dunthorn M. Comparing High-throughput Platforms for Sequencing the V4 Region of SSU-rDNA in Environmental Microbial Eukaryotic Diversity Surveys. J Eukaryot Microbiol 2014; 62:338-45. [PMID: 25312509 DOI: 10.1111/jeu.12187] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Revised: 08/11/2014] [Accepted: 09/19/2014] [Indexed: 01/25/2023]
Abstract
High-throughput sequencing platforms are continuing to increase resulting read lengths, which is allowing for a deeper and more accurate depiction of environmental microbial diversity. With the nascent Reagent Kit v3, Illumina MiSeq now has the ability to sequence the eukaryotic hyper-variable V4 region of the SSU-rDNA locus with paired-end reads. Using DNA collected from soils with analyses of strictly- and nearly identical amplicons, here we ask how the new Illumina MiSeq data compares with what we can obtain with Roche/454 GS FLX with regard to quantity and quality, presence and absence, and abundance perspectives. We show that there is an easy qualitative transition from the Roche/454 to the Illumina MiSeq platforms. The ease of this transition is more nuanced quantitatively for low-abundant amplicons, although estimates of abundances are known to also vary within platforms.
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Affiliation(s)
- Frédéric Mahé
- Department of Ecology, University of Kaiserslautern, D-67663, Kaiserslautern, Germany
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Pawlowski J, Lejzerowicz F, Esling P. Next-generation environmental diversity surveys of foraminifera: preparing the future. THE BIOLOGICAL BULLETIN 2014; 227:93-106. [PMID: 25411369 DOI: 10.1086/bblv227n2p93] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Foraminifera are commonly defined as marine testate protists, and their diversity is mainly assessed on the basis of the morphology of their agglutinated or mineralized tests. Diversity surveys based on environmental DNA (eDNA) have dramatically changed this view by revealing an unexpected diversity of naked and organic-walled lineages as well as detecting foraminiferal lineages in soil and freshwater environments. Moreover, single-cell analyses have allowed discrimination among genetically distinctive types within almost every described morphospecies. In view of these studies, the foraminiferal diversity appeared to be largely underestimated, but its accurate estimation was impeded by the low speed and coverage of a cloning-based eDNA approach. With the advent of high-throughput sequencing (HTS) technologies, these limitations disappeared in favor of exhaustive descriptions of foraminiferal diversity in numerous samples. Yet, the biases and errors identified in early HTS studies raised some questions about the accuracy of HTS data and their biological interpretation. Among the most controversial issues affecting the reliability of HTS diversity estimates are (1) the impact of technical and biological biases, (2) the sensitivity and specificity of taxonomic sequence assignment, (3) the ability to distinguish rare species, and (4) the quantitative interpretation of HTS data. Here, we document the lessons learned from previous HTS surveys and present the current advances and applications focusing on foraminiferal eDNA. We discuss the problems associated with HTS approaches and predict the future trends and avenues that hold promises for surveying foraminiferal diversity accurately and efficiently.
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Affiliation(s)
- J Pawlowski
- Department of Genetics and Evolution, University of Geneva, Switzerland; and
| | - F Lejzerowicz
- Department of Genetics and Evolution, University of Geneva, Switzerland; and
| | - P Esling
- IRCAM, UMR 9912, Université Pierre et Marie Curie, Paris, France
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Wu W, Huang B, Liao Y, Sun P. Picoeukaryotic diversity and distribution in the subtropical-tropical South China Sea. FEMS Microbiol Ecol 2014; 89:563-79. [PMID: 24849025 DOI: 10.1111/1574-6941.12357] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Revised: 04/27/2014] [Accepted: 05/16/2014] [Indexed: 11/27/2022] Open
Abstract
Little is known regarding the diversity and distribution of picoeukaryotes in the northwestern Pacific Ocean, although these organisms are vital components of their environment. Here, we used a culture-independent approach to assess the 18S rDNA diversity of picoeukaryotes at six sampling sites along a transcontinental section of the South China Sea. The Alveolata group comprised 58.6% of the clones and was mainly represented by the novel marine alveolates (MALV)-I (18.8%) and MALV-II (30.6%), corresponding to 66.5% of all operational taxonomic units. Sequences affiliated with seven clades of the novel marine stramenopiles (MAST) were widely distributed in different clone libraries. We report an entirely new group representing the deepest evolutionary branch of the Hacrobia; this finding suggests the existence of novel picoeukaryotes at a high taxonomic level. Many phylotypes could not be taxonomically assigned, indicating the presence of numerous previously unknown groups. Horizontally, picoeukaryotic assemblages in the coastal water characterized with the rare occurrence of MALV-I were distinct from offshore communities. Vertically, MAST-4 were mainly retrieved in surface waters; however, the Radiolaria (Rhizaria) were mainly detected in clone libraries from depths of 60 m. Our findings further emphasize the immense diversity of picoeukaryotes, especially in the subtropical-tropical northwestern Pacific Ocean.
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Affiliation(s)
- Wenxue Wu
- Key Laboratory of Coastal and Wetland Ecosystems (Ministry of Education), State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
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Logares R, Audic S, Bass D, Bittner L, Boutte C, Christen R, Claverie JM, Decelle J, Dolan JR, Dunthorn M, Edvardsen B, Gobet A, Kooistra WHCF, Mahé F, Not F, Ogata H, Pawlowski J, Pernice MC, Romac S, Shalchian-Tabrizi K, Simon N, Stoeck T, Santini S, Siano R, Wincker P, Zingone A, Richards TA, de Vargas C, Massana R. Patterns of rare and abundant marine microbial eukaryotes. Curr Biol 2014; 24:813-21. [PMID: 24704080 DOI: 10.1016/j.cub.2014.02.050] [Citation(s) in RCA: 292] [Impact Index Per Article: 29.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2013] [Revised: 01/27/2014] [Accepted: 02/20/2014] [Indexed: 01/17/2023]
Abstract
BACKGROUND Biological communities are normally composed of a few abundant and many rare species. This pattern is particularly prominent in microbial communities, in which most constituent taxa are usually extremely rare. Although abundant and rare subcommunities may present intrinsic characteristics that could be crucial for understanding community dynamics and ecosystem functioning, microbiologists normally do not differentiate between them. Here, we investigate abundant and rare subcommunities of marine microbial eukaryotes, a crucial group of organisms that remains among the least-explored biodiversity components of the biosphere. We surveyed surface waters of six separate coastal locations in Europe, independently considering the picoplankton, nanoplankton, and microplankton/mesoplankton organismal size fractions. RESULTS Deep Illumina sequencing of the 18S rRNA indicated that the abundant regional community was mostly structured by organismal size fraction, whereas the rare regional community was mainly structured by geographic origin. However, some abundant and rare taxa presented similar biogeography, pointing to spatiotemporal structure in the rare microeukaryote biosphere. Abundant and rare subcommunities presented regular proportions across samples, indicating similar species-abundance distributions despite taxonomic compositional variation. Several taxa were abundant in one location and rare in other locations, suggesting large oscillations in abundance. The substantial amount of metabolically active lineages found in the rare biosphere suggests that this subcommunity constitutes a diversity reservoir that can respond rapidly to environmental change. CONCLUSIONS We propose that marine planktonic microeukaryote assemblages incorporate dynamic and metabolically active abundant and rare subcommunities, with contrasting structuring patterns but fairly regular proportions, across space and time.
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Affiliation(s)
- Ramiro Logares
- Institut de Ciències del Mar (ICM), CSIC, Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Spain.
| | - Stéphane Audic
- ADMM UMR 7144, UPMC Paris 06, Station Biologique de Roscoff, 29682 Roscoff, France; ADMM UMR 7144, CNRS, Station Biologique de Roscoff, 29682 Roscoff, France
| | - David Bass
- Department of Life Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Lucie Bittner
- ADMM UMR 7144, UPMC Paris 06, Station Biologique de Roscoff, 29682 Roscoff, France; ADMM UMR 7144, CNRS, Station Biologique de Roscoff, 29682 Roscoff, France; Department of Ecology, University of Kaiserslautern, 67663 Kaiserslautern, Germany
| | - Christophe Boutte
- ADMM UMR 7144, UPMC Paris 06, Station Biologique de Roscoff, 29682 Roscoff, France; ADMM UMR 7144, CNRS, Station Biologique de Roscoff, 29682 Roscoff, France
| | - Richard Christen
- SAE UMR 7138, CNRS, Parc Valrose BP71, 06108 Nice Cedex 02, France; SAE UMR 7138, Université de Nice-Sophia Antipolis, Parc Valrose BP71, 06108 Nice Cedex 02, France
| | | | - Johan Decelle
- ADMM UMR 7144, UPMC Paris 06, Station Biologique de Roscoff, 29682 Roscoff, France; ADMM UMR 7144, CNRS, Station Biologique de Roscoff, 29682 Roscoff, France
| | - John R Dolan
- LOV UMR 7093, CNRS, UPMC Paris 06, 06230 Villefranche-sur-Mer, France
| | - Micah Dunthorn
- Department of Ecology, University of Kaiserslautern, 67663 Kaiserslautern, Germany
| | - Bente Edvardsen
- Department of Biosciences, University of Oslo, P.O. Box 1066 Blindern, 0316 Oslo, Norway
| | - Angélique Gobet
- ADMM UMR 7144, UPMC Paris 06, Station Biologique de Roscoff, 29682 Roscoff, France; ADMM UMR 7144, CNRS, Station Biologique de Roscoff, 29682 Roscoff, France
| | - Wiebe H C F Kooistra
- Ecology and Evolution of Plankton, Stazione Zoologica Anton Dohrn, Villa Comunale 1, 80121 Naples, Italy
| | - Frédéric Mahé
- ADMM UMR 7144, UPMC Paris 06, Station Biologique de Roscoff, 29682 Roscoff, France; ADMM UMR 7144, CNRS, Station Biologique de Roscoff, 29682 Roscoff, France; Department of Ecology, University of Kaiserslautern, 67663 Kaiserslautern, Germany
| | - Fabrice Not
- ADMM UMR 7144, UPMC Paris 06, Station Biologique de Roscoff, 29682 Roscoff, France; ADMM UMR 7144, CNRS, Station Biologique de Roscoff, 29682 Roscoff, France
| | - Hiroyuki Ogata
- IGS UMR 7256, CNRS, Aix-Marseille Université, 13288 Marseille, France; Education Academy of Computational Life Sciences, Tokyo Institute of Technology, Tokyo 152-8552, Japan
| | - Jan Pawlowski
- Department of Genetics and Evolution, University of Geneva, 1211 Geneva, Switzerland
| | - Massimo C Pernice
- Institut de Ciències del Mar (ICM), CSIC, Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Spain
| | - Sarah Romac
- ADMM UMR 7144, UPMC Paris 06, Station Biologique de Roscoff, 29682 Roscoff, France; ADMM UMR 7144, CNRS, Station Biologique de Roscoff, 29682 Roscoff, France
| | | | - Nathalie Simon
- ADMM UMR 7144, UPMC Paris 06, Station Biologique de Roscoff, 29682 Roscoff, France; ADMM UMR 7144, CNRS, Station Biologique de Roscoff, 29682 Roscoff, France
| | - Thorsten Stoeck
- Department of Ecology, University of Kaiserslautern, 67663 Kaiserslautern, Germany
| | - Sébastien Santini
- IGS UMR 7256, CNRS, Aix-Marseille Université, 13288 Marseille, France
| | - Raffaele Siano
- Ifremer, Centre de Brest, DYNECO/Pelagos BP70, 29280 Plouzané, France
| | | | - Adriana Zingone
- Ecology and Evolution of Plankton, Stazione Zoologica Anton Dohrn, Villa Comunale 1, 80121 Naples, Italy
| | - Thomas A Richards
- Biosciences, University of Exeter, Geoffrey Pope Building, Exeter EX4 4QD, UK
| | - Colomban de Vargas
- ADMM UMR 7144, UPMC Paris 06, Station Biologique de Roscoff, 29682 Roscoff, France; ADMM UMR 7144, CNRS, Station Biologique de Roscoff, 29682 Roscoff, France
| | - Ramon Massana
- Institut de Ciències del Mar (ICM), CSIC, Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Spain
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Dunthorn M, Otto J, Berger SA, Stamatakis A, Mahé F, Romac S, de Vargas C, Audic S, Stock A, Kauff F, Stoeck T. Placing environmental next-generation sequencing amplicons from microbial eukaryotes into a phylogenetic context. Mol Biol Evol 2014; 31:993-1009. [PMID: 24473288 DOI: 10.1093/molbev/msu055] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Nucleotide positions in the hypervariable V4 and V9 regions of the small subunit (SSU)-rDNA locus are normally difficult to align and are usually removed before standard phylogenetic analyses. Yet, with next-generation sequencing data, amplicons of these regions are all that are available to answer ecological and evolutionary questions that rely on phylogenetic inferences. With ciliates, we asked how inclusion of the V4 or V9 regions, regardless of alignment quality, affects tree topologies using distinct phylogenetic methods (including PairDist that is introduced here). Results show that the best approach is to place V4 amplicons into an alignment of full-length Sanger SSU-rDNA sequences and to infer the phylogenetic tree with RAxML. A sliding window algorithm as implemented in RAxML shows, though, that not all nucleotide positions in the V4 region are better than V9 at inferring the ciliate tree. With this approach and an ancestral-state reconstruction, we use V4 amplicons from European nearshore sampling sites to infer that rather than being primarily terrestrial and freshwater, colpodean ciliates may have repeatedly transitioned from terrestrial/freshwater to marine environments.
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Affiliation(s)
- Micah Dunthorn
- Department of Ecology, University of Kaiserslautern, Kaiserslautern, Germany
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