1
|
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: 4] [Impact Index Per Article: 4.0] [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.
Collapse
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
| |
Collapse
|
2
|
Da Silva O, Ayata SD, Ser-Giacomi E, Leconte J, Pelletier E, Fauvelot C, Madoui MA, Guidi L, Lombard F, Bittner L. Genomic differentiation of three pico-phytoplankton species in the Mediterranean Sea. Environ Microbiol 2022; 24:6086-6099. [PMID: 36053818 PMCID: PMC10087736 DOI: 10.1111/1462-2920.16171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 08/09/2022] [Indexed: 01/12/2023]
Abstract
For more than a decade, high-throughput sequencing has transformed the study of marine planktonic communities and has highlighted the extent of protist diversity in these ecosystems. Nevertheless, little is known relative to their genomic diversity at the species-scale as well as their major speciation mechanisms. An increasing number of data obtained from global scale sampling campaigns is becoming publicly available, and we postulate that metagenomic data could contribute to deciphering the processes shaping protist genomic differentiation in the marine realm. As a proof of concept, we developed a findable, accessible, interoperable and reusable (FAIR) pipeline and focused on the Mediterranean Sea to study three a priori abundant protist species: Bathycoccus prasinos, Pelagomonas calceolata and Phaeocystis cordata. We compared the genomic differentiation of each species in light of geographic, environmental and oceanographic distances. We highlighted that isolation-by-environment shapes the genomic differentiation of B. prasinos, whereas P. cordata is impacted by geographic distance (i.e. isolation-by-distance). At present time, the use of metagenomics to accurately estimate the genomic differentiation of protists remains challenging since coverages are lower compared to traditional population surveys. However, our approach sheds light on ecological and evolutionary processes occurring within natural marine populations and paves the way for future protist population metagenomic studies.
Collapse
Affiliation(s)
- Ophélie Da Silva
- Sorbonne Université, CNRS, Laboratoire d'Océanographie de Villefranche, LOV, Villefranche-sur-Mer, France.,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, CNRS, Laboratoire d'Océanographie de Villefranche, LOV, Villefranche-sur-Mer, France.,Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France.,Sorbonne Université, UMR 7159 CNRS-IRD-MNHN, LOCEAN-IPSL, Paris, France
| | - Enrico Ser-Giacomi
- Sorbonne Université, UMR 7159 CNRS-IRD-MNHN, LOCEAN-IPSL, Paris, France.,Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Jade Leconte
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Eric Pelletier
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France.,Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France
| | - Cécile Fauvelot
- Sorbonne Université, CNRS, Laboratoire d'Océanographie de Villefranche, LOV, Villefranche-sur-Mer, France.,Institut de Recherche pour le Développement (IRD), UMR ENTROPIE, Nouméa, New Caledonia
| | - Mohammed-Amin Madoui
- Service d'Etude des Prions et des Infections Atypiques (SEPIA), Institut François Jacob, Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Université Paris Saclay, Fontenay-aux-Roses, France
| | - Lionel Guidi
- Sorbonne Université, CNRS, Laboratoire d'Océanographie de Villefranche, LOV, Villefranche-sur-Mer, France.,Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France
| | - Fabien Lombard
- Sorbonne Université, CNRS, Laboratoire d'Océanographie de Villefranche, LOV, Villefranche-sur-Mer, France.,Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France.,Institut Universitaire de France (IUF), Paris, 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 (IUF), Paris, France
| |
Collapse
|
3
|
Lobanov V, Gobet A, Joyce A. Ecosystem-specific microbiota and microbiome databases in the era of big data. ENVIRONMENTAL MICROBIOME 2022; 17:37. [PMID: 35842686 PMCID: PMC9287977 DOI: 10.1186/s40793-022-00433-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 06/29/2022] [Indexed: 05/05/2023]
Abstract
The rapid development of sequencing methods over the past decades has accelerated both the potential scope and depth of microbiota and microbiome studies. Recent developments in the field have been marked by an expansion away from purely categorical studies towards a greater investigation of community functionality. As in-depth genomic and environmental coverage is often distributed unequally across major taxa and ecosystems, it can be difficult to identify or substantiate relationships within microbial communities. Generic databases containing datasets from diverse ecosystems have opened a new era of data accessibility despite costs in terms of data quality and heterogeneity. This challenge is readily embodied in the integration of meta-omics data alongside habitat-specific standards which help contextualise datasets both in terms of sample processing and background within the ecosystem. A special case of large genomic repositories, ecosystem-specific databases (ES-DB's), have emerged to consolidate and better standardise sample processing and analysis protocols around individual ecosystems under study, allowing independent studies to produce comparable datasets. Here, we provide a comprehensive review of this emerging tool for microbial community analysis in relation to current trends in the field. We focus on the factors leading to the formation of ES-DB's, their comparison to traditional microbial databases, the potential for ES-DB integration with meta-omics platforms, as well as inherent limitations in the applicability of ES-DB's.
Collapse
Affiliation(s)
- Victor Lobanov
- Department of Marine Sciences, University of Gothenburg, Box 461, 405 30, Gothenburg, Sweden
| | | | - Alyssa Joyce
- Department of Marine Sciences, University of Gothenburg, Box 461, 405 30, Gothenburg, Sweden.
| |
Collapse
|
4
|
Effects of Harmful Algal Blooms on Fish and Shellfish Species: A Case Study of New Zealand in a Changing Environment. Toxins (Basel) 2022; 14:toxins14050341. [PMID: 35622588 PMCID: PMC9147682 DOI: 10.3390/toxins14050341] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 05/11/2022] [Accepted: 05/12/2022] [Indexed: 12/03/2022] Open
Abstract
Harmful algal blooms (HABs) have wide-ranging environmental impacts, including on aquatic species of social and commercial importance. In New Zealand (NZ), strategic growth of the aquaculture industry could be adversely affected by the occurrence of HABs. This review examines HAB species which are known to bloom both globally and in NZ and their effects on commercially important shellfish and fish species. Blooms of Karenia spp. have frequently been associated with mortalities of both fish and shellfish in NZ and the sub-lethal effects of other genera, notably Alexandrium spp., on shellfish (which includes paralysis, a lack of byssus production, and reduced growth) are also of concern. Climate change and anthropogenic impacts may alter HAB population structure and dynamics, as well as the physiological responses of fish and shellfish, potentially further compromising aquatic species. Those HAB species which have been detected in NZ and have the potential to bloom and harm marine life in the future are also discussed. The use of environmental DNA (eDNA) and relevant bioassays are practical tools which enable early detection of novel, problem HAB species and rapid toxin/HAB screening, and new data from HAB monitoring of aquaculture production sites using eDNA are presented. As aquaculture grows to supply a sizable proportion of the world’s protein, the effects of HABs in reducing productivity is of increasing significance. Research into the multiple stressor effects of climate change and HABs on cultured species and using local, recent, HAB strains is needed to accurately assess effects and inform stock management strategies.
Collapse
|
5
|
Sun P, Liao Y, Wang Y, Yang EJ, Jiao N, Lee Y, Jung J, Cho KH, Moon JK, Xu D. Contrasting Community Composition and Co-Occurrence Relationships of the Active Pico-Sized Haptophytes in the Surface and Subsurface Chlorophyll Maximum Layers of the Arctic Ocean in Summer. Microorganisms 2022; 10:microorganisms10020248. [PMID: 35208705 PMCID: PMC8877492 DOI: 10.3390/microorganisms10020248] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 01/13/2022] [Accepted: 01/17/2022] [Indexed: 12/10/2022] Open
Abstract
Haptophytes (Hacrobia: Haptophyta), which can perform phototrophic, phagotrophic, or mixotrophic nutritional modes, are critical for element cycling in a variety of aquatic ecosystems. However, their diversity, particularly in the changing Arctic Ocean (AO), remains largely unknown. In the present study, the biodiversity, community composition, and co-occurrence networks of pico-sized haptophytes in the surface water and subsurface chlorophyll maximum (SCM) layer of the AO were explored. Our results found higher alpha diversity estimates in the surface water compared with in the SCM based on high-throughput sequencing of haptophyte specific 18S rRNA. The community composition of the surface water was significantly different from that of the SCM, and water temperature was identified as the primary factor shaping the community compositions. Prymnesiales (mostly Chrysochromulina), uncultured Prymnesiophyceae, and Phaeocystis dominated the surface water communities, whereas Phaeocystis dominated the SCM communities, followed by Chrysochromulina, uncultured Prymnesiophyceae, and the remaining taxa. The communities of the surface water and SCM layer developed relatively independent modules in the metacommunity network. Nodes in the surface water were more closely connected to one another than those in the SCM. Network stability analysis revealed that surface water networks were more stable than SCM networks. These findings suggest that SCM communities are more susceptible to environmental fluctuations than those in surface water and that future global changes (e.g., global warming) may profoundly influence the development, persistence, and service of SCM in the AO.
Collapse
Affiliation(s)
- Ping Sun
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361102, China; (P.S.); (Y.L.); (Y.W.); (N.J.)
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystem, College of the Environment and Ecology, Xiamen University, Xiamen 361102, China
- Fujian Provincial Key Laboratory for Coastal Ecology and Environmental Studies, Xiamen University, Xiamen 361102, China
| | - Yuyu Liao
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361102, China; (P.S.); (Y.L.); (Y.W.); (N.J.)
- Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Ying Wang
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361102, China; (P.S.); (Y.L.); (Y.W.); (N.J.)
- Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Eun-Jin Yang
- Division of Polar Ocean Science, Korea Polar Research Institute, 26, Songdomirae-ro, Yeonsu-gu, Incheon 21990, Korea; (E.-J.Y.); (Y.L.); (J.J.); (K.-H.C.); (J.-K.M.)
| | - Nianzhi Jiao
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361102, China; (P.S.); (Y.L.); (Y.W.); (N.J.)
- Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Youngju Lee
- Division of Polar Ocean Science, Korea Polar Research Institute, 26, Songdomirae-ro, Yeonsu-gu, Incheon 21990, Korea; (E.-J.Y.); (Y.L.); (J.J.); (K.-H.C.); (J.-K.M.)
| | - Jinyoung Jung
- Division of Polar Ocean Science, Korea Polar Research Institute, 26, Songdomirae-ro, Yeonsu-gu, Incheon 21990, Korea; (E.-J.Y.); (Y.L.); (J.J.); (K.-H.C.); (J.-K.M.)
| | - Kyoung-Ho Cho
- Division of Polar Ocean Science, Korea Polar Research Institute, 26, Songdomirae-ro, Yeonsu-gu, Incheon 21990, Korea; (E.-J.Y.); (Y.L.); (J.J.); (K.-H.C.); (J.-K.M.)
| | - Jong-Kuk Moon
- Division of Polar Ocean Science, Korea Polar Research Institute, 26, Songdomirae-ro, Yeonsu-gu, Incheon 21990, Korea; (E.-J.Y.); (Y.L.); (J.J.); (K.-H.C.); (J.-K.M.)
| | - Dapeng Xu
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361102, China; (P.S.); (Y.L.); (Y.W.); (N.J.)
- Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
- Correspondence:
| |
Collapse
|
6
|
Sandaa RA, Saltvedt MR, Dahle H, Wang H, Våge S, Blanc-Mathieu R, Steen IH, Grimsley N, Edvardsen B, Ogata H, Lawrence J. Adaptive evolution of viruses infecting marine microalgae (haptophytes), from acute infections to stable coexistence. Biol Rev Camb Philos Soc 2021; 97:179-194. [PMID: 34514703 DOI: 10.1111/brv.12795] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 08/27/2021] [Accepted: 09/01/2021] [Indexed: 12/13/2022]
Abstract
Collectively known as phytoplankton, photosynthetic microbes form the base of the marine food web, and account for up to half of the primary production on Earth. Haptophytes are key components of this phytoplankton community, playing important roles both as primary producers and as mixotrophs that graze on bacteria and protists. Viruses influence the ecology and diversity of phytoplankton in the ocean, with the majority of microalgae-virus interactions described as 'boom and bust' dynamics, which are characteristic of acute virus-host systems. Most haptophytes are, however, part of highly diverse communities and occur at low densities, decreasing their chance of being infected by viruses with high host specificity. Viruses infecting these microalgae have been isolated in the laboratory, and there are several characteristics that distinguish them from acute viruses infecting bloom-forming haptophytes. Herein we synthesise what is known of viruses infecting haptophyte hosts in the ocean, discuss the adaptive evolution of haptophyte-infecting viruses -from those that cause acute infections to those that stably coexist with their host - and identify traits of importance for successful survival in the ocean.
Collapse
Affiliation(s)
- Ruth-Anne Sandaa
- Department of Biological Sciences, University of Bergen, Postbox 7803, N-5020, Bergen, Norway
| | - Marius R Saltvedt
- Department of Biological Sciences, University of Bergen, Postbox 7803, N-5020, Bergen, Norway
| | - Håkon Dahle
- Department of Biological Sciences, University of Bergen, Postbox 7803, N-5020, Bergen, Norway
| | - Haina Wang
- Department of Biological Sciences, University of Bergen, Postbox 7803, N-5020, Bergen, Norway
| | - Selina Våge
- Department of Biological Sciences, University of Bergen, Postbox 7803, N-5020, Bergen, Norway
| | - Romain Blanc-Mathieu
- Laboratoire de Physiologie Cellulaire & Végétale, CEA, Université Grenoble Alpes, CNRS, INRA, IRIG, Grenoble, France
| | - Ida H Steen
- Department of Biological Sciences, University of Bergen, Postbox 7803, N-5020, Bergen, Norway
| | - Nigel Grimsley
- Sorbonne Université, CNRS, UMR 7232 Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, F-66650, Banyuls-sur-Mer, France
| | - Bente Edvardsen
- Department of Biosciences, University of Oslo, Postbox 1066, N-0316, Oslo, Norway
| | - Hiroyuki Ogata
- Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan
| | - Janice Lawrence
- Biology Department, University of New Brunswick, PO Box 4400, Fredericton, NB, E3B 5A3, Canada
| |
Collapse
|
7
|
Gaonkar CC, Piredda R, Sarno D, Zingone A, Montresor M, Kooistra WHCF. Species detection and delineation in the marine planktonic diatoms Chaetoceros and Bacteriastrum through metabarcoding: making biological sense of haplotype diversity. Environ Microbiol 2020; 22:1917-1929. [PMID: 32157787 DOI: 10.1111/1462-2920.14984] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 03/07/2020] [Indexed: 12/11/2022]
Abstract
High-throughput sequencing (HTS) metabarcoding is commonly applied to assess phytoplankton diversity. Usually, haplotypes are grouped into operational taxonomic units (OTUs) through clustering, whereby the resulting number of OTUs depends on chosen similarity thresholds. We applied, instead, a phylogenetic approach to infer taxa among 18S rDNA V4-metabarcode haplotypes gathered from 48 time-series samples using the marine planktonic diatoms Chaetoceros and Bacteriastrum as test case. The 73 recovered taxa comprised both solitary haplotypes and polytomies, the latter composed each of a highly abundant, dominant haplotype and one to several minor, peripheral haplotypes. The solitary and dominant haplotypes usually matched reference sequences, enabling species assignation of taxa. We hypothesise that the super-abundance of reads in dominant haplotypes results from the homogenization effect of concerted evolution. Reads of populous peripheral haplotypes and dominant haplotypes show comparable distribution patterns over the sample dates, suggesting that they are part of the same population. Many taxa revealed marked seasonality, with closely related ones generally showing distinct periodicity, whereas others occur year-round. Phylogenies inferred from metabarcode haplotypes enable delineation of biologically meaningful taxa, whereas OTUs resulting from clustering algorithms often deviate markedly from such taxa.
Collapse
Affiliation(s)
- Chetan C Gaonkar
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Naples, Italy
| | - Roberta Piredda
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Naples, Italy
| | - Diana Sarno
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Naples, Italy
| | - Adriana Zingone
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Naples, Italy
| | - Marina Montresor
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Naples, Italy
| | - Wiebe H C F Kooistra
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Naples, Italy
| |
Collapse
|
8
|
Armeli Minicante S, Piredda R, Quero GM, Finotto S, Bernardi Aubry F, Bastianini M, Pugnetti A, Zingone A. Habitat Heterogeneity and Connectivity: Effects on the Planktonic Protist Community Structure at Two Adjacent Coastal Sites (the Lagoon and the Gulf of Venice, Northern Adriatic Sea, Italy) Revealed by Metabarcoding. Front Microbiol 2019; 10:2736. [PMID: 32038505 PMCID: PMC6988810 DOI: 10.3389/fmicb.2019.02736] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 11/11/2019] [Indexed: 11/28/2022] Open
Abstract
The Lagoon of Venice (LoV) and the Gulf of Venice (GoV), two adjacent coastal Long Term Ecological Research (LTER) sites in the northern Adriatic Sea, represent a transitional/marine coupled ecosystem under the influence of regional and local factors. In this study, these sites were sampled on four dates from April 2016 to February 2017 for environmental DNA and relevant abiotic variables, aiming to assess the relative importance of habitat heterogeneity and connectivity in structuring the protist community. High Throughput Sequencing of V4-18S rRNA gene from 56 samples collected at seven stations produced ca 6 million reads, grouped into 7,336 Operational Taxonomic Units (OTUs) at 97% similarity, which were affiliated to protists belonging to 34 taxonomic groups. The whole community was dominated by Bacillariophyta, especially in spring-summer in the LoV, and by Dinophyta, mainly in the GoV. Ciliophora, Syndiniales, and Cryptophyceae were the next more abundant groups. The community structure varied across the seasons and was different in the two ecosystems, which shared 96% of the reads but showed a high proportion of OTUs distributed preferentially in one of the two sites (specialists) and a different partitioning of trophic categories. GoV specialists were mainly Dinophyceae (>56%), followed by Syndiniales and Bacillariophyta, while the LoV specialists were distributed among several groups, including Bacillariophyta, Syndiniales, Ciliophora, Cryptophyceae, and Trebouxiophyceae. The main abiotic drivers of the differences between protist communities were salinity and temperature, which however explained a minor part of the variance (17%), pointing at a higher relevance of biotic factors and inter-taxa relationships. This was more evident in the LoV, where the network analysis highlighted a higher number of OTUs’ connections than in the GoV. Overall, the metabarcoding approach allowed to depict the composition of the whole protist community in the lagoon and adjacent coastal waters with high resolution, revealing many taxa so far not reported in the area. In addition, despite no clear barrier to dispersal processes, differences in the relative abundance and temporal variability of local protist communities indicate that environmental heterogeneity, in these adjacent and connected ecosystems, can be strong enough to allow for ecological segregation.
Collapse
Affiliation(s)
| | - Roberta Piredda
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Grazia Marina Quero
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Stefania Finotto
- Institute of Marine Sciences, National Research Council, Venice, Italy
| | | | - Mauro Bastianini
- Institute of Marine Sciences, National Research Council, Venice, Italy
| | | | - Adriana Zingone
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Naples, Italy
| |
Collapse
|
9
|
Sildever S, Kawakami Y, Kanno N, Kasai H, Shiomoto A, Katakura S, Nagai S. Toxic HAB species from the Sea of Okhotsk detected by a metagenetic approach, seasonality and environmental drivers. HARMFUL ALGAE 2019; 87:101631. [PMID: 31349888 DOI: 10.1016/j.hal.2019.101631] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 05/30/2019] [Accepted: 06/10/2019] [Indexed: 06/10/2023]
Abstract
During recent decades, the distribution of harmful algal bloom (HAB) species has expanded worldwide together with the increase of blooms and toxicity events. In this study, the presence of toxic HAB species in the Sea of Okhotsk was investigated based on metagenetic data collected during 6 years of weekly monitoring. Operational taxonomic units (OTUs) associated with the toxic HAB species were detected based on amplifying 18S V7-V9 and 28S D1 rRNA gene regions. In total, 43 unique OTUs associated with toxic HAB species were revealed, with 26 of those previously not reported from the Sea of Okhotsk. More OTUs belonging to dinoflagellates were detected by 18S, whereas a similar number of OTUs associated with dinoflagellates and diatoms were detected by targeting the 28S region. Species belonging to genera Alexandrium, Karenia and Karlodinium were mainly associated with OTUs under Dinophyceae, whereas Bacillariophyceae was represented by the species belonging to genus Pseudo-nitzschia. From the detected OTUs, 22 showed a clear seasonal pattern with the majority of those appearing during summer-autumn. For Alexandrium pacificum, Aureococcus anophagefferens, and Pseudo-nitzschia pungens, the seasonal pattern was detected based on both rRNA regions. Additionally, 14 OTUs were detected during all seasons and two OTUs appeared sporadically. OTUs associated with the toxic species had low relative read abundances, which together with other factors such as similar and variable morphology as well as usage of fixatives, may explain why those species have previously not been detected by light microscopy. Environmental parameters, especially water temperature, significantly (<0.05) influenced the variability in OTU relative abundances and displayed significant (<0.05) correlations with the unique OTUs. The results of this study demonstrate the usefulness of the metagenetic approach for phytoplankton monitoring, which is especially relevant for detecting toxic HAB species.
Collapse
Affiliation(s)
- Sirje Sildever
- National Research Institute of Fisheries Science, Yokohama Kanagawa, 236-8648, Japan
| | - Yoko Kawakami
- AXIOHELIX Co. Ltd, Chiyoda-ku, Tokyo, 101-0024, Japan
| | - Nanako Kanno
- National Research Institute of Fisheries Science, Yokohama Kanagawa, 236-8648, Japan
| | - Hiromi Kasai
- Hokkaido National Fisheries Research Institute, Kushiro, Hokkaido, 085-0802, Japan
| | | | | | - Satoshi Nagai
- National Research Institute of Fisheries Science, Yokohama Kanagawa, 236-8648, Japan.
| |
Collapse
|
10
|
Deodato CR, Barlow SB, Hovde BT, Cattolico RA. Naked Chrysochromulina (Haptophyta) isolates from lake and river ecosystems: An electron microscopic comparison including new observations on the type species of this taxon. ALGAL RES 2019. [DOI: 10.1016/j.algal.2019.101492] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
11
|
Zingone A, D'Alelio D, Mazzocchi MG, Montresor M, Sarno D, team LTERMC. Time series and beyond: multifaceted plankton research at a marine Mediterranean LTER site. NATURE CONSERVATION 2019. [DOI: 10.3897/natureconservation.34.30789] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Plankton are a pivotal component of the diversity and functioning of coastal marine ecosystems. A long time-series of observations is the best tool to trace their patterns and variability over multiple scales, ultimately providing a sound foundation for assessing, modelling and predicting the effects of anthropogenic and natural environmental changes on pelagic communities. At the same time, a long time-series constitutes a formidable asset for different kinds of research on specific questions that emerge from the observations, whereby the results of these complementary studies provide precious interpretative tools that augment the informative value of the data collected. In this paper, we review more than 140 studies that have been developed around a Mediterranean plankton time series gathered in the Gulf of Naples at the station LTER-MC since 1984. These studies have addressed different topics concerning marine plankton, which have included: i) seasonal patterns and trends; ii) taxonomic diversity, with a focus on key or harmful algal species and the discovery of many new taxa; iii) molecular diversity of selected species, groups of species or the whole planktonic community; iv) life cycles of several phyto- and zooplankton species; and v) interactions among species through trophic relationships, parasites and viruses. Overall, the products of this research demonstrate the great value of time series besides the record of fluctuations and trends, and highlight their primary role in the development of the scientific knowledge of plankton much beyond the local scale.
Collapse
|
12
|
Richter N, Longo WM, George S, Shipunova A, Huang Y, Amaral‐Zettler L. Phylogenetic diversity in freshwater-dwelling Isochrysidales haptophytes with implications for alkenone production. GEOBIOLOGY 2019; 17:272-280. [PMID: 30720914 PMCID: PMC6590312 DOI: 10.1111/gbi.12330] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Revised: 11/30/2018] [Accepted: 12/06/2018] [Indexed: 06/09/2023]
Abstract
Members of the order Isochrysidales are unique among haptophyte lineages in being the exclusive producers of alkenones, long-chain ketones that are commonly used for paleotemperature reconstructions. Alkenone-producing haptophytes are divided into three major groups based largely on molecular ecological data: Group I is found in freshwater lakes, Group II commonly occurs in brackish and coastal marine environments, and Group III consists of open ocean species. Each group has distinct alkenone distributions; however, only Groups II and III Isochrysidales currently have cultured representatives. The uncultured Group I Isochrysidales are distinguished geochemically by the presence of tri-unsaturated alkenone isomers (C37:3b Me, C38:3b Et, C38:3b Me, C39:3b Et) present in water column and sediment samples, yet their genetic diversity, morphology, and environmental controls are largely unknown. Using small-subunit (SSU) ribosomal RNA (rRNA) marker gene amplicon high-throughput sequencing of environmental water column and sediment samples, we show that Group I is monophyletic with high phylogenetic diversity and contains a well-supported clade separating the previously described "EV" clade from the "Greenland" clade. We infer the first partial large-subunit (LSU) rRNA gene Group I sequence phylogeny, which uncovered additional well-supported clades embedded within Group I. Relative to Group II, Group I revealed higher levels of genetic diversity despite conservation of alkenone signatures and a closer evolutionary relationship with Group III. In Group I, the presence of the tri-unsaturated alkenone isomers appears to be conserved, which is not the case for Group II. This suggests differing environmental influences on Group I and II and perhaps uncovers evolutionary constraints on alkenone biosynthesis.
Collapse
Affiliation(s)
- Nora Richter
- Department of Earth, Environmental and Planetary SciencesBrown UniversityProvidenceRhode Island
- The Josephine Bay Paul Center for Comparative Molecular Biology and EvolutionMarine Biological LaboratoryWoods HoleMassachusetts
| | - William M. Longo
- Department of Earth, Environmental and Planetary SciencesBrown UniversityProvidenceRhode Island
- Department of Marine Chemistry and GeochemistryWoods Hole Oceanographic InstitutionWoods HoleMassachusetts
| | - Sarabeth George
- Department of Earth, Environmental and Planetary SciencesBrown UniversityProvidenceRhode Island
- The Josephine Bay Paul Center for Comparative Molecular Biology and EvolutionMarine Biological LaboratoryWoods HoleMassachusetts
| | - Anna Shipunova
- The Josephine Bay Paul Center for Comparative Molecular Biology and EvolutionMarine Biological LaboratoryWoods HoleMassachusetts
| | - Yongsong Huang
- Department of Earth, Environmental and Planetary SciencesBrown UniversityProvidenceRhode Island
| | - Linda Amaral‐Zettler
- Department of Earth, Environmental and Planetary SciencesBrown UniversityProvidenceRhode Island
- The Josephine Bay Paul Center for Comparative Molecular Biology and EvolutionMarine Biological LaboratoryWoods HoleMassachusetts
- Department of Marine Microbiology and BiogeochemistryNIOZ Royal Netherlands Institute for Sea Research and Utrecht UniversityTexelThe Netherlands
- Department of Freshwater and Marine EcologyInstitute for Biodiversity and Ecosystem DynamicsUniversity of AmsterdamAmsterdamNetherlands
| |
Collapse
|
13
|
Chan YF, Chiang KP, Ku Y, Gong GC. Abiotic and Biotic Factors Affecting the Ingestion Rates of Mixotrophic Nanoflagellates (Haptophyta). MICROBIAL ECOLOGY 2019; 77:607-615. [PMID: 30187089 DOI: 10.1007/s00248-018-1249-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 08/27/2018] [Indexed: 06/08/2023]
Abstract
Mixotrophic haptophytes comprise one of several important groups of mixotrophic nanoflagellates in the pelagic environment. This study aimed to investigate if phagotrophy in mixotrophic haptophytes is regulated by light or other factors in the surface (SE) and bottom (BE) of the euphotic zone in the subtropical northwestern Pacific Ocean. We estimated the rates of bacterial ingestion by haptophytes using fluorescently labeled bacteria (FLBs) and fluorescence in situ hybridization. Haptophyte diversity and abundance were also investigated in the same sampling area. The annual mean abundance of haptophytes was 419 ± 85.6 cells mL-1 in both SE and BE. Cells 3-5 μm in size were the dominant group in all haptophytes and accounted for majority of bacteria standing stock removed by haptophytes (53%). Most haptophyte ingestion rates (IRs) were not significantly different between the two layers (average SE ingestion rate: 12.5 ± 2.29 bac Hap-1 h-1; BE: 14.7 ± 3.03 bac Hap-1 h-1). Furthermore, the haptophyte IRs were negatively correlated with nitrate concentrations in the SE and positively correlated with bacterial abundances in the BE, which accounts for the significantly high IRs in August 2012 and 2013. These findings imply that mixotrophic haptophytes in this region had different factors affecting phagotrophy to adapt to the ambient light intensity alterations between SE and BE.
Collapse
Affiliation(s)
- Ya-Fan Chan
- Biodiversity Research Center, Academia Sinica, Nankang, Taipei, 115, Taiwan
| | - Kuo-Ping Chiang
- Institute of Marine Environment and Ecology, National Taiwan Ocean University, 2 Pei-Ning Road, Keelung, 202-24, Taiwan.
- Center of Excellence for the Oceans, National Taiwan Ocean University, 2 Pei-Ning Road, Keelung, 202-24, Taiwan.
| | - Yun Ku
- Institute of Marine Environment and Ecology, National Taiwan Ocean University, 2 Pei-Ning Road, Keelung, 202-24, Taiwan
| | - Gwo-Ching Gong
- Institute of Marine Environment and Ecology, National Taiwan Ocean University, 2 Pei-Ning Road, Keelung, 202-24, Taiwan
- Center of Excellence for the Oceans, National Taiwan Ocean University, 2 Pei-Ning Road, Keelung, 202-24, Taiwan
| |
Collapse
|
14
|
Faure E, Not F, Benoiston AS, Labadie K, Bittner L, Ayata SD. Mixotrophic protists display contrasted biogeographies in the global ocean. ISME JOURNAL 2019; 13:1072-1083. [PMID: 30643201 DOI: 10.1038/s41396-018-0340-5] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 12/13/2018] [Accepted: 12/13/2018] [Indexed: 12/21/2022]
Abstract
Mixotrophy, or the ability to acquire carbon from both auto- and heterotrophy, is a widespread ecological trait in marine protists. Using a metabarcoding dataset of marine plankton from the global ocean, 318,054 mixotrophic metabarcodes represented by 89,951,866 sequences and belonging to 133 taxonomic lineages were identified and classified into four mixotrophic functional types: constitutive mixotrophs (CM), generalist non-constitutive mixotrophs (GNCM), endo-symbiotic specialist non-constitutive mixotrophs (eSNCM), and plastidic specialist non-constitutive mixotrophs (pSNCM). Mixotrophy appeared ubiquitous, and the distributions of the four mixotypes were analyzed to identify the abiotic factors shaping their biogeographies. Kleptoplastidic mixotrophs (GNCM and pSNCM) were detected in new zones compared to previous morphological studies. Constitutive and non-constitutive mixotrophs had similar ranges of distributions. Most lineages were evenly found in the samples, yet some of them displayed strongly contrasted distributions, both across and within mixotypes. Particularly divergent biogeographies were found within endo-symbiotic mixotrophs, depending on the ability to form colonies or the mode of symbiosis. We showed how metabarcoding can be used in a complementary way with previous morphological observations to study the biogeography of mixotrophic protists and to identify key drivers of their biogeography.
Collapse
Affiliation(s)
- Emile Faure
- Sorbonne Université, CNRS, Laboratoire d'océanographie de Villefranche, LOV, 06230, Villefranche-sur-Mer, France. .,Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, CP 50, 57 rue Cuvier, 75005, Paris, France.
| | - Fabrice Not
- Sorbonne Université, CNRS, UMR7144 Adaptation and Diversity in Marine Environment (AD2M) Laboratory, Ecology of Marine Plankton team, Station Biologique de Roscoff, Place Georges Teissier, 29680, Roscoff, France
| | - Anne-Sophie Benoiston
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, CP 50, 57 rue Cuvier, 75005, Paris, France
| | - Karine Labadie
- Genoscope, Institut de biologie François-Jacob, Commissariat à l'Energie Atomique (CEA), Evry, France, 91057, Evry, France
| | - Lucie Bittner
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, CP 50, 57 rue Cuvier, 75005, Paris, France
| | - Sakina-Dorothée Ayata
- Sorbonne Université, CNRS, Laboratoire d'océanographie de Villefranche, LOV, 06230, Villefranche-sur-Mer, France.,Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, CP 50, 57 rue Cuvier, 75005, Paris, France
| |
Collapse
|
15
|
Carrier G, Baroukh C, Rouxel C, Duboscq-Bidot L, Schreiber N, Bougaran G. Draft genomes and phenotypic characterization of Tisochrysis lutea strains. Toward the production of domesticated strains with high added value. ALGAL RES 2018. [DOI: 10.1016/j.algal.2017.10.017] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
16
|
Leray M, Knowlton N. Censusing marine eukaryotic diversity in the twenty-first century. Philos Trans R Soc Lond B Biol Sci 2017; 371:rstb.2015.0331. [PMID: 27481783 PMCID: PMC4971183 DOI: 10.1098/rstb.2015.0331] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/26/2016] [Indexed: 11/12/2022] Open
Abstract
The ocean constitutes one of the vastest and richest biomes on our planet. Most recent estimations, all based on indirect approaches, suggest that there are millions of marine eukaryotic species. Moreover, a large majority of these are small (less than 1 mm), cryptic and still unknown to science. However, this knowledge gap, caused by the lack of diagnostic morphological features in small organisms and the limited sampling of the global ocean, is currently being filled, thanks to new DNA-based approaches. The molecular technique of PCR amplification of homologous gene regions combined with high-throughput sequencing, routinely used to census unculturable prokaryotes, is now also being used to characterize whole communities of marine eukaryotes. Here, we review how this methodological advancement has helped to better quantify the magnitude and patterns of marine eukaryotic diversity, with an emphasis on taxonomic groups previously largely overlooked. We then discuss obstacles remaining to achieve a global understanding of marine eukaryotic diversity. In particular, we argue that 18S variable regions do not provide sufficient taxonomic resolution to census marine life, and suggest combining broad eukaryotic surveys targeting the 18S rRNA region with more taxon-focused analyses of hypervariable regions to improve our understanding of the diversity of species, the functional units of marine ecosystems. This article is part of the themed issue ‘From DNA barcodes to biomes’.
Collapse
Affiliation(s)
- Matthieu Leray
- National Museum of Natural History, Smithsonian Institution, Washington, DC 20013, USA
| | - Nancy Knowlton
- National Museum of Natural History, Smithsonian Institution, Washington, DC 20013, USA
| |
Collapse
|
17
|
Gran-Stadniczeñko S, Šupraha L, Egge ED, Edvardsen B. Haptophyte Diversity and Vertical Distribution Explored by 18S and 28S Ribosomal RNA Gene Metabarcoding and Scanning Electron Microscopy. J Eukaryot Microbiol 2017; 64:514-532. [PMID: 27973742 PMCID: PMC5574017 DOI: 10.1111/jeu.12388] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Revised: 12/06/2016] [Accepted: 12/07/2016] [Indexed: 02/01/2023]
Abstract
Haptophyta encompasses more than 300 species of mostly marine pico‐ and nanoplanktonic flagellates. Our aims were to investigate the Oslofjorden haptophyte diversity and vertical distribution by metabarcoding, and to improve the approach to study haptophyte community composition, richness and proportional abundance by comparing two rRNA markers and scanning electron microscopy (SEM). Samples were collected in August 2013 at the Outer Oslofjorden, Norway. Total RNA/cDNA was amplified by haptophyte‐specific primers targeting the V4 region of the 18S, and the D1‐D2 region of the 28S rRNA. Taxonomy was assigned using curated haptophyte reference databases and phylogenetic analyses. Both marker genes showed Chrysochromulinaceae and Prymnesiaceae to be the families with highest number of Operational Taxonomic Units (OTUs), as well as proportional abundance. The 18S rRNA data set also contained OTUs assigned to eight supported and defined clades consisting of environmental sequences only, possibly representing novel lineages from family to class. We also recorded new species for the area. Comparing coccolithophores by SEM with metabarcoding shows a good correspondence with the 18S rRNA gene proportional abundances. Our results contribute to link morphological and molecular data and 28S to 18S rRNA gene sequences of haptophytes without cultured representatives, and to improve metabarcoding methodology.
Collapse
Affiliation(s)
| | - Luka Šupraha
- Department of Earth Sciences, Uppsala University, Villavägen 16, Uppsala, SE-75236, Sweden
| | - Elianne D Egge
- Department of Biosciences, University of Oslo, PO Box 1066 Blindern, Oslo, 0316, Norway
| | - Bente Edvardsen
- Department of Biosciences, University of Oslo, PO Box 1066 Blindern, Oslo, 0316, Norway
| |
Collapse
|
18
|
Patchiness of Ciliate Communities Sampled at Varying Spatial Scales along the New England Shelf. PLoS One 2016; 11:e0167659. [PMID: 27936137 PMCID: PMC5147948 DOI: 10.1371/journal.pone.0167659] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Accepted: 11/17/2016] [Indexed: 11/29/2022] Open
Abstract
Although protists (microbial eukaryotes) provide an important link between bacteria and Metazoa in food webs, we do not yet have a clear understanding of the spatial scales on which protist diversity varies. Here, we use a combination of DNA fingerprinting (denaturant gradient gel electrophoresis or DGGE) and high-throughput sequencing (HTS) to assess the ciliate community in the class Spirotrichea at varying scales of 1–3 km sampled in three locations separated by at least 25 km—offshore, midshelf and inshore—along the New England shelf. Analyses of both abundant community (DGGE) and the total community (HTS) members reveal that: 1) ciliate communities are patchily distributed inshore (i.e. the middle station of a transect is distinct from its two neighboring stations), whereas communities are more homogeneous among samples within the midshelf and offshore stations; 2) a ciliate closely related to Pelagostrobilidium paraepacrum ‘blooms’ inshore and; 3) environmental factors may differentially impact the distributions of individual ciliates (i.e. OTUs) rather than the community as a whole as OTUs tend to show distinct biogeographies (e.g. some OTUs are restricted to the offshore locations, some to the surface, etc.). Together, these data show the complexity underlying the spatial distributions of marine protists, and suggest that biogeography may be a property of ciliate species rather than communities.
Collapse
|
19
|
Piredda R, Tomasino MP, D'Erchia AM, Manzari C, Pesole G, Montresor M, Kooistra WHCF, Sarno D, Zingone A. Diversity and temporal patterns of planktonic protist assemblages at a Mediterranean Long Term Ecological Research site. FEMS Microbiol Ecol 2016; 93:fiw200. [DOI: 10.1093/femsec/fiw200] [Citation(s) in RCA: 105] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/25/2016] [Indexed: 11/13/2022] Open
|
20
|
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]
|
21
|
Forster D, Dunthorn M, Mahé F, Dolan JR, Audic S, Bass D, Bittner L, Boutte C, Christen R, Claverie JM, Decelle J, Edvardsen B, Egge E, Eikrem W, Gobet A, Kooistra WHCF, Logares R, Massana R, Montresor M, Not F, Ogata H, Pawlowski J, Pernice MC, Romac S, Shalchian-Tabrizi K, Simon N, Richards TA, Santini S, Sarno D, Siano R, Vaulot D, Wincker P, Zingone A, de Vargas C, Stoeck T. Benthic protists: the under-charted majority. FEMS Microbiol Ecol 2016; 92:fiw120. [PMID: 27267932 DOI: 10.1093/femsec/fiw120] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/30/2016] [Indexed: 11/13/2022] Open
Abstract
Marine protist diversity inventories have largely focused on planktonic environments, while benthic protists have received relatively little attention. We therefore hypothesize that current diversity surveys have only skimmed the surface of protist diversity in marine sediments, which may harbor greater diversity than planktonic environments. We tested this by analyzing sequences of the hypervariable V4 18S rRNA from benthic and planktonic protist communities sampled in European coastal regions. Despite a similar number of OTUs in both realms, richness estimations indicated that we recovered at least 70% of the diversity in planktonic protist communities, but only 33% in benthic communities. There was also little overlap of OTUs between planktonic and benthic communities, as well as between separate benthic communities. We argue that these patterns reflect the heterogeneity and diversity of benthic habitats. A comparison of all OTUs against the Protist Ribosomal Reference database showed that a higher proportion of benthic than planktonic protist diversity is missing from public databases; similar results were obtained by comparing all OTUs against environmental references from NCBI's Short Read Archive. We suggest that the benthic realm may therefore be the world's largest reservoir of marine protist diversity, with most taxa at present undescribed.
Collapse
Affiliation(s)
- Dominik Forster
- Department of Ecology, University of Kaiserslautern, Erwin-Schrödinger Str. 14, D-67663 Kaiserslautern, Germany
| | - Micah Dunthorn
- Department of Ecology, University of Kaiserslautern, Erwin-Schrödinger Str. 14, D-67663 Kaiserslautern, Germany
| | - Fréderic Mahé
- Department of Ecology, University of Kaiserslautern, Erwin-Schrödinger Str. 14, D-67663 Kaiserslautern, Germany
| | - John R Dolan
- Sorbonne Universités, UPMC Univ. Paris 06, CNRS, UMR CNRS UMR 7093 and Laboratoire d'Océanographie de Villefranche-sur-Mer, Université Paris 06, F-06230 Villefranche-sur-Mer, France
| | - Stéphane Audic
- Sorbonne Universités, UPMC Univ. Paris 06, CNRS, UMR 7144, Station Biologique, Place Georges Teissier, 29680 Roscoff, France
| | - David Bass
- Department of Life Sciences, the Natural History Museum London, Cromwell Road, London SW7 5BD, UK Centre for Environment, Fisheries and Aquaculture Science (Cefas), Barrack Road, the Nothe, Weymouth, Dorset DT4 8UB, UK
| | - Lucie Bittner
- Department of Ecology, University of Kaiserslautern, Erwin-Schrödinger Str. 14, D-67663 Kaiserslautern, Germany Sorbonne Universités, UPMC Univ. Paris 06, CNRS, UMR 7144, Station Biologique, Place Georges Teissier, 29680 Roscoff, France Sorbonne Universités, UPMC, CNRS, Institut de Biologie Paris-Seine (IBPS), Evolution Paris Seine, F-75005 Paris, France
| | - Christophe Boutte
- Sorbonne Universités, UPMC Univ. Paris 06, CNRS, UMR 7144, Station Biologique, Place Georges Teissier, 29680 Roscoff, France
| | - Richard Christen
- CNRS, UMR 7138 & Université de Nice-Sophia Antipolis, F-06103 Nice cedex 2, France Université de Nice-Sophia Antipolis & CNRS, UMR 7138 F-06103 Nice cedex 2, France
| | | | - Johan Decelle
- Sorbonne Universités, UPMC Univ. Paris 06, CNRS, UMR 7144, Station Biologique, Place Georges Teissier, 29680 Roscoff, France
| | - Bente Edvardsen
- Department of BioSciences, University of Oslo, Blindern, 0316 N-Oslo, Norway
| | - Elianne Egge
- Department of BioSciences, University of Oslo, Blindern, 0316 N-Oslo, Norway
| | - Wenche Eikrem
- Department of BioSciences, University of Oslo, Blindern, 0316 N-Oslo, Norway
| | - Angélique Gobet
- Sorbonne Universités, UPMC Univ. Paris 06, CNRS, UMR 7144, Station Biologique, Place Georges Teissier, 29680 Roscoff, France CNRS, UMR 8227 & UPMC Université Paris 06, Station Biologique de Roscoff, F-29682 Roscoff, France
| | | | - Ramiro Logares
- Institut de Ciències del Mar (CSIC), Passeig Marítim de la Barceloneta, 37-49, ES-08003, Barcelona, Catalonia, Spain
| | - Ramon Massana
- Institut de Ciències del Mar (CSIC), Passeig Marítim de la Barceloneta, 37-49, ES-08003, Barcelona, Catalonia, Spain
| | - Marina Montresor
- Stazione Zoologica Anton Dohrn, Villa Comunale 1, I-80121, Naples, Italy
| | - Fabrice Not
- Sorbonne Universités, UPMC Univ. Paris 06, CNRS, UMR 7144, Station Biologique, Place Georges Teissier, 29680 Roscoff, France
| | - Hiroyuki Ogata
- Sorbonne Universités, UPMC Univ. Paris 06, CNRS, UMR CNRS UMR 7093 and Laboratoire d'Océanographie de Villefranche-sur-Mer, Université Paris 06, F-06230 Villefranche-sur-Mer, France Institute for Chemical Research, Kyoto University, Uji, 611-0011, Japan
| | - Jan Pawlowski
- Department of Genetics and Evolution, University of Geneva, 4, Boulevard d'Yvoy, CH-1211 Geneva, Switzerland
| | - Massimo C Pernice
- Institut de Ciències del Mar (CSIC), Passeig Marítim de la Barceloneta, 37-49, ES-08003, Barcelona, Catalonia, Spain
| | - Sarah Romac
- Sorbonne Universités, UPMC Univ. Paris 06, CNRS, UMR 7144, Station Biologique, Place Georges Teissier, 29680 Roscoff, France
| | | | - Nathalie Simon
- Sorbonne Universités, UPMC Univ. Paris 06, CNRS, UMR 7144, Station Biologique, Place Georges Teissier, 29680 Roscoff, France
| | | | - Sébastien Santini
- CNRS, Aix-Marseille Université, IGS UMR7256, F-13288 Marseille, France
| | - Diana Sarno
- Stazione Zoologica Anton Dohrn, Villa Comunale 1, I-80121, Naples, Italy
| | - Raffaele Siano
- Ifremer, Centre de Brest DYNECO/Pelagos Technopôle Brest Iroise, BP 7029280 Plouzané, France
| | - Daniel Vaulot
- Sorbonne Universités, UPMC Univ. Paris 06, CNRS, UMR 7144, Station Biologique, Place Georges Teissier, 29680 Roscoff, France
| | | | - Adriana Zingone
- Stazione Zoologica Anton Dohrn, Villa Comunale 1, I-80121, Naples, Italy
| | - Colomban de Vargas
- Sorbonne Universités, UPMC Univ. Paris 06, CNRS, UMR 7144, Station Biologique, Place Georges Teissier, 29680 Roscoff, France
| | - Thorsten Stoeck
- Department of Ecology, University of Kaiserslautern, Erwin-Schrödinger Str. 14, D-67663 Kaiserslautern, Germany
| |
Collapse
|
22
|
Endo H, Sugie K, Yoshimura T, Suzuki K. Response of Spring Diatoms to CO2 Availability in the Western North Pacific as Determined by Next-Generation Sequencing. PLoS One 2016; 11:e0154291. [PMID: 27124280 PMCID: PMC4849754 DOI: 10.1371/journal.pone.0154291] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 04/12/2016] [Indexed: 11/18/2022] Open
Abstract
Next-generation sequencing (NGS) technologies have enabled us to determine phytoplankton community compositions at high resolution. However, few studies have adopted this approach to assess the responses of natural phytoplankton communities to environmental change. Here, we report the impact of different CO2 levels on spring diatoms in the Oyashio region of the western North Pacific as estimated by NGS of the diatom-specific rbcL gene (DNA), which encodes the large subunit of RubisCO. We also examined the abundance and composition of rbcL transcripts (cDNA) in diatoms to assess their physiological responses to changing CO2 levels. A short-term (3-day) incubation experiment was carried out on-deck using surface Oyashio waters under different pCO2 levels (180, 350, 750, and 1000 μatm) in May 2011. During the incubation, the transcript abundance of the diatom-specific rbcL gene decreased with an increase in seawater pCO2 levels. These results suggest that CO2 fixation capacity of diatoms decreased rapidly under elevated CO2 levels. In the high CO2 treatments (750 and 1000 μatm), diversity of diatom-specific rbcL gene and its transcripts decreased relative to the control treatment (350 μatm), as well as contributions of Chaetocerataceae, Thalassiosiraceae, and Fragilariaceae to the total population, but the contributions of Bacillariaceae increased. In the low CO2 treatment, contributions of Bacillariaceae also increased together with other eukaryotes. These suggest that changes in CO2 levels can alter the community composition of spring diatoms in the Oyashio region. Overall, the NGS technology provided us a deeper understanding of the response of diatoms to changes in CO2 levels in terms of their community composition, diversity, and photosynthetic physiology.
Collapse
Affiliation(s)
- Hisashi Endo
- Faculty of Environmental Earth Science/Graduate School of Environmental Science, Hokkaido University, Sapporo, Hokkaido, Japan.,CREST, Japan Science and Technology, Sapporo, Hokkaido, Japan
| | - Koji Sugie
- Central Research Institute of Electric Power Industry, Abiko, Chiba, Japan.,Research and Development Center for Global Change, Japan Agency for Marine Earth-Science and Technology (JAMSTEC), Yokosuka, Kanagawa, Japan
| | - Takeshi Yoshimura
- Central Research Institute of Electric Power Industry, Abiko, Chiba, Japan
| | - Koji Suzuki
- Faculty of Environmental Earth Science/Graduate School of Environmental Science, Hokkaido University, Sapporo, Hokkaido, Japan.,CREST, Japan Science and Technology, Sapporo, Hokkaido, Japan
| |
Collapse
|
23
|
Insights into global diatom distribution and diversity in the world's ocean. Proc Natl Acad Sci U S A 2016; 113:E1516-25. [PMID: 26929361 DOI: 10.1073/pnas.1509523113] [Citation(s) in RCA: 298] [Impact Index Per Article: 37.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Diatoms (Bacillariophyta) constitute one of the most diverse and ecologically important groups of phytoplankton. They are considered to be particularly important in nutrient-rich coastal ecosystems and at high latitudes, but considerably less so in the oligotrophic open ocean. The Tara Oceans circumnavigation collected samples from a wide range of oceanic regions using a standardized sampling procedure. Here, a total of ∼12 million diatom V9-18S ribosomal DNA (rDNA) ribotypes, derived from 293 size-fractionated plankton communities collected at 46 sampling sites across the global ocean euphotic zone, have been analyzed to explore diatom global diversity and community composition. We provide a new estimate of diversity of marine planktonic diatoms at 4,748 operational taxonomic units (OTUs). Based on the total assigned ribotypes, Chaetoceros was the most abundant and diverse genus, followed by Fragilariopsis, Thalassiosira, and Corethron We found only a few cosmopolitan ribotypes displaying an even distribution across stations and high abundance, many of which could not be assigned with confidence to any known genus. Three distinct communities from South Pacific, Mediterranean, and Southern Ocean waters were identified that share a substantial percentage of ribotypes within them. Sudden drops in diversity were observed at Cape Agulhas, which separates the Indian and Atlantic Oceans, and across the Drake Passage between the Atlantic and Southern Oceans, indicating the importance of these ocean circulation choke points in constraining diatom distribution and diversity. We also observed high diatom diversity in the open ocean, suggesting that diatoms may be more relevant in these oceanic systems than generally considered.
Collapse
|
24
|
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.
Collapse
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
| |
Collapse
|
25
|
Hovde BT, Deodato CR, Hunsperger HM, Ryken SA, Yost W, Jha RK, Patterson J, Monnat RJ, Barlow SB, Starkenburg SR, Cattolico RA. Genome Sequence and Transcriptome Analyses of Chrysochromulina tobin: Metabolic Tools for Enhanced Algal Fitness in the Prominent Order Prymnesiales (Haptophyceae). PLoS Genet 2015; 11:e1005469. [PMID: 26397803 PMCID: PMC4580454 DOI: 10.1371/journal.pgen.1005469] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Accepted: 07/27/2015] [Indexed: 12/11/2022] Open
Abstract
Haptophytes are recognized as seminal players in aquatic ecosystem function. These algae are important in global carbon sequestration, form destructive harmful blooms, and given their rich fatty acid content, serve as a highly nutritive food source to a broad range of eco-cohorts. Haptophyte dominance in both fresh and marine waters is supported by the mixotrophic nature of many taxa. Despite their importance the nuclear genome sequence of only one haptophyte, Emiliania huxleyi (Isochrysidales), is available. Here we report the draft genome sequence of Chrysochromulina tobin (Prymnesiales), and transcriptome data collected at seven time points over a 24-hour light/dark cycle. The nuclear genome of C. tobin is small (59 Mb), compact (∼40% of the genome is protein coding) and encodes approximately 16,777 genes. Genes important to fatty acid synthesis, modification, and catabolism show distinct patterns of expression when monitored over the circadian photoperiod. The C. tobin genome harbors the first hybrid polyketide synthase/non-ribosomal peptide synthase gene complex reported for an algal species, and encodes potential anti-microbial peptides and proteins involved in multidrug and toxic compound extrusion. A new haptophyte xanthorhodopsin was also identified, together with two “red” RuBisCO activases that are shared across many algal lineages. The Chrysochromulina tobin genome sequence provides new information on the evolutionary history, ecology and economic importance of haptophytes. Microalgae are important contributors to global ecological balance, and process nearly half of the world’s carbon each year. Additionally, these organisms are deeply rooted in the earths’ evolutionary history. To better understand why algae are such strong survivors in aquatic environments and to better understand their contribution to global ecology, we sequenced the genome of a microalga that is abundant in both fresh and salt water environments, but poorly represented by current genomic information. We identify protein-coding genes responsible for the synthesis of potential toxins as well as those that produce antibiotics, and describe gene products that enhanced the ability of the alga to use light energy. We observed that a day-night cycle, similar to that found in natural environments, significantly impacts the expression of algal genes whose products are responsible for synthesizing fats—a rich source of nutrition for many other organisms.
Collapse
Affiliation(s)
- Blake T. Hovde
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
- * E-mail: (BTH); (RAC)
| | - Chloe R. Deodato
- Department of Biology, University of Washington, Seattle, Washington, United States of America
| | - Heather M. Hunsperger
- Department of Biology, University of Washington, Seattle, Washington, United States of America
| | - Scott A. Ryken
- Department of Biology, University of Washington, Seattle, Washington, United States of America
| | - Will Yost
- Department of Biology, University of Washington, Seattle, Washington, United States of America
| | - Ramesh K. Jha
- Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Johnathan Patterson
- Department of Biology, University of Washington, Seattle, Washington, United States of America
| | - Raymond J. Monnat
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
- University of Washington, Department of Pathology, Seattle, Washington, United States of America
| | - Steven B. Barlow
- Electron Microscope Facility, San Diego State University, San Diego, California, United States of America
| | - Shawn R. Starkenburg
- Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Rose Ann Cattolico
- Department of Biology, University of Washington, Seattle, Washington, United States of America
- * E-mail: (BTH); (RAC)
| |
Collapse
|
26
|
Gimmler A, Stoeck T. Mining environmental high-throughput sequence data sets to identify divergent amplicon clusters for phylogenetic reconstruction and morphotype visualization. ENVIRONMENTAL MICROBIOLOGY REPORTS 2015; 7:679-686. [PMID: 26061246 DOI: 10.1111/1758-2229.12307] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2015] [Accepted: 06/03/2015] [Indexed: 06/04/2023]
Abstract
Environmental high-throughput sequencing (envHTS) is a very powerful tool, which in protistan ecology is predominantly used for the exploration of diversity and its geographic and local patterns. We here used a pyrosequenced V4-SSU rDNA data set from a solar saltern pond as test case to exploit such massive protistan amplicon data sets beyond this descriptive purpose. Therefore, we combined a Swarm-based blastn network including 11 579 ciliate V4 amplicons to identify divergent amplicon clusters with targeted polymerase chain reaction (PCR) primer design for full-length small subunit of the ribosomal DNA retrieval and probe design for fluorescence in situ hybridization (FISH). This powerful strategy allows to benefit from envHTS data sets to (i) reveal the phylogenetic position of the taxon behind divergent amplicons; (ii) improve phylogenetic resolution and evolutionary history of specific taxon groups; (iii) solidly assess an amplicons (species') degree of similarity to its closest described relative; (iv) visualize the morphotype behind a divergent amplicons cluster; (v) rapidly FISH screen many environmental samples for geographic/habitat distribution and abundances of the respective organism and (vi) to monitor the success of enrichment strategies in live samples for cultivation and isolation of the respective organisms.
Collapse
Affiliation(s)
- Anna Gimmler
- Department of Ecology, University of Kaiserslautern, Erwin-Schrödinger-Straße 14, Kaiserslautern, D-67633, Germany
| | - Thorsten Stoeck
- Department of Ecology, University of Kaiserslautern, Erwin-Schrödinger-Straße 14, Kaiserslautern, D-67633, Germany
| |
Collapse
|
27
|
Egge ES, Johannessen TV, Andersen T, Eikrem W, Bittner L, Larsen A, Sandaa RA, Edvardsen B. Seasonal diversity and dynamics of haptophytes in the Skagerrak, Norway, explored by high-throughput sequencing. Mol Ecol 2015; 24:3026-42. [PMID: 25893259 PMCID: PMC4692090 DOI: 10.1111/mec.13160] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2014] [Revised: 02/06/2015] [Accepted: 02/13/2015] [Indexed: 11/28/2022]
Abstract
Microalgae in the division Haptophyta play key roles in the marine ecosystem and in global biogeochemical processes. Despite their ecological importance, knowledge on seasonal dynamics, community composition and abundance at the species level is limited due to their small cell size and few morphological features visible under the light microscope. Here, we present unique data on haptophyte seasonal diversity and dynamics from two annual cycles, with the taxonomic resolution and sampling depth obtained with high-throughput sequencing. From outer Oslofjorden, S Norway, nano- and picoplanktonic samples were collected monthly for 2 years, and the haptophytes targeted by amplification of RNA/cDNA with Haptophyta-specific 18S rDNA V4 primers. We obtained 156 operational taxonomic units (OTUs), from c. 400.000 454 pyrosequencing reads, after rigorous bioinformatic filtering and clustering at 99.5%. Most OTUs represented uncultured and/or not yet 18S rDNA-sequenced species. Haptophyte OTU richness and community composition exhibited high temporal variation and significant yearly periodicity. Richness was highest in September–October (autumn) and lowest in April–May (spring). Some taxa were detected all year, such as Chrysochromulina simplex, Emiliania huxleyi and Phaeocystis cordata, whereas most calcifying coccolithophores only appeared from summer to early winter. We also revealed the seasonal dynamics of OTUs representing putative novel classes (clades HAP-3–5) or orders (clades D, E, F). Season, light and temperature accounted for 29% of the variation in OTU composition. Residual variation may be related to biotic factors, such as competition and viral infection. This study provides new, in-depth knowledge on seasonal diversity and dynamics of haptophytes in North Atlantic coastal waters.
Collapse
Affiliation(s)
| | - Torill Vik Johannessen
- Marine Microbiology, Department of Biology, University of Bergen, PO Box 7803, 5006, Bergen, Norway
| | - Tom Andersen
- Department of Biosciences, University of Oslo, PO Box 1066, 0316, Oslo, Norway
| | - Wenche Eikrem
- Department of Biosciences, University of Oslo, PO Box 1066, 0316, Oslo, Norway.,Norwegian Institute for Water Research, Gaustadalléen 21, 0349, Oslo, Norway
| | - Lucie Bittner
- CNRS FR3631, Institut de Biologie Paris-Seine, F-75005, Paris, France.,Sorbonne Universités, UPMC Univ Paris 06, Institut de Biologie Paris-Seine (IBPS), F-75005, Paris, France
| | - Aud Larsen
- Uni Research Environment, Thormøhlensgate 49b, N-5006, Bergen, Norway.,Hjort Centre for Marine Ecosystem Dynamics, N-5006, Bergen, Norway
| | - Ruth-Anne Sandaa
- Marine Microbiology, Department of Biology, University of Bergen, PO Box 7803, 5006, Bergen, Norway
| | - Bente Edvardsen
- Department of Biosciences, University of Oslo, PO Box 1066, 0316, Oslo, Norway
| |
Collapse
|
28
|
Decelle J, Romac S, Stern RF, Bendif EM, Zingone A, Audic S, Guiry MD, Guillou L, Tessier D, Le Gall F, Gourvil P, Dos Santos AL, Probert I, Vaulot D, de Vargas C, Christen R. PhytoREF: a reference database of the plastidial 16S rRNA gene of photosynthetic eukaryotes with curated taxonomy. Mol Ecol Resour 2015; 15:1435-45. [PMID: 25740460 DOI: 10.1111/1755-0998.12401] [Citation(s) in RCA: 102] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Revised: 02/20/2015] [Accepted: 03/02/2015] [Indexed: 11/30/2022]
Abstract
Photosynthetic eukaryotes have a critical role as the main producers in most ecosystems of the biosphere. The ongoing environmental metabarcoding revolution opens the perspective for holistic ecosystems biological studies of these organisms, in particular the unicellular microalgae that often lack distinctive morphological characters and have complex life cycles. To interpret environmental sequences, metabarcoding necessarily relies on taxonomically curated databases containing reference sequences of the targeted gene (or barcode) from identified organisms. To date, no such reference framework exists for photosynthetic eukaryotes. In this study, we built the PhytoREF database that contains 6490 plastidial 16S rDNA reference sequences that originate from a large diversity of eukaryotes representing all known major photosynthetic lineages. We compiled 3333 amplicon sequences available from public databases and 879 sequences extracted from plastidial genomes, and generated 411 novel sequences from cultured marine microalgal strains belonging to different eukaryotic lineages. A total of 1867 environmental Sanger 16S rDNA sequences were also included in the database. Stringent quality filtering and a phylogeny-based taxonomic classification were applied for each 16S rDNA sequence. The database mainly focuses on marine microalgae, but sequences from land plants (representing half of the PhytoREF sequences) and freshwater taxa were also included to broaden the applicability of PhytoREF to different aquatic and terrestrial habitats. PhytoREF, accessible via a web interface (http://phytoref.fr), is a new resource in molecular ecology to foster the discovery, assessment and monitoring of the diversity of photosynthetic eukaryotes using high-throughput sequencing.
Collapse
Affiliation(s)
- Johan Decelle
- UMR 7144 - Sorbonne Universités, UPMC Univ Paris 06, Station Biologique de Roscoff, Roscoff, 29680, France.,CNRS, UMR 7144, Station Biologique de Roscoff, Roscoff, 29680, France
| | - Sarah Romac
- UMR 7144 - Sorbonne Universités, UPMC Univ Paris 06, Station Biologique de Roscoff, Roscoff, 29680, France.,CNRS, UMR 7144, Station Biologique de Roscoff, Roscoff, 29680, France
| | - Rowena F Stern
- Sir Alister Hardy Foundation for Ocean Science, The Laboratory, Citadel Hill, Plymouth, PL1 2PB, UK
| | - El Mahdi Bendif
- Marine Biological Association, The Laboratory, Citadel Hill, Plymouth, PL1 2PB, UK
| | - Adriana Zingone
- Stazione Zoologica Anton Dohrn, Villa Comunale, Naples, 80121, Italy
| | - Stéphane Audic
- UMR 7144 - Sorbonne Universités, UPMC Univ Paris 06, Station Biologique de Roscoff, Roscoff, 29680, France.,CNRS, UMR 7144, Station Biologique de Roscoff, Roscoff, 29680, France
| | - Michael D Guiry
- The AlgaeBase Foundation, c/o Ryan Institute, National University of Ireland, University Road, Galway, Ireland
| | - Laure Guillou
- UMR 7144 - Sorbonne Universités, UPMC Univ Paris 06, Station Biologique de Roscoff, Roscoff, 29680, France.,CNRS, UMR 7144, Station Biologique de Roscoff, Roscoff, 29680, France
| | - Désiré Tessier
- CNRS, UMR 7138, Systématique Adaptation Evolution, Parc Valrose, BP71, Nice, F06108, France.,Université de Nice-Sophia Antipolis, UMR 7138, Systématique Adaptation Evolution, Parc Valrose, BP71, Nice, F06108, France
| | - Florence Le Gall
- UMR 7144 - Sorbonne Universités, UPMC Univ Paris 06, Station Biologique de Roscoff, Roscoff, 29680, France.,CNRS, UMR 7144, Station Biologique de Roscoff, Roscoff, 29680, France
| | - Priscillia Gourvil
- UMR 7144 - Sorbonne Universités, UPMC Univ Paris 06, Station Biologique de Roscoff, Roscoff, 29680, France.,CNRS, UMR 7144, Station Biologique de Roscoff, Roscoff, 29680, France
| | - Adriana L Dos Santos
- UMR 7144 - Sorbonne Universités, UPMC Univ Paris 06, Station Biologique de Roscoff, Roscoff, 29680, France.,CNRS, UMR 7144, Station Biologique de Roscoff, Roscoff, 29680, France
| | - Ian Probert
- UMR 7144 - Sorbonne Universités, UPMC Univ Paris 06, Station Biologique de Roscoff, Roscoff, 29680, France.,CNRS, UMR 7144, Station Biologique de Roscoff, Roscoff, 29680, France
| | - Daniel Vaulot
- UMR 7144 - Sorbonne Universités, UPMC Univ Paris 06, Station Biologique de Roscoff, Roscoff, 29680, France.,CNRS, UMR 7144, Station Biologique de Roscoff, Roscoff, 29680, France
| | - Colomban de Vargas
- UMR 7144 - Sorbonne Universités, UPMC Univ Paris 06, Station Biologique de Roscoff, Roscoff, 29680, France.,CNRS, UMR 7144, Station Biologique de Roscoff, Roscoff, 29680, France
| | - Richard Christen
- CNRS, UMR 7138, Systématique Adaptation Evolution, Parc Valrose, BP71, Nice, F06108, France.,Université de Nice-Sophia Antipolis, UMR 7138, Systématique Adaptation Evolution, Parc Valrose, BP71, Nice, F06108, France
| |
Collapse
|
29
|
Forster D, Bittner L, Karkar S, Dunthorn M, Romac S, Audic S, Lopez P, Stoeck T, Bapteste E. Testing ecological theories with sequence similarity networks: marine ciliates exhibit similar geographic dispersal patterns as multicellular organisms. BMC Biol 2015; 13:16. [PMID: 25762112 PMCID: PMC4381497 DOI: 10.1186/s12915-015-0125-5] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Accepted: 01/28/2015] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND High-throughput sequencing technologies are lifting major limitations to molecular-based ecological studies of eukaryotic microbial diversity, but analyses of the resulting millions of short sequences remain a major bottleneck for these approaches. Here, we introduce the analytical and statistical framework of sequence similarity networks, increasingly used in evolutionary studies and graph theory, into the field of ecology to analyze novel pyrosequenced V4 small subunit rDNA (SSU-rDNA) sequence data sets in the context of previous studies, including SSU-rDNA Sanger sequence data from cultured ciliates and from previous environmental diversity inventories. RESULTS Our broadly applicable protocol quantified the progress in the description of genetic diversity of ciliates by environmental SSU-rDNA surveys, detected a fundamental historical bias in the tendency to recover already known groups in these surveys, and revealed substantial amounts of hidden microbial diversity. Moreover, network measures demonstrated that ciliates are not globally dispersed, but are structured by habitat and geographical location at intermediate geographical scale, as observed for bacteria, plants, and animals. CONCLUSIONS Currently available 'universal' primers used for local in-depth sequencing surveys provide little hope to exhaust the significantly higher ciliate (and most likely microbial) diversity than previously thought. Network analyses such as presented in this study offer a promising way to guide the design of novel primers and to further explore this vast and structured microbial diversity.
Collapse
Affiliation(s)
- Dominik Forster
- Department of Ecology, University of Kaiserslautern, Erwin-Schrödinger-Straße 14, Kaiserslautern, D-67633, Germany.
| | - Lucie Bittner
- Department of Ecology, University of Kaiserslautern, Erwin-Schrödinger-Straße 14, Kaiserslautern, D-67633, Germany.
- CNRS, FR3631, Institut de Biologie Paris-Seine, Paris, F-75005, France.
- Sorbonne Universités, UPMC Univ Paris 06, Institut de Biologie Paris-Seine (IBPS), Paris, F-75005, France.
| | - Slim Karkar
- Sorbonne Universités, UPMC Univ Paris 06, Institut de Biologie Paris-Seine (IBPS), Paris, F-75005, France.
- CNRS, UMR7138, Institut de Biologie Paris-Seine, Paris, F-75005, France.
| | - Micah Dunthorn
- Department of Ecology, University of Kaiserslautern, Erwin-Schrödinger-Straße 14, Kaiserslautern, D-67633, Germany.
| | - Sarah Romac
- CNRS, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, Roscoff, F-29680, France.
- Sorbonne Universités, UPMC Univ Paris 06, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, Roscoff, F-29680, France.
| | - Stéphane Audic
- CNRS, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, Roscoff, F-29680, France.
- Sorbonne Universités, UPMC Univ Paris 06, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, Roscoff, F-29680, France.
| | - Philippe Lopez
- Sorbonne Universités, UPMC Univ Paris 06, Institut de Biologie Paris-Seine (IBPS), Paris, F-75005, France.
- CNRS, UMR7138, Institut de Biologie Paris-Seine, Paris, F-75005, France.
| | - Thorsten Stoeck
- Department of Ecology, University of Kaiserslautern, Erwin-Schrödinger-Straße 14, Kaiserslautern, D-67633, Germany.
| | - Eric Bapteste
- Sorbonne Universités, UPMC Univ Paris 06, Institut de Biologie Paris-Seine (IBPS), Paris, F-75005, France.
- CNRS, UMR7138, Institut de Biologie Paris-Seine, Paris, F-75005, France.
| |
Collapse
|
30
|
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.
Collapse
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
| |
Collapse
|
31
|
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.
Collapse
Affiliation(s)
- Frédéric Mahé
- Department of Ecology, University of Kaiserslautern, D-67663, Kaiserslautern, Germany
| | | | | | | | | | | | | | | | | | | |
Collapse
|
32
|
Mahé F, Rognes T, Quince C, de Vargas C, Dunthorn M. Swarm: robust and fast clustering method for amplicon-based studies. PeerJ 2014; 2:e593. [PMID: 25276506 PMCID: PMC4178461 DOI: 10.7717/peerj.593] [Citation(s) in RCA: 491] [Impact Index Per Article: 49.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Accepted: 09/03/2014] [Indexed: 11/20/2022] Open
Abstract
Popular de novo amplicon clustering methods suffer from two fundamental flaws: arbitrary global clustering thresholds, and input-order dependency induced by centroid selection. Swarm was developed to address these issues by first clustering nearly identical amplicons iteratively using a local threshold, and then by using clusters' internal structure and amplicon abundances to refine its results. This fast, scalable, and input-order independent approach reduces the influence of clustering parameters and produces robust operational taxonomic units.
Collapse
Affiliation(s)
- Frédéric Mahé
- CNRS, UMR 7144, EPEP - Évolution des Protistes et des Écosystèmes Pélagiques, Station Biologique de Roscoff , Roscoff , France ; Sorbonne Universités, UPMC Univ Paris 06, UMR 7144, Station Biologique de Roscoff , Roscoff , France ; Department of Ecology, University of Kaiserslautern , Kaiserslautern , Germany
| | - Torbjørn Rognes
- Department of Microbiology, Oslo University Hospital, Rikshospitalet , Oslo , Norway ; Department of Informatics, University of Oslo , Oslo , Norway
| | | | - Colomban de Vargas
- CNRS, UMR 7144, EPEP - Évolution des Protistes et des Écosystèmes Pélagiques, Station Biologique de Roscoff , Roscoff , France ; Sorbonne Universités, UPMC Univ Paris 06, UMR 7144, Station Biologique de Roscoff , Roscoff , France
| | - Micah Dunthorn
- Department of Ecology, University of Kaiserslautern , Kaiserslautern , Germany
| |
Collapse
|
33
|
Egge ES, Eikrem W, Edvardsen B. Deep-branching novel lineages and high diversity of haptophytes in the Skagerrak (Norway) uncovered by 454 pyrosequencing. J Eukaryot Microbiol 2014; 62:121-40. [PMID: 25099994 PMCID: PMC4344818 DOI: 10.1111/jeu.12157] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Revised: 06/04/2014] [Accepted: 06/06/2014] [Indexed: 01/14/2023]
Abstract
Microalgae in the division Haptophyta may be difficult to identify to species by microscopy because they are small and fragile. Here, we used high-throughput sequencing to explore the diversity of haptophytes in outer Oslofjorden, Skagerrak, and supplemented this with electron microscopy. Nano- and picoplanktonic subsurface samples were collected monthly for 2 yr, and the haptophytes were targeted by amplification of RNA/cDNA with Haptophyta-specific 18S ribosomal DNA V4 primers. Pyrosequencing revealed higher species richness of haptophytes than previously observed in the Skagerrak by microscopy. From ca. 400,000 reads we obtained 156 haptophyte operational taxonomic units (OTUs) after rigorous filtering and 99.5% clustering. The majority (84%) of the OTUs matched environmental sequences not linked to a morphological species, most of which were affiliated with the order Prymnesiales. Phylogenetic analyses including Oslofjorden OTUs and available cultured and environmental haptophyte sequences showed that several of the OTUs matched sequences forming deep-branching lineages, potentially representing novel haptophyte classes. Pyrosequencing also retrieved cultured species not previously reported by microscopy in the Skagerrak. Electron microscopy revealed species not yet genetically characterised and some potentially novel taxa. This study contributes to linking genotype to phenotype within this ubiquitous and ecologically important protist group, and reveals great, unknown diversity.
Collapse
Affiliation(s)
- Elianne S Egge
- Department of Biosciences, University of Oslo, P.O. Box 1066 Blindern, 0316, Oslo, Norway
| | | | | |
Collapse
|
34
|
Nanjappa D, Audic S, Romac S, Kooistra WHCF, Zingone A. Assessment of species diversity and distribution of an ancient diatom lineage using a DNA metabarcoding approach. PLoS One 2014; 9:e103810. [PMID: 25133638 PMCID: PMC4136930 DOI: 10.1371/journal.pone.0103810] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2014] [Accepted: 07/04/2014] [Indexed: 11/30/2022] Open
Abstract
Background Continuous efforts to estimate actual diversity and to trace the species distribution and ranges in the natural environments have gone in equal pace with advancements of the technologies in the study of microbial species diversity from microscopic observations to DNA-based barcoding. DNA metabarcoding based on Next Generation Sequencing (NGS) constitutes the latest advancement in these efforts. Here we use NGS data from different sites to investigate the geographic range of six species of the diatom family Leptocylindraceae and to identify possible new taxa within the family. Methodology/Principal Findings We analysed the V4 and V9 regions of the nuclear-encoded SSU rDNA gene region in the NGS database of the European ERA-Biodiversa project BioMarKs, collected in plankton and sediments at six coastal sites in European coastal waters, as well as environmental sequences from the NCBI database. All species known in the family Leptocylindraceae were detected in both datasets, but the much larger Illumina V9 dataset showed a higher species coverage at the various sites than the 454 V4 dataset. Sequences identical or similar to the references of Leptocylindrus aporus, L. convexus, L. danicus/hargravesii and Tenuicylindrus belgicus were found in the Mediterranean Sea, North Atlantic Ocean and Black Sea as well as at locations outside Europe. Instead, sequences identical or close to that of L. minimus were found in the North Atlantic Ocean and the Black Sea but not in the Mediterranean Sea, while sequences belonging to a yet undescribed taxon were encountered only in Oslo Fjord and Baffin Bay. Conclusions/Significance Identification of Leptocylindraceae species in NGS datasets has expanded our knowledge of the species biogeographic distribution and of the overall diversity of this diatom family. Individual species appear to be widespread, but not all of them are found everywhere. Despite the sequencing depth allowed by NGS and the wide geographic area covered by this study, the diversity of this ancient diatom family appears to be low, at least at the level of the marker used in this study.
Collapse
Affiliation(s)
- Deepak Nanjappa
- Stazione Zoologica Anton Dohrn, Naples, Italy
- * E-mail: (DN); (AZ)
| | - Stephane Audic
- CNRS, UMR EPEP – Évolution des Protistes et des Écosystèmes Pélagiques, UPMC Sorbonne Universités, Station Biologique de Roscoff, Roscoff, France
| | - Sarah Romac
- CNRS, UMR EPEP – Évolution des Protistes et des Écosystèmes Pélagiques, UPMC Sorbonne Universités, Station Biologique de Roscoff, Roscoff, France
| | | | - Adriana Zingone
- Stazione Zoologica Anton Dohrn, Naples, Italy
- * E-mail: (DN); (AZ)
| |
Collapse
|
35
|
Hovde BT, Starkenburg SR, Hunsperger HM, Mercer LD, Deodato CR, Jha RK, Chertkov O, Monnat RJ, Cattolico RA. The mitochondrial and chloroplast genomes of the haptophyte Chrysochromulina tobin contain unique repeat structures and gene profiles. BMC Genomics 2014; 15:604. [PMID: 25034814 PMCID: PMC4226036 DOI: 10.1186/1471-2164-15-604] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Accepted: 07/09/2014] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Haptophytes are widely and abundantly distributed in both marine and freshwater ecosystems. Few genomic analyses of representatives within this taxon have been reported, despite their early evolutionary origins and their prominent role in global carbon fixation. RESULTS The complete mitochondrial and chloroplast genome sequences of the haptophyte Chrysochromulina tobin (Prymnesiales) provide insight into the architecture and gene content of haptophyte organellar genomes. The mitochondrial genome (~34 kb) encodes 21 protein coding genes and contains a complex, 9 kb tandem repeat region. Similar to other haptophytes and rhodophytes, but not cryptophytes or stramenopiles, the mitochondrial genome has lost the nad7, nad9 and nad11 genes. The ~105 kb chloroplast genome encodes 112 protein coding genes, including ycf39 which has strong structural homology to NADP-binding nitrate transcriptional regulators; a divergent 'CheY-like' two-component response regulator (ycf55) and Tic/Toc (ycf60 and ycf80) membrane transporters. Notably, a zinc finger domain has been identified in the rpl36 ribosomal protein gene of all chloroplasts sequenced to date with the exception of haptophytes and cryptophytes--algae that have gained (via lateral gene transfer) an alternative rpl36 lacking the zinc finger motif. The two C. tobin chloroplast ribosomal RNA operon spacer regions differ in tRNA content. Additionally, each ribosomal operon contains multiple single nucleotide polymorphisms (SNPs)--a pattern observed in rhodophytes and cryptophytes, but few stramenopiles. Analysis of small (<200 bp) chloroplast encoded tandem and inverted repeats in C. tobin and 78 other algal chloroplast genomes show that repeat type, size and location are correlated with gene identity and taxonomic clade. CONCLUSION The Chrysochromulina tobin organellar genomes provide new insight into organellar function and evolution. These are the first organellar genomes to be determined for the prymnesiales, a taxon that is present in both oceanic and freshwater systems and represents major primary photosynthetic producers and contributors to global ecosystem stability.
Collapse
|
36
|
Hirai J, Kuriyama M, Ichikawa T, Hidaka K, Tsuda A. A metagenetic approach for revealing community structure of marine planktonic copepods. Mol Ecol Resour 2014; 15:68-80. [DOI: 10.1111/1755-0998.12294] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2013] [Revised: 06/07/2014] [Accepted: 06/09/2014] [Indexed: 11/30/2022]
Affiliation(s)
- J. Hirai
- National Research Institute of Fisheries Science; Fisheries Research Agency; 2-12-4 Fukuura Kanazawa Yokohama Kanagawa 236-8648 Japan
| | - M. Kuriyama
- National Research Institute of Fisheries Science; Fisheries Research Agency; 2-12-4 Fukuura Kanazawa Yokohama Kanagawa 236-8648 Japan
| | - T. Ichikawa
- National Research Institute of Fisheries Science; Fisheries Research Agency; 2-12-4 Fukuura Kanazawa Yokohama Kanagawa 236-8648 Japan
| | - K. Hidaka
- National Research Institute of Fisheries Science; Fisheries Research Agency; 2-12-4 Fukuura Kanazawa Yokohama Kanagawa 236-8648 Japan
| | - A. Tsuda
- Atmosphere and Ocean Research Institution; The University of Tokyo; 5-1-5 Kashiwanoha Kashiwa Chiba 277-8564 Japan
| |
Collapse
|
37
|
Dunthorn M, Stoeck T, Clamp J, Warren A, Mahé F. Ciliates and the Rare Biosphere: A Review. J Eukaryot Microbiol 2014; 61:404-9. [DOI: 10.1111/jeu.12121] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2014] [Revised: 03/14/2014] [Accepted: 03/14/2014] [Indexed: 11/27/2022]
Affiliation(s)
- Micah Dunthorn
- Department of Ecology; University of Kaiserslautern; D-67663 Kaiserslautern Germany
| | - Thorsten Stoeck
- Department of Ecology; University of Kaiserslautern; D-67663 Kaiserslautern Germany
| | - John Clamp
- Department of Biology; North Carolina Central University; Durham North Carolina 27707 USA
| | - Alan Warren
- Department of Life Sciences Department; Natural History Museum; London SW7 5BD United Kingdom
| | - Frédéric Mahé
- Department of Ecology; University of Kaiserslautern; D-67663 Kaiserslautern Germany
| |
Collapse
|
38
|
Santoferrara LF, Grattepanche JD, Katz LA, McManus GB. Pyrosequencing for assessing diversity of eukaryotic microbes: analysis of data on marine planktonic ciliates and comparison with traditional methods. Environ Microbiol 2014; 16:2752-63. [PMID: 24444191 DOI: 10.1111/1462-2920.12380] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2013] [Revised: 12/18/2013] [Accepted: 12/31/2013] [Indexed: 11/29/2022]
Abstract
Assessing microbial diversity requires analysis of all three domains of life, including eukaryotic microbes. We examined the diversity of two ecologically important clades of microbial eukaryotes, ciliates in the subclasses Oligotrichia and Choreotrichia (class Spirotrichea), by comparing pyrosequencing to Sanger-sequenced clone libraries and microscopy. Using samples from a large temperate estuary (Long Island Sound, USA), we gained three major insights. First, richness estimates varied by up to one order of magnitude either using different criteria for pyrosequence processing or among pyrosequencing, cloning and microscopy, while taxon identification was almost always coherent. Error-correcting algorithms for pyrosequences ('denoising') reduced discrepancies in richness but also removed known morphospecies from the data. Second, although most of the pyrosequenced operational taxonomic units (OTUs) were distributed within known orders and families, we found evidence of a previously uncharacterized or unknown clade even in these ciliate lineages that have a rich history of morphological description. Third, pyrosequencing allowed the detection of OTUs that were either dominant or extremely rare in different samples. Our findings confirm the potential of pyrosequencing for quantifying microbial diversity, but also highlight the importance of careful evaluation of pyrosequence processing for using this method to address ecological questions.
Collapse
|
39
|
Massive difference in synonymous substitution rates among mitochondrial, plastid, and nuclear genes of Phaeocystis algae. Mol Phylogenet Evol 2014; 71:36-40. [DOI: 10.1016/j.ympev.2013.10.018] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2013] [Revised: 10/22/2013] [Accepted: 10/24/2013] [Indexed: 01/11/2023]
|
40
|
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.
Collapse
Affiliation(s)
- Micah Dunthorn
- Department of Ecology, University of Kaiserslautern, Kaiserslautern, Germany
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
41
|
Christaki U, Kormas KA, Genitsaris S, Georges C, Sime-Ngando T, Viscogliosi E, Monchy S. Winter-summer succession of unicellular eukaryotes in a meso-eutrophic coastal system. MICROBIAL ECOLOGY 2014; 67:13-23. [PMID: 24081282 DOI: 10.1007/s00248-013-0290-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2013] [Accepted: 09/03/2013] [Indexed: 06/02/2023]
Abstract
The objective of this study was to explore the succession of planktonic unicellular eukaryotes by means of 18S rRNA gene tag pyrosequencing in the eastern English Channel (EEC) during the winter to summer transition. The 59 most representative (>0.1%, representing altogether 95% of total reads), unique operational taxonomic units (OTUs) from all samples belonged to 18 known high-level taxonomic groups and 1 unaffiliated clade. The five most abundant OTUs (69.2% of total reads) belonged to Dinophyceae, Cercozoa, Haptophyceae, marine alveolate group I, and Fungi. Cluster and network analysis between samples distinguished the winter, the pre-bloom, the Phaeocystis globosa bloom and the post-bloom early summer conditions. The OTUs-based network revealed that P. globosa showed a relatively low number of connections-most of them negative-with all other OTUs. Fungi were linked to all major taxonomic groups, except Dinophyceae. Cercozoa mostly co-occurred with the Fungi, the Bacillariophyceae and several of the miscellaneous OTUs. This study provided a more detailed exploration into the planktonic succession pattern of the EEC due to its increased depth of taxonomic sampling over previous efforts based on classical monitoring observations. Data analysis implied that the food web concept in a coastal system based on predator-prey (e.g. grazer-phytoplankton) relationships is just a part of the ecological picture; and those organisms exploiting a variety of strategies, such as saprotrophy and parasitism, are persistent and abundant members of the community.
Collapse
Affiliation(s)
- Urania Christaki
- Laboratoire d'Océanologie et Géosciences (LOG), UMR CNRS 8187, Université du Littoral Côte d'Opale (ULCO), 32 av. Foch, 62930, Wimereux, France,
| | | | | | | | | | | | | |
Collapse
|
42
|
Egge E, Bittner L, Andersen T, Audic S, de Vargas C, Edvardsen B. 454 pyrosequencing to describe microbial eukaryotic community composition, diversity and relative abundance: a test for marine haptophytes. PLoS One 2013; 8:e74371. [PMID: 24069303 PMCID: PMC3771978 DOI: 10.1371/journal.pone.0074371] [Citation(s) in RCA: 103] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2013] [Accepted: 08/05/2013] [Indexed: 11/19/2022] Open
Abstract
Next generation sequencing of ribosomal DNA is increasingly used to assess the diversity and structure of microbial communities. Here we test the ability of 454 pyrosequencing to detect the number of species present, and assess the relative abundance in terms of cell numbers and biomass of protists in the phylum Haptophyta. We used a mock community consisting of equal number of cells of 11 haptophyte species and compared targeting DNA and RNA/cDNA, and two different V4 SSU rDNA haptophyte-biased primer pairs. Further, we tested four different bioinformatic filtering methods to reduce errors in the resulting sequence dataset. With sequencing depth of 11000–20000 reads and targeting cDNA with Haptophyta specific primers Hap454 we detected all 11 species. A rarefaction analysis of expected number of species recovered as a function of sampling depth suggested that minimum 1400 reads were required here to recover all species in the mock community. Relative read abundance did not correlate to relative cell numbers. Although the species represented with the largest biomass was also proportionally most abundant among the reads, there was generally a weak correlation between proportional read abundance and proportional biomass of the different species, both with DNA and cDNA as template. The 454 sequencing generated considerable spurious diversity, and more with cDNA than DNA as template. With initial filtering based only on match with barcode and primer we observed 100-fold more operational taxonomic units (OTUs) at 99% similarity than the number of species present in the mock community. Filtering based on quality scores, or denoising with PyroNoise resulted in ten times more OTU99% than the number of species. Denoising with AmpliconNoise reduced the number of OTU99% to match the number of species present in the mock community. Based on our analyses, we propose a strategy to more accurately depict haptophyte diversity using 454 pyrosequencing.
Collapse
Affiliation(s)
- Elianne Egge
- University of Oslo, Department of Biosciences, Marine Biology, Oslo, Norway
- * E-mail: (EE); (BE)
| | - Lucie Bittner
- CNRS UMR7144 & UPMC, Station Biologique de Roscoff, Roscoff, France
- University of Kaiserslautern, Department of Ecology, Kaiserslautern, Germany
| | - Tom Andersen
- University of Oslo, Department of Biosciences, Integrative Biology, Oslo, Norway
| | - Stéphane Audic
- CNRS UMR7144 & UPMC, Station Biologique de Roscoff, Roscoff, France
| | | | - Bente Edvardsen
- University of Oslo, Department of Biosciences, Marine Biology, Oslo, Norway
- * E-mail: (EE); (BE)
| |
Collapse
|
43
|
Stoeck T, Breiner HW, Filker S, Ostermaier V, Kammerlander B, Sonntag B. A morphogenetic survey on ciliate plankton from a mountain lake pinpoints the necessity of lineage-specific barcode markers in microbial ecology. Environ Microbiol 2013; 16:430-44. [PMID: 23848238 PMCID: PMC4208686 DOI: 10.1111/1462-2920.12194] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Revised: 06/11/2013] [Accepted: 06/11/2013] [Indexed: 02/03/2023]
Abstract
Analyses of high-throughput environmental sequencing data have become the 'gold-standard' to address fundamental questions of microbial diversity, ecology and biogeography. Findings that emerged from sequencing are, e.g. the discovery of the extensive 'rare microbial biosphere' and its potential function as a seed-bank. Even though applied since several years, results from high-throughput environmental sequencing have hardly been validated. We assessed how well pyrosequenced amplicons [the hypervariable eukaryotic V4 region of the small subunit ribosomal RNA (SSU rRNA) gene] reflected morphotype ciliate plankton. Moreover, we assessed if amplicon sequencing had the potential to detect the annual ciliate plankton stock. In both cases, we identified significant quantitative and qualitative differences. Our study makes evident that taxon abundance distributions inferred from amplicon data are highly biased and do not mirror actual morphotype abundances at all. Potential reasons included cell losses after fixation, cryptic morphotypes, resting stages, insufficient sequence data availability of morphologically described species and the unsatisfying resolution of the V4 SSU rRNA fragment for accurate taxonomic assignments. The latter two underline the necessity of barcoding initiatives for eukaryotic microbes to better and fully exploit environmental amplicon data sets, which then will also allow studying the potential of seed-bank taxa as a buffer for environmental changes.
Collapse
Affiliation(s)
- Thorsten Stoeck
- Department of Ecology, Faculty of Biology, University of Kaiserslautern, Kaiserslautern, Germany
| | | | | | | | | | | |
Collapse
|