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Anderson SR, Blanco-Bercial L, Carlson CA, Harvey EL. Role of Syndiniales parasites in depth-specific networks and carbon flux in the oligotrophic ocean. ISME COMMUNICATIONS 2024; 4:ycae014. [PMID: 38419659 PMCID: PMC10900894 DOI: 10.1093/ismeco/ycae014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 01/18/2024] [Accepted: 01/18/2024] [Indexed: 03/02/2024]
Abstract
Microbial associations that result in phytoplankton mortality are important for carbon transport in the ocean. This includes parasitism, which in microbial food webs is dominated by the marine alveolate group, Syndiniales. Parasites are expected to contribute to carbon recycling via host lysis; however, knowledge on host dynamics and correlation to carbon export remain unclear and limit the inclusion of parasitism in biogeochemical models. We analyzed a 4-year 18S rRNA gene metabarcoding dataset (2016-19), performing network analysis for 12 discrete depths (1-1000 m) to determine Syndiniales-host associations in the seasonally oligotrophic Sargasso Sea. Analogous water column and sediment trap data were included to define environmental drivers of Syndiniales and their correlation with particulate carbon flux (150 m). Syndiniales accounted for 48-74% of network edges, most often associated with Dinophyceae and Arthropoda (mainly copepods) at the surface and Rhizaria (Polycystinea, Acantharea, and RAD-B) in the aphotic zone. Syndiniales were the only eukaryote group to be significantly (and negatively) correlated with particulate carbon flux, indicating their contribution to flux attenuation via remineralization. Examination of Syndiniales amplicons revealed a range of depth patterns, including specific ecological niches and vertical connection among a subset (19%) of the community, the latter implying sinking of parasites (infected hosts or spores) on particles. Our findings elevate the critical role of Syndiniales in marine microbial systems and reveal their potential use as biomarkers for carbon export.
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Affiliation(s)
- Sean R Anderson
- Department of Biological Sciences, University of New Hampshire, Durham, NH 03824, United States
- Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, Falmouth, MA 02543, United States
| | | | - Craig A Carlson
- Department of Ecology, Evolution and Marine Biology and the Marine Science Institute, University of California, Santa Barbara, CA 93106, United States
| | - Elizabeth L Harvey
- Department of Biological Sciences, University of New Hampshire, Durham, NH 03824, United States
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2
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Rizos I, Debeljak P, Finet T, Klein D, Ayata SD, Not F, Bittner L. Beyond the limits of the unassigned protist microbiome: inferring large-scale spatio-temporal patterns of Syndiniales marine parasites. ISME COMMUNICATIONS 2023; 3:16. [PMID: 36854980 PMCID: PMC9975217 DOI: 10.1038/s43705-022-00203-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 11/15/2022] [Accepted: 11/16/2022] [Indexed: 03/02/2023]
Abstract
Marine protists are major components of the oceanic microbiome that remain largely unrepresented in culture collections and genomic reference databases. The exploration of this uncharted protist diversity in oceanic communities relies essentially on studying genetic markers from the environment as taxonomic barcodes. Here we report that across 6 large scale spatio-temporal planktonic surveys, half of the genetic barcodes remain taxonomically unassigned at the genus level, preventing a fine ecological understanding for numerous protist lineages. Among them, parasitic Syndiniales (Dinoflagellata) appear as the least described protist group. We have developed a computational workflow, integrating diverse 18S rDNA gene metabarcoding datasets, in order to infer large-scale ecological patterns at 100% similarity of the genetic marker, overcoming the limitation of taxonomic assignment. From a spatial perspective, we identified 2171 unassigned clusters, i.e., Syndiniales sequences with 100% similarity, exclusively shared between the Tropical/Subtropical Ocean and the Mediterranean Sea among all Syndiniales orders and 25 ubiquitous clusters shared within all the studied marine regions. From a temporal perspective, over 3 time-series, we highlighted 39 unassigned clusters that follow rhythmic patterns of recurrence and are the best indicators of parasite community's variation. These clusters withhold potential as ecosystem change indicators, mirroring their associated host community responses. Our results underline the importance of Syndiniales in structuring planktonic communities through space and time, raising questions regarding host-parasite association specificity and the trophic mode of persistent Syndiniales, while providing an innovative framework for prioritizing unassigned protist taxa for further description.
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Affiliation(s)
- Iris Rizos
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France.
- Sorbonne Université, CNRS, AD2M-UMR7144 Station Biologique de Roscoff, 29680, Roscoff, France.
| | - Pavla Debeljak
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France
| | - Thomas Finet
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France
| | - Dylan Klein
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France
| | - Sakina-Dorothée Ayata
- Sorbonne Université, Laboratoire d'Océanographie et du Climat: Expérimentation et Analyses Numériques (LOCEAN, SU/CNRS/IRD/MNHN), 75252, Paris Cedex 05, France
| | - Fabrice Not
- Sorbonne Université, CNRS, AD2M-UMR7144 Station Biologique de Roscoff, 29680, Roscoff, France
| | - Lucie Bittner
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France
- Institut Universitaire de France, Paris, France
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3
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Guillou L, Szymczak J, Alves-de-Souza C. Amoebophrya ceratii. Trends Parasitol 2023; 39:152-153. [PMID: 36522232 DOI: 10.1016/j.pt.2022.11.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 11/22/2022] [Accepted: 11/23/2022] [Indexed: 12/15/2022]
Affiliation(s)
- Laure Guillou
- Sorbonne Université, CNRS, UMR7144 Adaptation et Diversité en Milieu Marin, Ecology of Marine Plankton (ECOMAP), Station Biologique de Roscoff, 29680 Roscoff, France.
| | - Jeremy Szymczak
- Sorbonne Université, CNRS, UMR7144 Adaptation et Diversité en Milieu Marin, Ecology of Marine Plankton (ECOMAP), Station Biologique de Roscoff, 29680 Roscoff, France
| | - Catharina Alves-de-Souza
- Algal Resources Collection, Center for Marine Science, University of North Carolina Wilmington, Wilmington, NC 28409, USA
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4
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Holt CC, Boscaro V, Van Steenkiste NWL, Herranz M, Mathur V, Irwin NAT, Buckholtz G, Leander BS, Keeling PJ. Microscopic marine invertebrates are reservoirs for cryptic and diverse protists and fungi. MICROBIOME 2022; 10:161. [PMID: 36180959 PMCID: PMC9523941 DOI: 10.1186/s40168-022-01363-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 09/02/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Microbial symbioses in marine invertebrates are commonplace. However, characterizations of invertebrate microbiomes are vastly outnumbered by those of vertebrates. Protists and fungi run the gamut of symbiosis, yet eukaryotic microbiome sequencing is rarely undertaken, with much of the focus on bacteria. To explore the importance of microscopic marine invertebrates as potential symbiont reservoirs, we used a phylogenetic-focused approach to analyze the host-associated eukaryotic microbiomes of 220 animal specimens spanning nine different animal phyla. RESULTS Our data expanded the traditional host range of several microbial taxa and identified numerous undescribed lineages. A lack of comparable reference sequences resulted in several cryptic clades within the Apicomplexa and Ciliophora and emphasized the potential for microbial invertebrates to harbor novel protistan and fungal diversity. CONCLUSIONS Microscopic marine invertebrates, spanning a wide range of animal phyla, host various protist and fungal sequences and may therefore serve as a useful resource in the detection and characterization of undescribed symbioses. Video Abstract.
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Affiliation(s)
- Corey C Holt
- Department of Botany, University of British Columbia, Vancouver, Canada.
- Hakai Institute, Heriot Bay, Canada.
| | - Vittorio Boscaro
- Department of Botany, University of British Columbia, Vancouver, Canada
- Hakai Institute, Heriot Bay, Canada
| | - Niels W L Van Steenkiste
- Department of Botany, University of British Columbia, Vancouver, Canada
- Hakai Institute, Heriot Bay, Canada
- Department of Zoology, University of British Columbia, Vancouver, Canada
| | - Maria Herranz
- Department of Botany, University of British Columbia, Vancouver, Canada
- Hakai Institute, Heriot Bay, Canada
- Department of Zoology, University of British Columbia, Vancouver, Canada
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Varsha Mathur
- Department of Botany, University of British Columbia, Vancouver, Canada
| | | | - Gracy Buckholtz
- Department of Botany, University of British Columbia, Vancouver, Canada
| | - Brian S Leander
- Department of Botany, University of British Columbia, Vancouver, Canada
- Department of Zoology, University of British Columbia, Vancouver, Canada
| | - Patrick J Keeling
- Department of Botany, University of British Columbia, Vancouver, Canada.
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5
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Ott BM, Litaker RW, Holland WC, Delwiche CF. Using RDNA sequences to define dinoflagellate species. PLoS One 2022; 17:e0264143. [PMID: 35213572 PMCID: PMC8880924 DOI: 10.1371/journal.pone.0264143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 02/03/2022] [Indexed: 11/18/2022] Open
Abstract
Dinoflagellate species are traditionally defined using morphological characters, but molecular evidence accumulated over the past several decades indicates many morphologically-based descriptions are inaccurate. This recognition led to an increasing reliance on DNA sequence data, particularly rDNA gene segments, in defining species. The validity of this approach assumes the divergence in rDNA or other selected genes parallels speciation events. Another concern is whether single gene rDNA phylogenies by themselves are adequate for delineating species or if multigene phylogenies are required instead. Currently, few studies have directly assessed the relative utility of multigene versus rDNA-based phylogenies for distinguishing species. To address this, the current study examined D1-D3 and ITS/5.8S rDNA gene regions, a multi-gene phylogeny, and morphological characters in Gambierdiscus and other related dinoflagellate genera to determine if they produce congruent phylogenies and identify the same species. Data for the analyses were obtained from previous sequencing efforts and publicly available dinoflagellate transcriptomic libraries as well from the additional nine well-characterized Gambierdiscus species transcriptomic libraries generated in this study. The D1-D3 and ITS/5.8S phylogenies successfully identified the described Gambierdiscus and Alexandrium species. Additionally, the data showed that the D1-D3 and multigene phylogenies were equally capable of identifying the same species. The multigene phylogenies, however, showed different relationships among species and are likely to prove more accurate at determining phylogenetic relationships above the species level. These data indicated that D1-D3 and ITS/5.8S rDNA region phylogenies are generally successful for identifying species of Gambierdiscus, and likely those of other dinoflagellates. To assess how broadly general this finding is likely to be, rDNA molecular phylogenies from over 473 manuscripts representing 232 genera and 863 described species of dinoflagellates were reviewed. Results showed the D1-D3 rDNA and ITS phylogenies in combination are capable of identifying 97% of dinoflagellate species including all the species belonging to the genera Alexandrium, Ostreopsis and Gambierdiscus, although it should be noted that multi-gene phylogenies are preferred for inferring relationships among these species. A protocol is presented for determining when D1-D3, confirmed by ITS/5.8S rDNA sequence data, would take precedence over morphological features when describing new dinoflagellate species. This protocol addresses situations such as: a) when a new species is both morphologically and molecularly distinct from other known species; b) when a new species and closely related species are morphologically indistinguishable, but genetically distinct; and c) how to handle potentially cryptic species and cases where morphotypes are clearly distinct but have the same rDNA sequence. The protocol also addresses other molecular, morphological, and genetic approaches required to resolve species boundaries in the small minority of species where the D1-D3/ITS region phylogenies fail.
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Affiliation(s)
- Brittany M. Ott
- Joint Institute for Food Safety and Applied Nutrition (JIFSAN), University of Maryland—College Park, College Park, MD, United States of America
- Cell Biology and Molecular Genetics, University of Maryland—College Park, College Park, MD, United States of America
- * E-mail: (BMO); (RWL)
| | - R. Wayne Litaker
- CSS, Inc. Under Contract to National Oceanic and Atmospheric Administration (NOAA), National Ocean Service, National Centers for Coastal Ocean Science, Beaufort Laboratory, Beaufort, North Carolina, United States of America
- * E-mail: (BMO); (RWL)
| | - William C. Holland
- National Oceanic and Atmospheric Administration, National Ocean Service, National Centers for Coastal Ocean Science, Beaufort Laboratory, Beaufort, North Carolina, United States of America
| | - Charles F. Delwiche
- Cell Biology and Molecular Genetics, University of Maryland—College Park, College Park, MD, United States of America
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6
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Zhang Y, Huang N, Wang M, Liu H, Jing H. Microbial Eukaryotes Associated With Sediments in Deep-Sea Cold Seeps. Front Microbiol 2021; 12:782004. [PMID: 35003010 PMCID: PMC8740301 DOI: 10.3389/fmicb.2021.782004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 11/19/2021] [Indexed: 11/30/2022] Open
Abstract
Microbial eukaryotes are key components of the marine food web, but their distribution in deep-sea chemosynthetic ecosystems has not been well studied. Here, high-throughput sequencing of the 18S rRNA gene and network analysis were applied to investigate the diversity, distribution and potential relationships between microbial eukaryotes in samples collected from two cold seeps and one trough in the northern South China Sea. SAR (i.e., Stramenopiles, Alveolata, and Rhizaria) was the predominant group in all the samples, and it was highly affiliated to genotypes with potential symbiotic and parasitic strategies identified from other deep-sea extreme environments (e.g., oxygen deficient zones, bathypelagic waters, and hydrothermal vents). Our findings indicated that specialized lineages of deep-sea microbial eukaryotes exist in chemosynthetic cold seeps, where microbial eukaryotes affiliated with parasitic/symbiotic taxa were prevalent in the community. The biogeographic pattern of the total community was best represented by the intermediate operational taxonomic unit (OTU) category, whose relative abundance ranged 0.01–1% within a sample, and the communities of the two cold seeps were distinct from the trough, which suggests that geographical proximity has no critical impact on the distribution of deep-sea microbial eukaryotes. Overall, this study has laid the foundations for future investigations regarding the ecological function and in situ trophic relationships of microbial eukaryotes in deep-sea ecosystems.
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Affiliation(s)
- Yue Zhang
- CAS Key Laboratory for Experimental Study Under Deep-Sea Extreme Conditions, Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | - Ning Huang
- CAS Key Laboratory for Experimental Study Under Deep-Sea Extreme Conditions, Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | - Minxiao Wang
- Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Hongbin Liu
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, Hong Kong SAR, China
- HKUST-CAS Sanya Joint Laboratory of Marine Science Research, Chinese Academy of Sciences, Sanya, China
- Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, China
| | - Hongmei Jing
- CAS Key Laboratory for Experimental Study Under Deep-Sea Extreme Conditions, Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
- HKUST-CAS Sanya Joint Laboratory of Marine Science Research, Chinese Academy of Sciences, Sanya, China
- Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, China
- *Correspondence: Hongmei Jing,
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7
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Long M, Marie D, Szymczak J, Toullec J, Bigeard E, Sourisseau M, Le Gac M, Guillou L, Jauzein C. Dinophyceae can use exudates as weapons against the parasite Amoebophrya sp. (Syndiniales). ISME COMMUNICATIONS 2021; 1:34. [PMID: 37938261 PMCID: PMC9723556 DOI: 10.1038/s43705-021-00035-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 05/21/2021] [Accepted: 06/02/2021] [Indexed: 05/09/2023]
Abstract
Parasites in the genus Amoebophrya sp. infest dinoflagellate hosts in marine ecosystems and can be determining factors in the demise of blooms, including toxic red tides. These parasitic protists, however, rarely cause the total collapse of Dinophyceae blooms. Experimental addition of parasite-resistant Dinophyceae (Alexandrium minutum or Scrippsiella donghaienis) or exudates into a well-established host-parasite coculture (Scrippsiella acuminata-Amoebophrya sp.) mitigated parasite success and increased the survival of the sensitive host. This effect was mediated by waterborne molecules without the need for a physical contact. The strength of the parasite defenses varied between dinoflagellate species, and strains of A. minutum and was enhanced with increasing resistant host cell concentrations. The addition of resistant strains or exudates never prevented the parasite transmission entirely. Survival time of Amoebophrya sp. free-living stages (dinospores) decreased in presence of A. minutum but not of S. donghaienis. Parasite progeny drastically decreased with both species. Integrity of the dinospore membrane was altered by A. minutum, providing a first indication on the mode of action of anti-parasitic molecules. These results demonstrate that extracellular defenses can be an effective strategy against parasites that protects not only the resistant cells producing them, but also the surrounding community.
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Affiliation(s)
- Marc Long
- IFREMER, Centre de Brest, DYNECO Pelagos, F-29280, Plouzané, France.
| | - Dominique Marie
- UMR 7144 Sorbonne Université & Centre National pour la Recherche Scientifique, «Adaptation and Diversity in Marine Environment», Team «Ecology of Marine Plankton, ECOMAP», Station Biologique de Roscoff, 29680, Roscoff, France
| | - Jeremy Szymczak
- UMR 7144 Sorbonne Université & Centre National pour la Recherche Scientifique, «Adaptation and Diversity in Marine Environment», Team «Ecology of Marine Plankton, ECOMAP», Station Biologique de Roscoff, 29680, Roscoff, France
| | - Jordan Toullec
- IFREMER, Centre de Brest, DYNECO Pelagos, F-29280, Plouzané, France
| | - Estelle Bigeard
- UMR 7144 Sorbonne Université & Centre National pour la Recherche Scientifique, «Adaptation and Diversity in Marine Environment», Team «Ecology of Marine Plankton, ECOMAP», Station Biologique de Roscoff, 29680, Roscoff, France
| | - Marc Sourisseau
- IFREMER, Centre de Brest, DYNECO Pelagos, F-29280, Plouzané, France
| | - Mickael Le Gac
- IFREMER, Centre de Brest, DYNECO Pelagos, F-29280, Plouzané, France
| | - Laure Guillou
- UMR 7144 Sorbonne Université & Centre National pour la Recherche Scientifique, «Adaptation and Diversity in Marine Environment», Team «Ecology of Marine Plankton, ECOMAP», Station Biologique de Roscoff, 29680, Roscoff, France
| | - Cécile Jauzein
- IFREMER, Centre de Brest, DYNECO Pelagos, F-29280, Plouzané, France
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8
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Jayatunga DPW, Harischandra IN, Chandrasekharan NV, de Silva BGDNK. Compensatory Base Changes Reveal Sexual Incompatibility among Members of the Anopheles subpictus Sensu Lato (Diptera: Culicidae) Species Complex in Sri Lanka. Life (Basel) 2021; 11:life11030211. [PMID: 33800295 PMCID: PMC7998985 DOI: 10.3390/life11030211] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 02/23/2021] [Accepted: 03/02/2021] [Indexed: 11/16/2022] Open
Abstract
The mosquito Anopheles (Cellia) subpictus sensu lato (s.l.) is a major secondary vector of malaria in Sri Lanka. The sibling species composition in this species complex in Sri Lanka remains debatable. Compensatory base changes (CBCs) in the secondary structures of internal transcribed spacer 2 (ITS2) are reliable sources to predict sexual incompatibility among closely related species. The objective of the present study was to investigate the An. subpictus s.l. populations in Sri Lanka using the CBC analysis. Mosquito DNA was amplified and sequenced for the ITS2 region. The sequences were annotated using ITS2 Database. ITS2 secondary structures were constructed and analyzed for CBCs using various bioinformatics tools. The ITS2 regions consisted of two different lengths, 575 bp and 480 bp. The two CBCs and three hemi CBCs identified in the present study suggest that there may be at least two sexually incompatible sibling species. In conclusion, it is likely that there may be only two reproductively isolated sibling species in the An. subpictus species complex in Sri Lanka. However, due to high divergence of ITS2 in these species, it is reasonable to assume that they may be undergoing a speciation event to separate as a distinct species.
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Affiliation(s)
- D. P. W. Jayatunga
- Center for Biotechnology, Department of Zoology, Faculty of Applied Sciences, University of Sri Jayewardenepura, Gangodawila, Nugegoda 10250, Sri Lanka;
| | - I. N. Harischandra
- Genetics and Molecular Biology Unit, Faculty of Applied Sciences, University of Sri Jayewardenepura, Gangodawila, Nugegoda 10250, Sri Lanka;
| | - N. V. Chandrasekharan
- Department of Chemistry, Faculty of Science, University of Colombo, Colombo 00300, Sri Lanka;
| | - B. G. D. N. K. de Silva
- Center for Biotechnology, Department of Zoology, Faculty of Applied Sciences, University of Sri Jayewardenepura, Gangodawila, Nugegoda 10250, Sri Lanka;
- Genetics and Molecular Biology Unit, Faculty of Applied Sciences, University of Sri Jayewardenepura, Gangodawila, Nugegoda 10250, Sri Lanka;
- Correspondence: ; Tel.: +94-112804515 or +94-774467277
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9
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Farhat S, Le P, Kayal E, Noel B, Bigeard E, Corre E, Maumus F, Florent I, Alberti A, Aury JM, Barbeyron T, Cai R, Da Silva C, Istace B, Labadie K, Marie D, Mercier J, Rukwavu T, Szymczak J, Tonon T, Alves-de-Souza C, Rouzé P, Van de Peer Y, Wincker P, Rombauts S, Porcel BM, Guillou L. Rapid protein evolution, organellar reductions, and invasive intronic elements in the marine aerobic parasite dinoflagellate Amoebophrya spp. BMC Biol 2021; 19:1. [PMID: 33407428 PMCID: PMC7789003 DOI: 10.1186/s12915-020-00927-9] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Accepted: 11/12/2020] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Dinoflagellates are aquatic protists particularly widespread in the oceans worldwide. Some are responsible for toxic blooms while others live in symbiotic relationships, either as mutualistic symbionts in corals or as parasites infecting other protists and animals. Dinoflagellates harbor atypically large genomes (~ 3 to 250 Gb), with gene organization and gene expression patterns very different from closely related apicomplexan parasites. Here we sequenced and analyzed the genomes of two early-diverging and co-occurring parasitic dinoflagellate Amoebophrya strains, to shed light on the emergence of such atypical genomic features, dinoflagellate evolution, and host specialization. RESULTS We sequenced, assembled, and annotated high-quality genomes for two Amoebophrya strains (A25 and A120), using a combination of Illumina paired-end short-read and Oxford Nanopore Technology (ONT) MinION long-read sequencing approaches. We found a small number of transposable elements, along with short introns and intergenic regions, and a limited number of gene families, together contribute to the compactness of the Amoebophrya genomes, a feature potentially linked with parasitism. While the majority of Amoebophrya proteins (63.7% of A25 and 59.3% of A120) had no functional assignment, we found many orthologs shared with Dinophyceae. Our analyses revealed a strong tendency for genes encoded by unidirectional clusters and high levels of synteny conservation between the two genomes despite low interspecific protein sequence similarity, suggesting rapid protein evolution. Most strikingly, we identified a large portion of non-canonical introns, including repeated introns, displaying a broad variability of associated splicing motifs never observed among eukaryotes. Those introner elements appear to have the capacity to spread over their respective genomes in a manner similar to transposable elements. Finally, we confirmed the reduction of organelles observed in Amoebophrya spp., i.e., loss of the plastid, potential loss of a mitochondrial genome and functions. CONCLUSION These results expand the range of atypical genome features found in basal dinoflagellates and raise questions regarding speciation and the evolutionary mechanisms at play while parastitism was selected for in this particular unicellular lineage.
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Affiliation(s)
- Sarah Farhat
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ. Evry, Université Paris-Saclay, 91057, Evry, France
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, New York, 11794, USA
| | - Phuong Le
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Ehsan Kayal
- Sorbonne Université, CNRS, FR2424, Station Biologique de Roscoff, Place Georges Teissier, 29680, Roscoff, France
| | - Benjamin Noel
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ. Evry, Université Paris-Saclay, 91057, Evry, France
| | - 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, Station Biologique de Roscoff, Place Georges Teissier, 29680, Roscoff, France
| | - Florian Maumus
- URGI, INRA, Université Paris-Saclay, 78026, Versailles, France
| | - Isabelle Florent
- Unité Molécules de Communication et Adaptation des Microorganismes (MCAM, UMR7245), Muséum national d'Histoire naturelle, CNRS, CP 52, 57 rue Cuvier, 75005, Paris, France
| | - Adriana Alberti
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ. Evry, Université Paris-Saclay, 91057, Evry, France
| | - Jean-Marc Aury
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ. Evry, Université Paris-Saclay, 91057, Evry, France
| | - Tristan Barbeyron
- Sorbonne Université, CNRS, UMR 8227, Station Biologique de Roscoff, Place Georges Teissier, 29680, Roscoff, France
| | - 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
| | - Corinne Da Silva
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ. Evry, Université Paris-Saclay, 91057, Evry, France
| | - Benjamin Istace
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ. Evry, Université Paris-Saclay, 91057, Evry, France
| | - Karine Labadie
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ. Evry, Université Paris-Saclay, 91057, Evry, 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
| | - Jonathan Mercier
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ. Evry, Université Paris-Saclay, 91057, Evry, France
| | - Tsinda Rukwavu
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ. Evry, Université Paris-Saclay, 91057, Evry, France
| | - Jeremy Szymczak
- Sorbonne Université, CNRS, FR2424, Station Biologique de Roscoff, Place Georges Teissier, 29680, Roscoff, France
- Sorbonne Université, CNRS, UMR7144 Adaptation et Diversité en Milieu Marin, Ecology of Marine Plankton (ECOMAP), Station Biologique de Roscoff SBR, 29680, Roscoff, France
| | - Thierry Tonon
- Centre for Novel Agricultural Products, Department of Biology, University of York, Heslington, York, YO10 5DD, UK
| | - 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, USA
| | - Pierre Rouzé
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ. Evry, Université Paris-Saclay, 91057, Evry, France
| | - Stephane Rombauts
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Betina M Porcel
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ. Evry, Université Paris-Saclay, 91057, Evry, France.
| | - 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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Kayal E, Alves-de-Souza C, Farhat S, Velo-Suarez L, Monjol J, Szymczak J, Bigeard E, Marie D, Noel B, Porcel BM, Corre E, Six C, Guillou L. Dinoflagellate Host Chloroplasts and Mitochondria Remain Functional During Amoebophrya Infection. Front Microbiol 2020; 11:600823. [PMID: 33424803 PMCID: PMC7793755 DOI: 10.3389/fmicb.2020.600823] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 11/19/2020] [Indexed: 11/13/2022] Open
Abstract
Dinoflagellates are major components of phytoplankton that play critical roles in many microbial food webs, many of them being hosts of countless intracellular parasites. The phototrophic dinoflagellate Scrippsiella acuminata (Dinophyceae) can be infected by the microeukaryotic parasitoids Amoebophrya spp. (Syndiniales), some of which primarily target and digest the host nucleus. Early digestion of the nucleus at the beginning of the infection is expected to greatly impact the host metabolism, inducing the knockout of the organellar machineries that highly depend upon nuclear gene expression, such as the mitochondrial OXPHOS pathway and the plastid photosynthetic carbon fixation. However, previous studies have reported that chloroplasts remain functional in swimming host cells infected by Amoebophrya. We report here a multi-approach monitoring study of S. acuminata organelles over a complete infection cycle by nucleus-targeting Amoebophrya sp. strain A120. Our results show sustained and efficient photosystem II activity as a hallmark of functional chloroplast throughout the infection period despite the complete digestion of the host nucleus. We also report the importance played by light on parasite production, i.e., the amount of host biomass converted to parasite infective propagules. Using a differential gene expression analysis, we observed an apparent increase of all 3 mitochondrial and 9 out of the 11 plastidial genes involved in the electron transport chains (ETC) of the respiration pathways during the first stages of the infection. The longer resilience of organellar genes compared to those encoded by the nucleus suggests that both mitochondria and chloroplasts remain functional throughout most of the infection. This extended organelle functionality, along with higher parasite production under light conditions, suggests that host bioenergetic organelles likely benefit the parasite Amoebophrya sp. A120 and improve its fitness during the intracellular infective stage.
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Affiliation(s)
- Ehsan Kayal
- Fédération de Recherche 2424 Sorbonne Université & Centre National pour la Recherche Scientifique, Station Biologique de Roscoff, Roscoff, France
| | - Catharina Alves-de-Souza
- Algal Resources Collection, Center for Marine Sciences, University of North Carolina Wilmington, Wilmington, NC, United States
| | - Sarah Farhat
- Génomique Métabolique, Génoscope, Institut François Jacob, CEA, CNRS, Université d'Evry, Université Paris-Saclay, Evry, France
| | - Lourdes Velo-Suarez
- UMR 1078, Genetics, Functional Genomics and Biotechnology, INSERM. UFR Médecine, Brest, France
| | - Joanne Monjol
- UMR 7144 Sorbonne Université & Centre National pour la Recherche Scientifique, «Adaptation and Diversity in Marine Environment», Team «Ecology of Marine Plankton, ECOMAP», Station Biologique de Roscoff, Roscoff, France
| | - Jeremy Szymczak
- UMR 7144 Sorbonne Université & Centre National pour la Recherche Scientifique, «Adaptation and Diversity in Marine Environment», Team «Ecology of Marine Plankton, ECOMAP», Station Biologique de Roscoff, Roscoff, France
| | - Estelle Bigeard
- UMR 7144 Sorbonne Université & Centre National pour la Recherche Scientifique, «Adaptation and Diversity in Marine Environment», Team «Ecology of Marine Plankton, ECOMAP», Station Biologique de Roscoff, Roscoff, France
| | - Dominique Marie
- UMR 7144 Sorbonne Université & Centre National pour la Recherche Scientifique, «Adaptation and Diversity in Marine Environment», Team «Ecology of Marine Plankton, ECOMAP», Station Biologique de Roscoff, Roscoff, France
| | - Benjamin Noel
- Génomique Métabolique, Génoscope, Institut François Jacob, CEA, CNRS, Université d'Evry, Université Paris-Saclay, Evry, France
| | - Betina M Porcel
- Génomique Métabolique, Génoscope, Institut François Jacob, CEA, CNRS, Université d'Evry, Université Paris-Saclay, Evry, France
| | - Erwan Corre
- Fédération de Recherche 2424 Sorbonne Université & Centre National pour la Recherche Scientifique, Station Biologique de Roscoff, Roscoff, France
| | - Christophe Six
- UMR 7144 Sorbonne Université & Centre National pour la Recherche Scientifique, «Adaptation and Diversity in Marine Environment», Team «Ecology of Marine Plankton, ECOMAP», Station Biologique de Roscoff, Roscoff, France
| | - Laure Guillou
- UMR 7144 Sorbonne Université & Centre National pour la Recherche Scientifique, «Adaptation and Diversity in Marine Environment», Team «Ecology of Marine Plankton, ECOMAP», Station Biologique de Roscoff, Roscoff, France
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