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Ouyang H, Chen J, Lin L, Zheng H, Xie C, Wang C, Wang Z. Metabarcoding and co-occurrence network reveal significant effects of mariculture on benthic eukaryotic microalgal community: A case study in Daya Bay of the South China Sea. MARINE POLLUTION BULLETIN 2024; 207:116832. [PMID: 39128232 DOI: 10.1016/j.marpolbul.2024.116832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2024] [Revised: 07/19/2024] [Accepted: 08/06/2024] [Indexed: 08/13/2024]
Abstract
Benthic eukaryotic microalgae were analyzed by metabarcoding the partial 18S rRNA gene in Daya Bay bi-monthly in 2021. Altogether 941 eukaryotic microalgal OTUs were detected, belonging to 27 classes of 8 phyla. Dinophyta and Chlorophyta were the dominant phyla. Microalgal community in the mariculture zone differed significantly from those in non-mariculture zone, reflected by low alpha diversity indexes and increasing abundance and richness of chlorophytes and correspondingly decreasing of dinoflagellates. The abundant occurrences of the pico- and nano-sized taxa such as the chlorophyte Picochlorum in the mariculture zone suggested that nutrient enrichment might result in the miniaturization of the benthic eukaryotic microalgae. The co-occurrence network suggested more negative interactions between taxa in the mariculture zone. A total of 41 algal bloom and/or harmful algal bloom (HAB) species were detected in this study, suggesting a high potential risk of HABs in Daya Bay, especially for the recurrent bloom species Scrippsiella acuminata.
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Affiliation(s)
- Hong Ouyang
- College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Jiazhuo Chen
- College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Lanping Lin
- College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Hu Zheng
- College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Changliang Xie
- College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Chaofan Wang
- College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Zhaohui Wang
- College of Life Science and Technology, Jinan University, Guangzhou 510632, China.
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Stuart J, Ryan KG, Pearman JK, Thomson-Laing J, Hampton HG, Smith KF. A comparison of two gene regions for assessing community composition of eukaryotic marine microalgae from coastal ecosystems. Sci Rep 2024; 14:6442. [PMID: 38499675 PMCID: PMC10948787 DOI: 10.1038/s41598-024-56993-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 03/13/2024] [Indexed: 03/20/2024] Open
Abstract
Two gene regions commonly used to characterise the diversity of eukaryotic communities using metabarcoding are the 18S ribosomal DNA V4 and V9 gene regions. We assessed the effectiveness of these two regions for characterising diverisity of coastal eukaryotic microalgae communities (EMCs) from tropical and temperate sites. We binned amplicon sequence variants (ASVs) into the high level taxonomic groups: dinoflagellates, pennate diatoms, radial centric diatoms, polar centric diatoms, chlorophytes, haptophytes and 'other microalgae'. When V4 and V9 generated ASV abundances were compared, the V9 region generated a higher number of raw reads, captured more diversity from all high level taxonomic groups and was more closely aligned with the community composition determined using light microscopy. The V4 region did resolve more ASVs to a deeper taxonomic resolution within the dinoflagellates, but did not effectively resolve other major taxonomic divisions. When characterising these communities via metabarcoding, the use of multiple gene regions is recommended, but the V9 gene region can be used in isolation to provide high-level community biodiversity to reflect relative abundances within groups. This approach reduces the cost of sequencing multiple gene regions whilst still providing important baseline ecosystem function information.
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Affiliation(s)
- Jacqui Stuart
- School of Biological Sciences, Victoria University of Wellington, PO Box 600, Wellington, 6140, New Zealand.
- Cawthron Institute, Private Bag 2, Nelson, 7042, New Zealand.
| | - Ken G Ryan
- School of Biological Sciences, Victoria University of Wellington, PO Box 600, Wellington, 6140, New Zealand
| | - John K Pearman
- Cawthron Institute, Private Bag 2, Nelson, 7042, New Zealand
| | | | | | - Kirsty F Smith
- Cawthron Institute, Private Bag 2, Nelson, 7042, New Zealand
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Argyle PA, Rhodes LL, Smith KF, Harwood DT, Halafihi T, Marsden ID. Diversity and distribution of benthic dinoflagellates in Tonga include the potentially harmful genera Gambierdiscus and Fukuyoa. HARMFUL ALGAE 2023; 130:102524. [PMID: 38061817 DOI: 10.1016/j.hal.2023.102524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 10/01/2023] [Accepted: 10/07/2023] [Indexed: 12/18/2023]
Abstract
Benthic dinoflagellates that can cause illness, such as ciguatera poisoning (CP), are prevalent around the Pacific but are poorly described in many locations. This study represents the first ecological assessment of benthic harmful algae species in the Kingdom of Tonga, a country where CP occurs regularly. Surveys were conducted in June 2016 in the Tongatapu island group, and in June 2017 across three island groups: Ha'apai, Vava'u, and Tongatapu. Shallow subtidal coastal habitats were investigated by measuring water quality parameters and conducting quadrat surveys. Microalgae samples were collected using either macrophyte collection or the artificial substrate method. Benthic dinoflagellates (Gambierdiscus and/or Fukuyoa, Ostreopsis, and Prorocentrum) were counted using light microscopy, followed by molecular analyses (real-time PCR in 2016 and high throughput sequencing (metabarcoding) in 2017) to identify Gambierdiscus and Fukuyoa to species level. Six species were detected from the Tongatapu island group in 2016 (G. australes, G. carpenteri, G. honu, G. pacificus, F. paulensis, and F. ruetzleri) using real-time PCR. Using the metabarcoding approach in 2017, a total of eight species (G. australes, G. carpenteri, G. honu, G. pacificus, G. cheloniae, G. lewisii, G. polynesiensis, and F. yasumotoi) were detected. Species were detected in mixed assemblages of up to six species, with G. pacificus and G. carpenteri being the most frequently observed. Ha'apai had the highest diversity with eight species detected, which identifies this area as a Gambierdiscus diversity 'hotspot'. Vava'u and Tongatapu had three and six species found respectively. Gambierdiscus polynesiensis, a described ciguatoxin producer and proposed causative agent of CP was found only in Ha'apai and Vava'u in 2017, but not in Tongatapu in either year. Ostreopsis spp. and Prorocentrum spp. were also frequently observed, with Prorocentrum most abundant at the majority of sites. In 2016, the highest number of Gambierdiscus and/or Fukuyoa cells were observed on seagrass (Halodule uninervis) from Sopu, Tongatapu. In 2017, the highest numbers of Gambierdiscus and/or Fukuyoa from artificial substrate samples were recorded in the Halimeda dominant habitat at Neiafu Tahi, Vava'u, a low energy site. This raised the question of the effect of wave motion or currents on abundance measurements from artificial substrates. Differences in detection were noticed between macrophytes and artificial substrates, with higher numbers of species found on artificial substrates. This study provides a baseline of benthic dinoflagellate distributions and diversity for Tonga that may be used for future studies and the development of monitoring programmes.
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Affiliation(s)
- Phoebe A Argyle
- School of Biological Sciences, University of Canterbury, Private Bag 4800, 20 Kirkwood Ave, Christchurch 8041, New Zealand; Cawthron Institute, Private Bag 2, 98 Halifax St East, Nelson 7042, New Zealand; Ministry of Marine Resources, PO Box 85, Moss Rd, Avarua, Rarotonga, Cook Islands.
| | - Lesley L Rhodes
- Cawthron Institute, Private Bag 2, 98 Halifax St East, Nelson 7042, New Zealand
| | - Kirsty F Smith
- Cawthron Institute, Private Bag 2, 98 Halifax St East, Nelson 7042, New Zealand
| | - D Tim Harwood
- Cawthron Institute, Private Bag 2, 98 Halifax St East, Nelson 7042, New Zealand
| | | | - Islay D Marsden
- School of Biological Sciences, University of Canterbury, Private Bag 4800, 20 Kirkwood Ave, Christchurch 8041, New Zealand
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Ruvindy R, Barua A, Bolch CJS, Sarowar C, Savela H, Murray SA. Genomic copy number variability at the genus, species and population levels impacts in situ ecological analyses of dinoflagellates and harmful algal blooms. ISME COMMUNICATIONS 2023; 3:70. [PMID: 37422553 PMCID: PMC10329664 DOI: 10.1038/s43705-023-00274-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 06/18/2023] [Accepted: 06/20/2023] [Indexed: 07/10/2023]
Abstract
The application of meta-barcoding, qPCR, and metagenomics to aquatic eukaryotic microbial communities requires knowledge of genomic copy number variability (CNV). CNV may be particularly relevant to functional genes, impacting dosage and expression, yet little is known of the scale and role of CNV in microbial eukaryotes. Here, we quantify CNV of rRNA and a gene involved in Paralytic Shellfish Toxin (PST) synthesis (sxtA4), in 51 strains of 4 Alexandrium (Dinophyceae) species. Genomes varied up to threefold within species and ~7-fold amongst species, with the largest (A. pacificum, 130 ± 1.3 pg cell-1 /~127 Gbp) in the largest size category of any eukaryote. Genomic copy numbers (GCN) of rRNA varied by 6 orders of magnitude amongst Alexandrium (102- 108 copies cell-1) and were significantly related to genome size. Within the population CNV of rRNA was 2 orders of magnitude (105 - 107 cell-1) in 15 isolates from one population, demonstrating that quantitative data based on rRNA genes needs considerable caution in interpretation, even if validated against locally isolated strains. Despite up to 30 years in laboratory culture, rRNA CNV and genome size variability were not correlated with time in culture. Cell volume was only weakly associated with rRNA GCN (20-22% variance explained across dinoflagellates, 4% in Gonyaulacales). GCN of sxtA4 varied from 0-102 copies cell-1, was significantly related to PSTs (ng cell-1), displaying a gene dosage effect modulating PST production. Our data indicate that in dinoflagellates, a major marine eukaryotic group, low-copy functional genes are more reliable and informative targets for quantification of ecological processes than unstable rRNA genes.
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Affiliation(s)
- Rendy Ruvindy
- University of Technology Sydney, School of Life Sciences, Sydney, PO Box 123, Broadway, NSW, 2007, Australia
| | - Abanti Barua
- University of Technology Sydney, School of Life Sciences, Sydney, PO Box 123, Broadway, NSW, 2007, Australia
| | - Christopher J S Bolch
- Institute for Marine & Antarctic Studies, University of Tasmania, Launceston, 7248, TAS, Australia
| | - Chowdhury Sarowar
- Sydney Institute of Marine Science, Chowder Bay Rd, Mosman, NSW, Australia
| | - Henna Savela
- University of Technology Sydney, School of Life Sciences, Sydney, PO Box 123, Broadway, NSW, 2007, Australia
- Finnish Environment Institute, Marine Research Centre, Helsinki, Finland
| | - Shauna A Murray
- University of Technology Sydney, School of Life Sciences, Sydney, PO Box 123, Broadway, NSW, 2007, Australia.
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Veselá-Strejcová J, Scalco E, Zingone A, Colin S, Caputi L, Sarno D, Nebesářová J, Bowler C, Lukeš J. Diverse eukaryotic phytoplankton from around the Marquesas Islands documented by combined microscopy and molecular techniques. Protist 2023; 174:125965. [PMID: 37327684 DOI: 10.1016/j.protis.2023.125965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 04/21/2023] [Accepted: 05/02/2023] [Indexed: 06/18/2023]
Abstract
Oceanic phytoplankton serve as a base for the food webs within the largest planetary ecosystem. Despite this, surprisingly little is known about species composition, function and ecology of phytoplankton communities, especially for vast areas of the open ocean. In this study we focus on the marine phytoplankton microflora from the vicinity of the Marquesas Islands in the Southern Pacific Ocean collected during the Tara Oceans expedition. Multiple samples from four sites and two depths were studied in detail using light microscopy, scanning electron microscopy, and automated confocal laser scanning microscopy. In total 289 taxa were identified, with Dinophyceae and Bacillariophyceae contributing 60% and 32% of taxa, respectively, to phytoplankton community composition. Notwithstanding, a large number of cells could not be assigned to any known species. Coccolithophores and other flagellates together contributed less than 8% to the species list. Observed cell densities were generally low, but at sites of high autotrophic biomass, diatoms reached the highest cell densities (1.26 × 104 cells L-1). Overall, 18S rRNA metabarcode-based community compositions matched microscopy-based estimates, particularly for the main diatom taxa, indicating consistency and complementarity between different methods, while the wide range of microscopy-based methods permitted several unknown and poorly studied taxa to be revealed and identified.
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Affiliation(s)
- Jana Veselá-Strejcová
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 37005 České Budějovice (Budweis), Czech Republic
| | - Eleonora Scalco
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
| | - Adriana Zingone
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
| | - Sébastien Colin
- Max Planck Institute for Developmental Biology, 72076 Tuebingen, Germany
| | - Luigi Caputi
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
| | - Diana Sarno
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
| | - Jana Nebesářová
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 37005 České Budějovice (Budweis), Czech Republic
| | - Chris Bowler
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy; Institut de Biologie de l'École Normale Supérieure, CNRS, INSERM, PSL Université Paris, 75005 Paris, France
| | - Julius Lukeš
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 37005 České Budějovice (Budweis), Czech Republic; Faculty of Science, University of South Bohemia, 37005 České Budějovice (Budweis), Czech Republic.
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Kalu EI, Reyes-Prieto A, Barbeau MA. Community dynamics of microbial eukaryotes in intertidal mudflats in the hypertidal Bay of Fundy. ISME COMMUNICATIONS 2023; 3:21. [PMID: 36918616 PMCID: PMC10014957 DOI: 10.1038/s43705-023-00226-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 02/15/2023] [Accepted: 02/28/2023] [Indexed: 03/16/2023]
Abstract
Protists (microbial eukaryotes) are a critically important but understudied group of microorganisms. They are ubiquitous, represent most of the genetic and functional diversity among eukaryotes, and play essential roles in nutrient and energy cycling. Yet, protists remain a black box in marine sedimentary ecosystems like the intertidal mudflats in the Bay of Fundy. The harsh conditions of the intertidal zone and high energy nature of tides in the Bay of Fundy provide an ideal system for gaining insights into the major food web players, diversity patterns and potential structuring influences of protist communities. Our 18S rDNA metabarcoding study quantified seasonal variations and vertical stratification of protist communities in Bay of Fundy mudflat sediments. Three 'SAR' lineages were consistently dominant (in terms of abundance, richness, and prevalence), drove overall community dynamics and formed the core microbiome in sediments. They are Cercozoa (specifically thecate, benthic gliding forms), Bacillariophyta (mainly cosmopolitan, typically planktonic diatoms), and Dinophyceae (dominated by a toxigenic, bloom-forming species). Consumers were the dominant trophic functional group and were comprised mostly of eukaryvorous and bacterivorous Cercozoa, and omnivorous Ciliophora, while phototrophs were dominated by Bacillariophyta. The codominance of Apicomplexa (invertebrate parasites) and Syndiniales (protist parasites) in parasite assemblages, coupled with broader diversity patterns, highlighted the combined marine and terrestrial influences on microbial communities inhabiting intertidal sediments. Our findings, the most comprehensive in a hypertidal benthic system, suggest that synergistic interactions of both local and regional processes (notably benthic-pelagic coupling) may drive heterogenous microbial distribution in high-energy coastal systems.
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Affiliation(s)
- Eke I Kalu
- Department of Biology, University of New Brunswick, Fredericton, NB, Canada.
| | | | - Myriam A Barbeau
- Department of Biology, University of New Brunswick, Fredericton, NB, Canada
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Verma A, Hoppenrath M, Smith KF, Murray JS, Harwood DT, Hosking JM, Rongo T, Rhodes LL, Murray SA. Ostreopsis Schmidt and Coolia Meunier (Dinophyceae, Gonyaulacales) from Cook Islands and Niue (South Pacific Ocean), including description of Ostreopsis tairoto sp. nov. Sci Rep 2023; 13:3110. [PMID: 36813881 PMCID: PMC9947023 DOI: 10.1038/s41598-023-29969-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 02/14/2023] [Indexed: 02/24/2023] Open
Abstract
It is important to decipher the diversity and distribution of benthic dinoflagellates, as there are many morphologically indistinct taxa that differ from one another in production of potent toxins. To date, the genus Ostreopsis comprises twelve described species, of which seven are potentially toxic and produce compounds presenting a threat to human and environmental health. In this study, isolates previously identified as "Ostreopsis sp. 3" were sampled from the area where it was first reported, Rarotonga, Cook Islands, and have been taxonomically and phylogenetically characterised as Ostreopsis tairoto sp. nov. Phylogenetically, the species is closely related to "Ostreopsis sp. 8", O. mascarenensis, "O. sp. 4", O. fattorussoi, O. rhodesiae and O. cf. siamensis. Previously, it was considered a part of the O. cf. ovata complex but can be distinguished from O. cf. ovata based on the small pores identified on this study, and from O. fattorussoi and O. rhodesiae based on relative lengths of the 2' plates. No known palytoxin -like compounds were detected in strains investigated in this study. Strains of O. lenticularis, Coolia malayensis and C. tropicalis were also identified and described. This study advances our knowledge of biogeography, distribution, and toxins of Ostreopsis and Coolia species.
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Affiliation(s)
- A. Verma
- grid.117476.20000 0004 1936 7611School of Life Sciences, University of Technology, Broadway, Sydney, NSW 2007 Australia
| | - M. Hoppenrath
- grid.500026.10000 0004 0487 6958Senckenberg am Meer, German Center for Marine Biodiversity Research (DZMB), Südstrand 44, D-26382 Wilhelmshaven, Germany
| | - K. F. Smith
- grid.418703.90000 0001 0740 4700Cawthron Institute, Nelson, 7010 New Zealand
| | - J. S. Murray
- grid.418703.90000 0001 0740 4700Cawthron Institute, Nelson, 7010 New Zealand
| | - D. T. Harwood
- grid.418703.90000 0001 0740 4700Cawthron Institute, Nelson, 7010 New Zealand
| | - J. M. Hosking
- Te Ipukarea Society, PO Box 649, Rarotonga, Cook Islands
| | - T. Rongo
- Kōrero O Te `Ōrau, Avarua, PO Box 881, Avarua, Rarotonga, Cook Islands
| | - L. L. Rhodes
- grid.418703.90000 0001 0740 4700Cawthron Institute, Nelson, 7010 New Zealand
| | - S. A. Murray
- grid.117476.20000 0004 1936 7611School of Life Sciences, University of Technology, Broadway, Sydney, NSW 2007 Australia
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Liu X, Liu Y, Chai Z, Hu Z, Tang YZ. A combined approach detected novel species diversity and distribution of dinoflagellate cysts in the Yellow Sea, China. MARINE POLLUTION BULLETIN 2023; 187:114567. [PMID: 36640495 DOI: 10.1016/j.marpolbul.2022.114567] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 12/29/2022] [Accepted: 12/30/2022] [Indexed: 06/17/2023]
Abstract
Resting cysts of dinoflagellates seed harmful algal blooms (HABs) and their geographic expansion, which makes it fundamentally important to obtain comprehensive inventories of dinoflagellate resting cysts in HABs-prone regions. The Yellow Sea (YS) of China has observed numerous outbreaks of dinoflagellate HABs with some novel species recorded recently indicating an underestimated HABs-causing species diversity. We report our investigation of dinoflagellate cysts of YS via an approach combining metabarcoding sequencing and single-cyst morpho-molecular identification, which identified many novel cyst species and a significant controlling effect of the Yellow Sea Cold Water Mass on cyst composition. The metabarcoding and single cyst-based sequencing detected 11 cyst species never being unambiguously reported in China, 10 never reported as cyst producers, and 3 HABs-causing species never reported from YS. Our detections of many potentially toxic or HABs-causative, particularly novel, cysts and distribution pattern provide important insights into the risks and ecology of dinoflagellate HABs.
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Affiliation(s)
- Xiaohan Liu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuyang Liu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Zhaoyang Chai
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Zhangxi Hu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China.
| | - Ying Zhong Tang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China.
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Ciliate Morpho-Taxonomy and Practical Considerations before Deploying Metabarcoding to Ciliate Community Diversity Surveys in Urban Receiving Waters. Microorganisms 2022; 10:microorganisms10122512. [PMID: 36557765 PMCID: PMC9787992 DOI: 10.3390/microorganisms10122512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 12/12/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022] Open
Abstract
Disentangling biodiversity and community assembly effects on ecosystem function has always been an important topic in ecological research. The development and application of a DNA metabarcoding method has fundamentally changed the way we describe prokaryotic communities and estimate biodiversity. Compared to prokaryotes (bacteria and archaea), the eukaryotic microbes (unicellular eukaryotes) also fulfill extremely important ecological functions in different ecosystems regarding their intermediate trophic positions. For instance, ciliated microbes (accounting for a substantial portion of the diversity of unicellular eukaryotes) perform pivotal roles in microbial loops and are essential components in different ecosystems, especially in water purification processes. Therefore, the community composition of ciliated species has been widely utilized as a proxy for water quality and biological assessment in urban river ecosystems and WWTPs (wastewater treatment plants). Unfortunately, investigating the dynamic changes and compositions in ciliate communities relies heavily on existing morpho-taxonomical descriptions, which is limited by traditional microscopic approaches. To deal with this dilemma, we discuss the DNA-based taxonomy of ciliates, the relative merits and challenges of deploying its application using DNA metabarcoding for surveys of ciliate community diversity in urban waterbodies, and provide suggestions for minimizing relevant sources of biases in its implementation. We expect that DNA metabarcoding could untangle relationships between community assembly and environmental changes affecting ciliate communities. These analyses and discussions could offer a replicable method in support of the application of evaluating communities of ciliated protozoa as indicators of urban freshwater ecosystems.
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DNA metabarcoding data reveals harmful algal-bloom species undescribed previously at the northern Antarctic Peninsula region. Polar Biol 2022. [DOI: 10.1007/s00300-022-03084-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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Zhang Z, Li H, Shen W, Du X, Li S, Wei Z, Zhang Z, Feng K, Deng Y. The large-scale spatial patterns of ecological networks between phytoplankton and zooplankton in coastal marine ecosystems. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 827:154285. [PMID: 35248637 DOI: 10.1016/j.scitotenv.2022.154285] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 11/22/2021] [Accepted: 02/28/2022] [Indexed: 06/14/2023]
Abstract
Although autotrophic phytoplankton and heterotrophic zooplankton both play important roles in the food web of marine ecosystem, their comprehensive interactions and spatial patterns at continental scale remain poorly studied. Here, we collected 251 seawater samples along 13,000 km of Chinese coastline, and microscopically investigated the latitudinal gradients of planktonic diversities. In total, 307 phytoplanktonic and 311 zooplanktonic species were visually identified. Using the newly developed Inter-Domain Ecological Networks (IDENs) approach, the phytoplankton-zooplankton interaction networks were constructed. We found that the phyto-zooplankton network structure was varied across three regions, more complex and numerous connections along the southern coast than in the north. In addition, some particular associations between zooplanktonic and phytoplanktonic groups were found to be localized in specific regions. Furthermore, the seawater temperature and salinity were the major driving force for shaping planktonic interaction networks. These results provide a deeper understanding of planktonic biogeography and phytoplankton-zooplankton interaction patterns.
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Affiliation(s)
- Zheng Zhang
- Institute of Marine Science and Technology, Shandong University, Qingdao 266237, China
| | - Hongjun Li
- State Environmental Protection Key Laboratory of Coastal Ecosystem, National Marine Environmental Monitoring Center, Dalian, 116023, China
| | - Wenli Shen
- Institute of Marine Science and Technology, Shandong University, Qingdao 266237, China
| | - Xiongfeng Du
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Shuzhen Li
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China; Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education) and Dalian POCT Laboratory, School of Environmental Science and Technology, Dalian University of Technology, Dalian, 116024, China
| | - Ziyan Wei
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhaojing Zhang
- Institute of Marine Science and Technology, Shandong University, Qingdao 266237, China
| | - Kai Feng
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Ye Deng
- Institute of Marine Science and Technology, Shandong University, Qingdao 266237, China; CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China.
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Pseudocochlodinium profundisulcus Resting Cysts Detected in the Ballast Tank Sediment of Ships Arriving in the Ports of China and North America and the Implications in the Species' Geographic Distribution and Possible Invasion. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 19:ijerph19010299. [PMID: 35010560 PMCID: PMC8751027 DOI: 10.3390/ijerph19010299] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 12/23/2021] [Accepted: 12/24/2021] [Indexed: 11/17/2022]
Abstract
Over the past several decades, much attention has been focused on the dispersal of aquatic nonindigenous species via ballast tanks of shipping vessels worldwide. The recently reclassified dinoflagellate Pseudocochlodinium profundisulcus (previously identified as Cochlodinium sp., Cochlodinium geminatum, or Polykrikos geminatus) was not reported in China until 2006. However, algal blooming events caused by this organism have been reported almost every year since then in the Pearl River Estuary and its adjacent areas in China. Whether P. profundisulcus is an indigenous or an invasive species has thus become an ecological question of great scientific and practical significance. In this study, we collected the sediments from ballast tanks of ships arriving in the ports of China and North America and characterized dinoflagellate resting cysts via a combined approach. We germinated two dark brownish cysts from the tank of an international ship (Vessel A) arriving at the Jiangyin Port (China) into vegetative cells and identified them as P. profundisulcus by light and scanning electron microscopy and phylogenetic analyses for partial LSU rDNA sequences. We also identified P. profundisulcus cyst from the ballast tank sediment of a ship (Vessel B) arriving in the port of North America via single-cyst PCR and cloning sequencing, which indicated that this species could be transported as resting cyst via ship. Since phylogenetic analyses based on partial LSU rDNA sequences could not differentiate all sequences among our cysts from those deposited in the NCBI database into sub-groups, all populations from China, Australia, Japan, and the original sources from which the cysts in the two vessels arrived in China and North America were carried over appeared to share a very recent common ancestor, and the species may have experienced a worldwide expansion recently. These results indicate that P. profundisulcus cysts may have been extensively transferred to many regions of the world via ships’ ballast tank sediments. While our work provides an exemplary case for both the feasibility and complexity (in tracking the source) of the bio-invasion risk via the transport of live resting cysts by ship’s ballast tanks, it also points out an orientation for future investigation.
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Shuwang X, Sun J, Wei Y, Guo C. Size-Fractionated Filtration Combined with Molecular Methods Reveals the Size and Diversity of Picophytoplankton. BIOLOGY 2021; 10:biology10121280. [PMID: 34943195 PMCID: PMC8698306 DOI: 10.3390/biology10121280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 11/14/2021] [Accepted: 11/27/2021] [Indexed: 06/14/2023]
Abstract
In this study, flow cytometry (FCM) and size-fractionated filtration, together with high-throughput molecular sequencing methods (SM), were used to investigate picophytoplankton. A particle separation filter and a higher-throughput sequencing method were used to evaluate the composition of a euphotic zone of picophytoplankton-especially picoeukaryotic phytoplankton-in the Western Pacific, and the results of flow cytometry, which is a classic way to detect picophytoplankton, were used as a standard to evaluate the reliability of the results of the SMs. Within a water column of 200 m, six water depths (5, 25, 50, 113 (DCM), 150, and 200 m) were established. In order to further study the particle size spectra of the picophytoplankton, size-fractionated filtration was used to separate water samples from each water depth into three particle size ranges: 0.2-0.6, 0.6-1.2, and 1.2-2 μm. A total of 36 (6 × 3 × 2) samples were obtained through PCR amplification of the 18S rRNA V4 hypervariable region and 16S rRNA, which were biased toward phytoplankton plastids, and then high-throughput sequencing was performed. The estimation of the picophytoplankton diameter relied on forward scattering (FSC) through FCM. The estimation of the vertical distribution and diameter of the picophytoplankton using the SM was consistent with the results with FCM; thus, we believe that the estimation of picophytoplankton composition with the SM has value as a reference, although the size-fractionated filtration seemed to cause some deviations. In addition to Prochlorococcus and Synechococcus, the SM was used to evaluate the composition of picoeukaryotic phytoplankton, which mainly included Prymnesiophycea (Haptophyta) (38.15%), Cryptophyceae (Cryptophyta) (22.36%), Dictyochophyceae (Chrysophyta) (12.22%), and Mamiellophyceae (Chlorophyta) (3.31%). In addition, the SM also detected Dinophyceae (Dinoflagellata) (11.69%) sequences and a small number of Bacillariophyceae (Diatom) (1.64%) sequences, which are generally considered to have large particle sizes. The results of the SM also showed that the picoeukaryotic phytoplankton were not evenly distributed in the euphotic layer, and the vertical distributions of the different picoeukaryotic phytoplankton were different. An analysis of correlations with environmental factors showed that temperature was the main environmental factor controlling the vertical distribution of picophytoplankton.
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Affiliation(s)
- Xinze Shuwang
- Institute of Marine Science and Technology, Shandong University, Qingdao 266237, China; (X.S.); (C.G.)
| | - Jun Sun
- College of Marine Science and Technology, China University of Geosciences (Wuhan), Wuhan 430074, China
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences (Wuhan), Wuhan 430074, China
| | - Yuqiu Wei
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China;
| | - Congcong Guo
- Institute of Marine Science and Technology, Shandong University, Qingdao 266237, China; (X.S.); (C.G.)
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Burki F, Sandin MM, Jamy M. Diversity and ecology of protists revealed by metabarcoding. Curr Biol 2021; 31:R1267-R1280. [PMID: 34637739 DOI: 10.1016/j.cub.2021.07.066] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Protists are the dominant eukaryotes in the biosphere where they play key functional roles. While protists have been studied for over a century, it is the high-throughput sequencing of molecular markers from environmental samples - the approach of metabarcoding - that has revealed just how diverse, and abundant, these small organisms are. Metabarcoding is now routine to survey environmental diversity, so data have rapidly accumulated from a multitude of environments and at different sampling scales. This mass of data has provided unprecedented opportunities to study the taxonomic and functional diversity of protists, and how this diversity is organised in space and time. Here, we use metabarcoding as a common thread to discuss the state of knowledge in protist diversity research, from technical considerations of the approach to important insights gained on diversity patterns and the processes that might have structured this diversity. In addition to these insights, we conclude that metabarcoding is on the verge of an exciting added dimension thanks to the maturation of high-throughput long-read sequencing, so that a robust eco-evolutionary framework of protist diversity is within reach.
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Affiliation(s)
- Fabien Burki
- Department of Organismal Biology (Systematic Biology), Uppsala University, Norbyv. 18D, 75236 Uppsala, Sweden; Science For Life Laboratory, Uppsala University, 75236 Uppsala, Sweden.
| | - Miguel M Sandin
- Department of Organismal Biology (Systematic Biology), Uppsala University, Norbyv. 18D, 75236 Uppsala, Sweden
| | - Mahwash Jamy
- Department of Organismal Biology (Systematic Biology), Uppsala University, Norbyv. 18D, 75236 Uppsala, Sweden
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Cooney EC, Okamoto N, Cho A, Hehenberger E, Richards TA, Santoro AE, Worden AZ, Leander BS, Keeling PJ. Single-Cell Transcriptomics of Abedinium Reveals a New Early-Branching Dinoflagellate Lineage. Genome Biol Evol 2021; 12:2417-2428. [PMID: 33045041 DOI: 10.1093/gbe/evaa196] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/15/2020] [Indexed: 12/12/2022] Open
Abstract
Dinoflagellates possess many cellular characteristics with unresolved evolutionary histories. These include nuclei with greatly expanded genomes and chromatin packaged using histone-like proteins and dinoflagellate-viral nucleoproteins instead of histones, highly reduced mitochondrial genomes with extensive RNA editing, a mix of photosynthetic and cryptic secondary plastids, and tertiary plastids. Resolving the evolutionary origin of these traits requires understanding their ancestral states and early intermediates. Several early-branching dinoflagellate lineages are good candidates for such reconstruction, however these cells tend to be delicate and environmentally sparse, complicating such analyses. Here, we employ transcriptome sequencing from manually isolated and microscopically documented cells to resolve the placement of two cells of one such genus, Abedinium, collected by remotely operated vehicle in deep waters off the coast of Monterey Bay, CA. One cell corresponds to the only described species, Abedinium dasypus, whereas the second cell is distinct and formally described as Abedinium folium, sp. nov. Abedinium has classically been assigned to the early-branching dinoflagellate subgroup Noctilucales, which is weakly supported by phylogenetic analyses of small subunit ribosomal RNA, the single characterized gene from any member of the order. However, an analysis based on 221 proteins from the transcriptome places Abedinium as a distinct lineage, separate from and basal to Noctilucales and the rest of the core dinoflagellates. The transcriptome also contains evidence of a cryptic plastid functioning in the biosynthesis of isoprenoids, iron-sulfur clusters, and heme, a mitochondrial genome with all three expected protein-coding genes (cob, cox1, and cox3), and the presence of some but not all dinoflagellate-specific chromatin packaging proteins.
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Affiliation(s)
- Elizabeth C Cooney
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Noriko Okamoto
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Anna Cho
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Elisabeth Hehenberger
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
- Ocean Ecosystems Biology Unit, GEOMAR-Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | | | - Alyson E Santoro
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara
| | - Alexandra Z Worden
- Ocean Ecosystems Biology Unit, GEOMAR-Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
- Kiel University, Germany
| | - Brian S Leander
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Patrick J Keeling
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
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16
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Persson A, Smith BC, Alix JH, Li Y, Holohan BA, Wikfors GH. Differences in Specific Mass Density Between Dinoflagellate Life Stages and Relevance to Accumulation by Hydrodynamic Processes. JOURNAL OF PHYCOLOGY 2021; 57:1492-1503. [PMID: 33960400 PMCID: PMC8596432 DOI: 10.1111/jpy.13181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 03/31/2021] [Indexed: 06/12/2023]
Abstract
One previously unstudied aspect of differences between sexual and asexual life stages in large-scale transport and accumulation is density (mass per unit volume) of cells in each life stage. The specific density was determined for Scrippsiella lachrymosa cells in medium with and without nitrogen (N) enrichment through density-gradient centrifugation. Growth medium without N addition is often called "encystment medium" when used for the purpose of resting cyst formation in cyst-forming dinoflagellates; mating gametes are usually seen after 2-3 days. Significant differences in specific density were found after 2 days in encystment medium simultaneously with the observation of typical gamete swimming behavior and mating. The specific density of cells in encystment medium was 1.06 g · cm-3 ; whereas, the specific density of cells in growth medium was 1.11 g · cm-3 . Cells in encystment medium were found to have significantly increased lipid content, reduced chlorophyll content, and reduced internal complexity. The findings may explain differential transport of less dense and chemotactically aggregating gametes into surface blooms in contrast to denser vegetative cells that perform daily vertical migration and do not aggregate. Passive accumulation of non-migrating gametes into layers in stagnant water also can be explained, as well as sinking of zygotes when the storage of highly dense starch increases. Resting cysts had a density of over 1.14 g · cm-3 and would sink to become part of the silt fraction of the sediment. We suggest that differences in behavior and buoyancy between sexual and asexual life stages cause differences in cell accumulation, and therefore large-scale, environmental transport could be directly dependent upon life-cycle transitions.
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Affiliation(s)
- Agneta Persson
- Department of Biological and Environmental SciencesGöteborg UniversityBox 461405 30GöteborgSweden
- Smedjebacksvägen 13SE‐771 90LudvikaSweden
| | - Barry C. Smith
- National Oceanic and Atmospheric AdministrationNational Marine Fisheries ServiceNortheast Fisheries Science CenterMilford Laboratory212 Rogers AvenueMilfordConnecticut06460USA
| | - Jennifer H. Alix
- National Oceanic and Atmospheric AdministrationNational Marine Fisheries ServiceNortheast Fisheries Science CenterMilford Laboratory212 Rogers AvenueMilfordConnecticut06460USA
| | - Yaqin Li
- National Oceanic and Atmospheric AdministrationNational Marine Fisheries ServiceNortheast Fisheries Science CenterMilford Laboratory212 Rogers AvenueMilfordConnecticut06460USA
| | - Bridget A. Holohan
- Department of Marine SciencesUniversity of Connecticut1080 Shennecossett RoadGrotonConnecticut06340USA
| | - Gary H. Wikfors
- National Oceanic and Atmospheric AdministrationNational Marine Fisheries ServiceNortheast Fisheries Science CenterMilford Laboratory212 Rogers AvenueMilfordConnecticut06460USA
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Romano F, Pitta P. Relationships of pelagic ciliates with the microbial food web components at a coastal station in the oligotrophic Eastern Mediterranean Sea: temporal and vertical variability. JOURNAL OF PLANKTON RESEARCH 2021; 43:691-711. [PMID: 34584492 PMCID: PMC8461642 DOI: 10.1093/plankt/fbab053] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 08/02/2021] [Indexed: 06/13/2023]
Abstract
The annual/temporal and vertical dynamics of the microbial food web (MFW) was studied in a coastal station of the oligotrophic Eastern Mediterranean Sea. The present study analyzed the changes of all components of the MFW with a specific focus on the relationships between different size classes of heterotrophic and mixotrophic ciliates with their potential prey. The MFW was dominated by heterotrophic picoplankton in all months and depths analyzed, whereas autotrophic nanoplankton took advantage in cold months with higher nutrient availability. On the other hand, mixotrophic microplankton biomass was higher in summer when nutrients and chlorophyll-a were scarce. As part of the mixotrophic biomass, mixotrophic ciliates were correlated with their "potential" prey at the surface and deep chlorophyll maximum. Large mixotrophic ciliates (L. strobila) were more selective in terms of potential prey, showing a correlation with Synechococcus. On the other hand, mixotrophic nanociliates (Strombidium dalum) were correlated differently with different potential prey according to depth, supporting the idea that nanociliates could be more generalists in terms of prey selection. Because the relationships between mixotrophic ciliates and their potential prey are still poorly studied, this work represents the start for further investigation.
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Affiliation(s)
- Filomena Romano
- Marine Biological Section, University of Copenhagen, Helsingør DK-3000, Denmark
| | - Paraskevi Pitta
- Marine Biological Section, University of Copenhagen, Helsingør DK-3000, Denmark
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18
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Tang YZ, Gu H, Wang Z, Liu D, Wang Y, Lu D, Hu Z, Deng Y, Shang L, Qi Y. Exploration of resting cysts (stages) and their relevance for possibly HABs-causing species in China. HARMFUL ALGAE 2021; 107:102050. [PMID: 34456016 DOI: 10.1016/j.hal.2021.102050] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 04/30/2021] [Accepted: 05/10/2021] [Indexed: 06/13/2023]
Abstract
The studies on the species diversity, distribution, environmental implications, and molecular basis of resting cysts (stages) of dinoflagellates and a few species of other groups conducted in China during the last three decades are reviewed. The major achievements are summarized as the following five aspects: 1) The continual efforts in detecting the species diversity of resting cysts (spores) in dinoflagellates and other classes using either morphological or molecular approaches, or both, in the four seas of China, which led to identifications of 106 species of dinoflagellate resting cysts and 4 species of resting stages from other groups of microalgae, with a total of 64 species of dinoflagellate cysts and the resting stage of the brown tide-causing Aureococcus anophagefferens being unequivocally identified via molecular approaches from the sediments of Chinese coastal waters; 2) The well-known toxic and HABs-causing dinoflagellates Karenia mikimotoi, Karlodinium veneficum, Akashiwo sanguinea and the pelagophyte A. anophagefferens were proven to be resting cyst (stage) producers via laboratory studies on their life cycles and field detections of resting cysts (resting stage cells). And, via germination experiment and subsequent characterization of vegetative cells, numerous dinoflagellate species that had never been described or found to form cysts were discovered and characterized; 3) The distributions of the resting cysts of Alexandrium catenella, A. pacificum, Gymnodinium catenatum, K. mikimotoi, K. veneficum and Azadinium poporum and the resting stage cells of A. anophagefferens were morphologically and molecularly mapped in all four seas of China, with A. anophagefferens proven to have been present in the Bohai Sea for at least 1,500 years; 4) Obtaining important insights into the 'indicator' values of the dinoflagellate cyst assemblages in sediment cores for tracking eutrophication, environmental pollution and other anthropological influences in coastal waters; 5) Studies on the cyst-pertinent processes and genetic basis (transcriptomics together with physiological and chemical measurements) of resting cyst dormancy not only revealed the regulating patterns of some environmental factors in cyst formation and germination, but also identified many characteristically active or inactive metabolic pathways, differentially expressed genes, and the possibly vital regulating function of the phytohormone abscisic acid and a group of molecular chaperones in resting cysts. We also identified seven issues and three themes that should be addressed and explored by Chinese scientists working in the area in the future.
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Affiliation(s)
- Ying Zhong Tang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China.
| | - Haifeng Gu
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
| | - Zhaohui Wang
- Institute of Hydrology, College of Life Science and Technology, Ji'nan University, Guangzhou 510632, China
| | - Dongyan Liu
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai 200241, China
| | - Yan Wang
- Research Center of Red Tide and Marine Biology, College of Life Science and Technology, Ji'nan University, Guangzhou 510632, China
| | - Douding Lu
- Key Laboratory of Marine Ecosystem and Biogeochemistry, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, China
| | - Zhangxi Hu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Yunyan Deng
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Lixia Shang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Yuzao Qi
- Research Center of Red Tide and Marine Biology, College of Life Science and Technology, Ji'nan University, Guangzhou 510632, China
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Xiong W, Jousset A, Li R, Delgado-Baquerizo M, Bahram M, Logares R, Wilden B, de Groot GA, Amacker N, Kowalchuk GA, Shen Q, Geisen S. A global overview of the trophic structure within microbiomes across ecosystems. ENVIRONMENT INTERNATIONAL 2021; 151:106438. [PMID: 33621916 DOI: 10.1016/j.envint.2021.106438] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 01/14/2021] [Accepted: 02/01/2021] [Indexed: 06/12/2023]
Abstract
The colossal project of mapping the microbiome on Earth is rapidly advancing, with a focus on individual microbial groups. However, a global assessment of the associations between predatory protists and their bacterial prey is still missing at a cross-ecosystem level. This knowledge is critical to better understand the importance of top-down links in structuring microbiomes. Here, we examined 38 sequence-based datasets of paired bacterial and protistan taxa, covering 3,178 samples from diverse habitats including freshwater, marine and soils. We show that community profiles of protists and bacteria strongly correlated across and within habitats, with trophic microbiome structures fundamentally differing across habitats. Soils hosted the most heterogenous and diverse microbiomes. Protist communities were dominated by predators in soils and phototrophs in aquatic environments. This led to changes in the ratio of total protists to bacteria richness, which was highest in marine, while that of predatory protists to bacteria was highest in soils. Taxon richness and relative abundance of predatory protists positively correlated with bacterial richness in marine habitats. These links differed between soils, predatory protist richness and the relative abundance of predatory protists positively correlated with bacterial richness in forest and grassland soils, but not in agricultural soils. Our results suggested that anthropogenic pressure affects higher trophic levels more than lower ones leading to a decoupled trophic structure in microbiomes. Together, our cumulative overview of microbiome patterns of bacteria and protists at the global scale revealed major patterns and differences of the trophic structure of microbiomes across Earth's habitats, and show that anthropogenic factors might have negative effects on the trophic structure within microbiomes. Furthermore, the increased impact of anthropogenic factors on especially higher trophic levels suggests that often-observed reduced ecosystem functions in anthropogenic systems might be partly attributed to a reduction of trophic complexity.
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Affiliation(s)
- Wu Xiong
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, Jiangsu, People's Republic of China; Ecology and Biodiversity Group, Department of Biology, Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Alexandre Jousset
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, Jiangsu, People's Republic of China.
| | - Rong Li
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, Jiangsu, People's Republic of China
| | - Manuel Delgado-Baquerizo
- Departamento de Sistemas Físicos, Químicos y Naturales, Universidad Pablo de Olavide, 41013 Sevilla, Spain
| | - Mohammad Bahram
- Department of Ecology, Swedish University of Agricultural Sciences, Ulls väg 16, 756 51 Uppsala, Sweden; Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, 40 Lai St, Tartu, Estonia
| | - Ramiro Logares
- Institute of Marine Sciences (ICM), CSIC, 08003 Barcelona, Catalonia, Spain
| | - Benjamin Wilden
- University of Bielefeld, Department of Animal Ecology, Konsequenz 45, 33615 Bielefeld, Germany
| | - Gerard Arjen de Groot
- Wageningen Environmental Research, Wageningen University & Research, 6700 AA Wageningen, the Netherlands
| | - Nathalie Amacker
- Ecology and Biodiversity Group, Department of Biology, Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - George A Kowalchuk
- Ecology and Biodiversity Group, Department of Biology, Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Qirong Shen
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, Jiangsu, People's Republic of China.
| | - Stefan Geisen
- Laboratory of Nematology, Wageningen University & Research, 6700 ES Wageningen, the Netherlands.
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Huang H, Xu Q, Gibson K, Chen Y, Chen N. Molecular characterization of harmful algal blooms in the Bohai Sea using metabarcoding analysis. HARMFUL ALGAE 2021; 106:102066. [PMID: 34154783 DOI: 10.1016/j.hal.2021.102066] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Revised: 05/31/2021] [Accepted: 06/01/2021] [Indexed: 06/13/2023]
Abstract
Although the occurrences of harmful algal blooms (HABs) have been intensifying, many HABs in coastal waters may have been neglected despite their damaging impact directly on ecology and indirectly on human and animal health. The current detection of HABs depends primarily on the water coloration, chlorophyll intensity, cell density, and mortality due to HAB toxicity. Such methods may not be adequately sensitive to detecting HABs that are relatively transient or small scale. The Bohai Sea is the largest inlet of the Yellow Sea located on the northeast coast of China and famous for shipping and marine aquacultures. HABs frequently occur in the Bohai Sea. In this study, we explored the composition, diversity, and distribution of HAB species using the metabarcoding approach. Through sequencing and the analyzing the 18S rDNA V4 region of 15 samples collected from spatially isolated sites in the Bohai Sea during an expedition in the summer of 2019, we identified 74 potential HAB species including 34 that had not been reported in the Bohai Sea in previous studies. This project provided a detailed analysis of phytoplankton composition, and molecular detection of HAB species in the Bohai Sea. In particular, these analyses revealed extremely high relative abundances of the ichthyotoxic phytoplankton species Vicicitus globosus (Dictyochophyceae) at multiple adjacent sampling sites in the Bohai Bay, which were close to the Yellow River Estuary during the expedition. The results revealed the occurrence of a potential HAB event that would be otherwise undetected using conventional methods, highlighting the sensitivity and power of metabarcoding analysis in detecting HABs and HAB species. This research suggested the value for routine and long-term monitoring of HAB species as an approach for monitoring HABs.
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Affiliation(s)
- Hailong Huang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266200, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Qing Xu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266200, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China; College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Kate Gibson
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia, V5A 1S6, Canada
| | - Yang Chen
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266200, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Nansheng Chen
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266200, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China; Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia, V5A 1S6, Canada.
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21
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Zhang H, Zhou Y, Liu TQ, Yin XJ, Lin L, Lin Q, Wang DZ. Initiation of efficient C 4 pathway in response to low ambient CO 2 during the bloom period of a marine dinoflagellate. Environ Microbiol 2021; 23:3196-3211. [PMID: 33938118 DOI: 10.1111/1462-2920.15545] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Accepted: 04/26/2021] [Indexed: 11/29/2022]
Abstract
Dinoflagellates are important primary producers and major causative agents of harmful algal blooms in the global ocean. Despite the great ecological significance, the photosynthetic carbon acquisition by dinoflagellates is still poorly understood. The pathways of photosynthetic carbon assimilation in a marine dinoflagellate Prorocentrum donghaiense under both in situ and laboratory-simulated bloom conditions were investigated using a combination of metaproteomics, qPCR, stable carbon isotope and targeted metabolomics approaches. A rapid consumption of dissolved CO2 to generate high biomass was observed as the bloom proceeded. The carbon assimilation genes and proteins including intracellular carbonic anhydrase 2, phosphoenolpyruvate carboxylase, phosphoenolpyruvate carboxykinase and RubisCO as well as their enzyme activities were all highly expressed at the low CO2 level, indicating that C4 photosynthetic pathway functioned in the blooming P. donghaiense cells. Furthermore, δ13 C values and content of C4 compound (malate) significantly increased with the decreasing CO2 concentration. The transition from C3 to C4 pathway minimizes the internal CO2 leakage and guarantees efficient carbon fixation at the low CO2 level. This study demonstrates the existence of C4 photosynthetic pathway in a marine dinoflagellate and reveals its important complementary role to assist carbon assimilation for cell proliferation during the bloom period.
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Affiliation(s)
- Hao Zhang
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen, 361005, China.,CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Youping Zhou
- Isotopomics in Chemical Biology & Shaanxi Key Laboratory of Chemical Additives for Industry, School of Chemistry & Chemical Engineering, Shaanxi University of Science & Technology, Xi'an, 710021, China
| | - Tian-Qi Liu
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen, 361005, China
| | - Xi-Jie Yin
- Laboratory of Marine & Coastal Geology, MNR Third Institute of Oceanology, Xiamen, 361005, China
| | - Lin Lin
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen, 361005, China
| | - Qiang Lin
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Da-Zhi Wang
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen, 361005, China
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22
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García-Gómez C, Yebra L, Cortés D, Sánchez A, Alonso A, Valcárcel-Pérez N, Gómez-Jakobsen F, Herrera I, Johnstone C, Mercado JM. Shifts in the protist community associated with an anticyclonic gyre in the Alboran Sea (Mediterranean Sea). FEMS Microbiol Ecol 2021; 96:5911576. [PMID: 32975560 DOI: 10.1093/femsec/fiaa197] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 09/23/2020] [Indexed: 02/06/2023] Open
Abstract
The diversity of protists was researched in the Alboran Sea (SW Mediterranean Sea) by means of high-throughput sequencing technologies based on the amplification of the V9 region of 18S rRNA. Samples were collected at different depths in seven stations following an environmental gradient from a coastal upwelling zone to the core of an oligotrophic anticyclonic gyre (AG). Sampling was performed during summer, when the water column was stratified. The superphyla Alveolata, Stramenopila and Rhizaria accounted for 84% of the total operational taxonomic units (OTUs). The most diverse groups were Dinophyceae (21% of OTUs), Marine Alveolates-II (MALV-II; 20%), Ciliophora (9%) and MALV-I (6%). In terms of read abundance, the predominant groups were Dinophyceae (29%), Bacillariophyta (14%), MALV-II (11%) and Ciliophora (11%). Samples were clustered into three groups according to the sampling depth and position. The shallow community in coastal stations presented distinguishable patterns of diatoms and ciliates compared with AG stations. These results indicate that there was a strong horizontal coupling between phytoplankton and ciliate communities. Abundance of Radiolaria and Syndiniales increased with depth. Our analyses demonstrate that the stratification disruption produced by the AG caused shifts in the trophic ecology of the plankton assemblages inducing a transition from bottom-up to top-down control.
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Affiliation(s)
- Candela García-Gómez
- Centro Oceanográfico de Málaga, Instituto Español de Oceanografía, Puerto Pesquero s/n, 29640 Fuengirola, Spain
| | - Lidia Yebra
- Centro Oceanográfico de Málaga, Instituto Español de Oceanografía, Puerto Pesquero s/n, 29640 Fuengirola, Spain
| | - Dolores Cortés
- Centro Oceanográfico de Málaga, Instituto Español de Oceanografía, Puerto Pesquero s/n, 29640 Fuengirola, Spain
| | - Antonio Sánchez
- Centro Oceanográfico de Málaga, Instituto Español de Oceanografía, Puerto Pesquero s/n, 29640 Fuengirola, Spain
| | - Aitor Alonso
- Centro Oceanográfico de Málaga, Instituto Español de Oceanografía, Puerto Pesquero s/n, 29640 Fuengirola, Spain
| | - Nerea Valcárcel-Pérez
- Centro Oceanográfico de Málaga, Instituto Español de Oceanografía, Puerto Pesquero s/n, 29640 Fuengirola, Spain
| | - Francisco Gómez-Jakobsen
- Centro Oceanográfico de Málaga, Instituto Español de Oceanografía, Puerto Pesquero s/n, 29640 Fuengirola, Spain
| | - Inma Herrera
- Centro Oceanográfico de Málaga, Instituto Español de Oceanografía, Puerto Pesquero s/n, 29640 Fuengirola, Spain
| | - Carolina Johnstone
- Centro Oceanográfico de Málaga, Instituto Español de Oceanografía, Puerto Pesquero s/n, 29640 Fuengirola, Spain
| | - Jesús M Mercado
- Centro Oceanográfico de Málaga, Instituto Español de Oceanografía, Puerto Pesquero s/n, 29640 Fuengirola, Spain
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23
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Assessing the Use of Molecular Barcoding and qPCR for Investigating the Ecology of Prorocentrum minimum (Dinophyceae), a Harmful Algal Species. Microorganisms 2021; 9:microorganisms9030510. [PMID: 33670984 PMCID: PMC7997176 DOI: 10.3390/microorganisms9030510] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 02/12/2021] [Accepted: 02/19/2021] [Indexed: 01/04/2023] Open
Abstract
Prorocentrum minimum is a species of marine dinoflagellate that occurs worldwide and can be responsible for harmful algal blooms (HABs). Some studies have reported it to produce tetrodotoxin; however, results have been inconsistent. qPCR and molecular barcoding (amplicon sequencing) using high-throughput sequencing have been increasingly applied to quantify HAB species for ecological analyses and monitoring. Here, we isolated a strain of P. minimum from eastern Australian waters, where it commonly occurs, and developed and validated a qPCR assay for this species based on a region of ITS rRNA in relation to abundance estimates from the cultured strain as determined using light microscopy. We used this tool to quantify and examine ecological drivers of P. minimum in Botany Bay, an estuary in southeast Australia, for over ~14 months in 2016–2017. We compared abundance estimates using qPCR with those obtained using molecular barcoding based on an 18S rRNA amplicon. There was a significant correlation between the abundance estimates from amplicon sequencing and qPCR, but the estimates from light microscopy were not significantly correlated, likely due to the counting method applied. Using amplicon sequencing, ~600 unique actual sequence variants (ASVs) were found, much larger than the known phytoplankton diversity from this region. P. minimum abundance in Botany Bay was found to be significantly associated with lower salinities and higher dissolved CO2 levels.
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24
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Dinoflagellates alter their carbon and nutrient metabolic strategies across environmental gradients in the central Pacific Ocean. Nat Microbiol 2021; 6:173-186. [PMID: 33398100 DOI: 10.1038/s41564-020-00814-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 10/13/2020] [Indexed: 01/28/2023]
Abstract
Marine microeukaryotes play a fundamental role in biogeochemical cycling through the transfer of energy to higher trophic levels and vertical carbon transport. Despite their global importance, microeukaryote physiology, nutrient metabolism and contributions to carbon cycling across offshore ecosystems are poorly characterized. Here, we observed the prevalence of dinoflagellates along a 4,600-km meridional transect extending across the central Pacific Ocean, where oligotrophic gyres meet equatorial upwelling waters rich in macronutrients yet low in dissolved iron. A combined multi-omics and geochemical analysis provided a window into dinoflagellate metabolism across the transect, indicating a continuous taxonomic dinoflagellate community that shifted its functional transcriptome and proteome as it extended from the euphotic to the mesopelagic zone. In euphotic waters, multi-omics data suggested that a combination of trophic modes were utilized, while mesopelagic metabolism was marked by cytoskeletal investments and nutrient recycling. Rearrangement in nutrient metabolism was evident in response to variable nitrogen and iron regimes across the gradient, with no associated change in community assemblage. Total dinoflagellate proteins scaled with particulate carbon export, with both elevated in equatorial waters, suggesting a link between dinoflagellate abundance and total carbon flux. Dinoflagellates employ numerous metabolic strategies that enable broad occupation of central Pacific ecosystems and play a dual role in carbon transformation through both photosynthetic fixation in the euphotic zone and remineralization in the mesopelagic zone.
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25
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Gottschling M, Czech L, Mahé F, Adl S, Dunthorn M. The Windblown: Possible Explanations for Dinophyte DNA in Forest Soils. J Eukaryot Microbiol 2020; 68:e12833. [PMID: 33155377 DOI: 10.1111/jeu.12833] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 10/12/2020] [Accepted: 10/28/2020] [Indexed: 11/28/2022]
Abstract
Dinophytes are widely distributed in marine- and fresh-waters, but have yet to be conclusively documented in terrestrial environments. Here, we evaluated the presence of these protists from an environmental DNA metabarcoding dataset of Neotropical rainforest soils. Using a phylogenetic placement approach with a reference alignment and tree, we showed that the numerous sequencing reads that were phylogenetically placed as dinophytes did not correlate with taxonomic assignment, environmental preference, nutritional mode, or dormancy. All the dinophytes in the soils are rather windblown dispersal units of aquatic species and are not biologically active residents of terrestrial environments.
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Affiliation(s)
- Marc Gottschling
- Department Biologie, Systematische Botanik und Mykologie, GeoBio-Center, Ludwig-Maximilians-Universität München, Munich, D-80638, Germany
| | - Lucas Czech
- Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, Heidelberg, D-69118, Germany.,Department of Plant Biology, Carnegie Institution for Science, Stanford, California, 94305, USA
| | - Frédéric Mahé
- CIRAD, UMR BGPI, Montpellier, F-34398, France.,BGPI, Université de Montpellier, CIRAD, IRD, Montpellier SupAgro, , Montpellier, France
| | - Sina Adl
- Department of Soil Sciences, College of Agriculture and Bioresources, University of Saskatchewan, Saskatoon, SK, S7N 5A8, Canada
| | - Micah Dunthorn
- Eukaryotic Microbiology, Faculty of Biology, Universität Duisburg-Essen, Essen, D-45141, Germany.,Centre for Water and Environmental Research (ZWU), Universität Duisburg-Essen, Essen, D-45141, Germany
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26
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Santoferrara L, Burki F, Filker S, Logares R, Dunthorn M, McManus GB. Perspectives from Ten Years of Protist Studies by High-Throughput Metabarcoding. J Eukaryot Microbiol 2020; 67:612-622. [PMID: 32498124 DOI: 10.1111/jeu.12813] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 05/29/2020] [Accepted: 05/29/2020] [Indexed: 01/07/2023]
Abstract
During the last decade, high-throughput metabarcoding became routine for analyzing protistan diversity and distributions in nature. Amid a multitude of exciting findings, scientists have also identified and addressed technical and biological limitations, although problems still exist for inference of meaningful taxonomic and ecological knowledge based on short DNA sequences. Given the extensive use of this approach, it is critical to settle our understanding on its strengths and weaknesses and to synthesize up-to-date methodological and conceptual trends. This article summarizes key scientific and technical findings, and identifies current and future directions in protist research that uses metabarcoding.
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Affiliation(s)
- Luciana Santoferrara
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA.,Department of Marine Sciences, University of Connecticut, Groton, CT, USA
| | - Fabien Burki
- Department of Organismal Biology, Program in Systematic Biology, and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Sabine Filker
- Department of Molecular Ecology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Ramiro Logares
- Institute of Marine Sciences (ICM), CSIC, Barcelona, Spain
| | - Micah Dunthorn
- Department of Eukaryotic Microbiology, University of Duisburg-Essen, Essen, Germany
| | - George B McManus
- Department of Marine Sciences, University of Connecticut, Groton, CT, USA
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27
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Stephens TG, González-Pech RA, Cheng Y, Mohamed AR, Burt DW, Bhattacharya D, Ragan MA, Chan CX. Genomes of the dinoflagellate Polarella glacialis encode tandemly repeated single-exon genes with adaptive functions. BMC Biol 2020; 18:56. [PMID: 32448240 PMCID: PMC7245778 DOI: 10.1186/s12915-020-00782-8] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Accepted: 04/20/2020] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Dinoflagellates are taxonomically diverse and ecologically important phytoplankton that are ubiquitously present in marine and freshwater environments. Mostly photosynthetic, dinoflagellates provide the basis of aquatic primary production; most taxa are free-living, while some can form symbiotic and parasitic associations with other organisms. However, knowledge of the molecular mechanisms that underpin the adaptation of these organisms to diverse ecological niches is limited by the scarce availability of genomic data, partly due to their large genome sizes estimated up to 250 Gbp. Currently available dinoflagellate genome data are restricted to Symbiodiniaceae (particularly symbionts of reef-building corals) and parasitic lineages, from taxa that have smaller genome size ranges, while genomic information from more diverse free-living species is still lacking. RESULTS Here, we present two draft diploid genome assemblies of the free-living dinoflagellate Polarella glacialis, isolated from the Arctic and Antarctica. We found that about 68% of the genomes are composed of repetitive sequence, with long terminal repeats likely contributing to intra-species structural divergence and distinct genome sizes (3.0 and 2.7 Gbp). For each genome, guided using full-length transcriptome data, we predicted > 50,000 high-quality protein-coding genes, of which ~40% are in unidirectional gene clusters and ~25% comprise single exons. Multi-genome comparison unveiled genes specific to P. glacialis and a common, putatively bacterial origin of ice-binding domains in cold-adapted dinoflagellates. CONCLUSIONS Our results elucidate how selection acts within the context of a complex genome structure to facilitate local adaptation. Because most dinoflagellate genes are constitutively expressed, Polarella glacialis has enhanced transcriptional responses via unidirectional, tandem duplication of single-exon genes that encode functions critical to survival in cold, low-light polar environments. These genomes provide a foundational reference for future research on dinoflagellate evolution.
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Affiliation(s)
- Timothy G Stephens
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia.,Present Address: Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, 08901, USA
| | - Raúl A González-Pech
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia.,Present address: Department of Integrative Biology, University of South Florida, Tampa, FL, 33620, USA
| | - Yuanyuan Cheng
- UQ Genomics Initiative, The University of Queensland, Brisbane, QLD, 4072, Australia.,Present Address: Faculty of Science, School of Life and Environmental Sciences, The University of Sydney, Camperdown, NSW, 2006, Australia
| | - Amin R Mohamed
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Agriculture and Food, Queensland Bioscience Precinct, Brisbane, QLD, 4067, Australia
| | - David W Burt
- UQ Genomics, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Debashish Bhattacharya
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, 08901, USA
| | - Mark A Ragan
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Cheong Xin Chan
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia. .,School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, 4072, Australia. .,Australian Centre for Ecogenomics, The University of Queensland, Brisbane, QLD, 4072, Australia.
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28
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Sunagawa S, Acinas SG, Bork P, Bowler C, Eveillard D, Gorsky G, Guidi L, Iudicone D, Karsenti E, Lombard F, Ogata H, Pesant S, Sullivan MB, Wincker P, de Vargas C. Tara Oceans: towards global ocean ecosystems biology. Nat Rev Microbiol 2020; 18:428-445. [PMID: 32398798 DOI: 10.1038/s41579-020-0364-5] [Citation(s) in RCA: 143] [Impact Index Per Article: 35.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/27/2020] [Indexed: 12/14/2022]
Abstract
A planetary-scale understanding of the ocean ecosystem, particularly in light of climate change, is crucial. Here, we review the work of Tara Oceans, an international, multidisciplinary project to assess the complexity of ocean life across comprehensive taxonomic and spatial scales. Using a modified sailing boat, the team sampled plankton at 210 globally distributed sites at depths down to 1,000 m. We describe publicly available resources of molecular, morphological and environmental data, and discuss how an ecosystems biology approach has expanded our understanding of plankton diversity and ecology in the ocean as a planetary, interconnected ecosystem. These efforts illustrate how global-scale concepts and data can help to integrate biological complexity into models and serve as a baseline for assessing ecosystem changes and the future habitability of our planet in the Anthropocene epoch.
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Affiliation(s)
- Shinichi Sunagawa
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Zürich, Switzerland.
| | - Silvia G Acinas
- Department of Marine Biology and Oceanography, Institute of Marine Sciences-CSIC, Barcelona, Spain
| | - Peer Bork
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany.,Max Delbrück Center for Molecular Medicine, Berlin, Germany.,Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany
| | - Chris Bowler
- Institut de Biologie de l'ENS, Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France.,Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, Paris, France
| | | | - Damien Eveillard
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, Paris, France.,Université de Nantes, CNRS, UMR6004, LS2N, Nantes, France
| | - Gabriel Gorsky
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, Paris, France.,Sorbonne Université, CNRS, Laboratoire d'Océanographie de Villefranche, Villefranche-sur-Mer, France
| | - Lionel Guidi
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, Paris, France.,Sorbonne Université, CNRS, Laboratoire d'Océanographie de Villefranche, Villefranche-sur-Mer, France
| | | | - Eric Karsenti
- Institut de Biologie de l'ENS, Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France.,Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, Paris, France.,Directors' Research, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Fabien Lombard
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, Paris, France.,Sorbonne Université, CNRS, Laboratoire d'Océanographie de Villefranche, Villefranche-sur-Mer, France
| | - Hiroyuki Ogata
- Institute for Chemical Research, Kyoto University, Kyoto, Japan
| | - Stephane Pesant
- PANGAEA, University of Bremen, Bremen, Germany.,MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Matthew B Sullivan
- Department of Microbiology, The Ohio State University, Columbus, OH, USA.,Department of Civil, Environmental and Geodetic Engineering, The Ohio State University, Columbus, OH, USA.,Center for RNA Biology, The Ohio State University, Columbus, OH, USA
| | - Patrick Wincker
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, Paris, France.,Génomique Métabolique, Genoscope, Institut de Biologie Francois Jacob, Commissariat à l'Énergie Atomique, CNRS, Université Evry, Université Paris-Saclay, Evry, France
| | - Colomban de Vargas
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, Paris, France. .,Sorbonne Université and CNRS, UMR 7144 (AD2M), ECOMAP, Station Biologique de Roscoff, Roscoff, France.
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29
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Abstract
Photosynthesis evolved in the ocean more than 2 billion years ago and is now performed by a wide range of evolutionarily distinct organisms, including both prokaryotes and eukaryotes. Our appreciation of their abundance, distributions, and contributions to primary production in the ocean has been increasing since they were first discovered in the seventeenth century and has now been enhanced by data emerging from the Tara Oceans project, which performed a comprehensive worldwide sampling of plankton in the upper layers of the ocean between 2009 and 2013. Largely using recent data from Tara Oceans, here we review the geographic distributions of phytoplankton in the global ocean and their diversity, abundance, and standing stock biomass. We also discuss how omics-based information can be incorporated into studies of photosynthesis in the ocean and show the likely importance of mixotrophs and photosymbionts.
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Affiliation(s)
- Juan José Pierella Karlusich
- Institut de Biologie de l'École Normale Supérieure (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université de Recherche Paris Sciences et Lettres (Université PSL), 75005 Paris, France;
| | - Federico M Ibarbalz
- Institut de Biologie de l'École Normale Supérieure (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université de Recherche Paris Sciences et Lettres (Université PSL), 75005 Paris, France;
| | - Chris Bowler
- Institut de Biologie de l'École Normale Supérieure (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université de Recherche Paris Sciences et Lettres (Université PSL), 75005 Paris, France;
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30
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Esenkulova S, Sutherland BJ, Tabata A, Haigh N, Pearce CM, Miller KM. Comparing metabarcoding and morphological approaches to identify phytoplankton taxa associated with harmful algal blooms. Facets (Ott) 2020. [DOI: 10.1139/facets-2020-0025] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Molecular techniques are expected to be highly useful in detecting taxa causing harmful algal blooms (HABs). This is the first report in Canada evaluating HABs-related species identification using a combination of morphological and molecular approaches. Microscopy, quantitative polymerase chain reaction (qPCR), and metabarcoding with multiple markers (i.e., 16S, 18S-dinoflagellate and 18S-diatom, large subunit (28S) rDNA) were applied on samples ( n = 54) containing suspected harmful algae (e.g., Alexandrium spp., Chattonella sp., Chrysochromulina spp., Dictyocha spp., Heterosigma akashiwo, Protoceratium reticulatum, Pseudochattonella verruculosa, Pseudo-nitzschia spp., Pseudopedinella sp.). Owing to methodology limitations, qPCR result interpretation was limited, although good detectability occurred using previously published assays for Alexandrium tamarense, H. akashiwo, and P. verruculosa. Overall, the multiple-marker metabarcoding results were superior to the morphology-based methods, with the exception of taxa from the silicoflagellate group. The combined results using both 18S markers and the 28S marker together closely corresponded with morphological identification of targeted species, providing the best overall taxonomic coverage and resolution. The most numerous unique taxa were identified using the 18S-dinoflagellate amplicon, and the best resolution to the species level occurred using the 28S amplicon. Molecular techniques are therefore promising for HABs taxa detection but currently depend on deploying multiple markers for metabarcoding.
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Affiliation(s)
- Svetlana Esenkulova
- Pacific Salmon Foundation, #300 1682 West 7th Avenue, Vancouver, BC V6J 4S6, Canada
- Fisheries and Oceans Canada, Pacific Biological Station, Nanaimo, BC V9T 6N7, Canada
| | - Ben J.G. Sutherland
- Fisheries and Oceans Canada, Pacific Biological Station, Nanaimo, BC V9T 6N7, Canada
| | - Amy Tabata
- Fisheries and Oceans Canada, Pacific Biological Station, Nanaimo, BC V9T 6N7, Canada
| | - Nicola Haigh
- Microthalassia Inc., Nanaimo, BC V9T 1T4, Canada
| | - Christopher M. Pearce
- Fisheries and Oceans Canada, Pacific Biological Station, Nanaimo, BC V9T 6N7, Canada
| | - Kristina M. Miller
- Fisheries and Oceans Canada, Pacific Biological Station, Nanaimo, BC V9T 6N7, Canada
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31
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Wu PF, Li DX, Kong LF, Li YY, Zhang H, Xie ZX, Lin L, Wang DZ. The diversity and biogeography of microeukaryotes in the euphotic zone of the northwestern Pacific Ocean. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 698:134289. [PMID: 31514034 DOI: 10.1016/j.scitotenv.2019.134289] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 08/12/2019] [Accepted: 09/03/2019] [Indexed: 06/10/2023]
Abstract
Microeukaryotes are the key ecosystem drivers mediating marine productivity, the food web and biogeochemical cycles. The northwestern Pacific Ocean (NWPO), as one of the world's largest oligotrophic regions, remains largely unexplored regarding diversity and biogeography of microeukaryotes. Here, we investigated the community composition and geographical distribution of microeukaryotes collected from the euphotic zone of three different regions in the NWPO using high-throughput sequencing of the 18S rRNA gene and quantified the contributions of environmental factors on the distributions of microeukaryotes. The relative abundance of different group taxa, except for Ciliophora, presented distinct patterns in each region, and Metazoa and Dinoflagellata dominated the community, contributing approximately half of reads abundance. Spatial and environmental factors explained 66.01% of community variation in the NWPO. Temperature was the most important environmental factor significantly correlated with community structure. Bacterial biomass was also significantly correlated with microeukaryotic distribution, especially for Dinoflagellata and Diatomea. Network analysis showed strong correlations between microeukaryotic groups and free-living bacteria and different bacterial taxa were correlated with specific microeukaryotic groups, indicating that their interactions enabled microeukaryotic groups to adapt to diverse environments. This study provides a first glance at the diversity and geographical distribution of microeukaryotes in the NWPO and sheds light on the biotic and abiotic factors in shaping the microeukaryotic community in the ocean.
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Affiliation(s)
- Peng-Fei Wu
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen, 361005, China
| | - Dong-Xu Li
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen, 361005, China
| | - Ling-Fen Kong
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen, 361005, China
| | - Yuan-Yuan Li
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen, 361005, China
| | - Hao Zhang
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen, 361005, China
| | - Zhang-Xian Xie
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen, 361005, China
| | - Lin Lin
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen, 361005, China
| | - Da-Zhi Wang
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen, 361005, China; Key Laboratory of Marine Ecology & Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.
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32
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Polinski JM, Bucci JP, Gasser M, Bodnar AG. Metabarcoding assessment of prokaryotic and eukaryotic taxa in sediments from Stellwagen Bank National Marine Sanctuary. Sci Rep 2019; 9:14820. [PMID: 31616016 PMCID: PMC6794287 DOI: 10.1038/s41598-019-51341-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 09/27/2019] [Indexed: 12/30/2022] Open
Abstract
Stellwagen Bank National Marine Sanctuary (SBNMS) in the Gulf of Maine is a historic fishing ground renowned for remarkable productivity. Biodiversity conservation is a key management priority for SBNMS and yet data on the diversity of microorganisms, both prokaryotic and eukaryotic, is lacking. This study utilized next generation sequencing to characterize sedimentary communities within SBNMS at three sites over two seasons. Targeting 16S and 18S small subunit (SSU) rRNA genes and fungal Internal Transcribed Spacer (ITS) rDNA sequences, samples contained high diversity at all taxonomic levels and identified 127 phyla, including 115 not previously represented in the SBNMS Management Plan and Environmental Assessment. A majority of the diversity was bacterial, with 59 phyla, but also represented were nine Archaea, 18 Animalia, 14 Chromista, eight Protozoa, two Plantae, and 17 Fungi phyla. Samples from different sites and seasons were dominated by the same high abundance organisms but displayed considerable variation in rare taxa. The levels of biodiversity seen on this small spatial scale suggest that benthic communities of this area support a diverse array of micro- and macro-organisms, and provide a baseline for future studies to assess changes in community structure in response to rapid warming in the Gulf of Maine.
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Affiliation(s)
| | - John P Bucci
- Gloucester Marine Genomics Institute, Inc. Gloucester, Massachusetts, USA.,School of Marine Science and Ocean Engineering, University of New Hampshire, Durham, New Hampshire, USA
| | - Mark Gasser
- Gloucester Marine Genomics Institute, Inc. Gloucester, Massachusetts, USA.,The Johns Hopkins Applied Physics Laboratory, Laurel, Maryland, USA
| | - Andrea G Bodnar
- Gloucester Marine Genomics Institute, Inc. Gloucester, Massachusetts, USA
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33
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Verma A, Kazandjian A, Sarowar C, Harwood DT, Murray JS, Pargmann I, Hoppenrath M, Murray SA. Morphology and Phylogenetics of Benthic Prorocentrum Species (Dinophyceae) from Tropical Northwestern Australia. Toxins (Basel) 2019; 11:toxins11100571. [PMID: 31574958 PMCID: PMC6833055 DOI: 10.3390/toxins11100571] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 09/17/2019] [Accepted: 09/27/2019] [Indexed: 01/29/2023] Open
Abstract
Approximately 70 species of Prorocentrum are known, of which around 30 species are associated with benthic habitats. Some produce okadaic acid (OA), dinophysistoxin (DTX) and their derivatives, which are involved in diarrhetic shellfish poisoning. In this study, we isolated and characterized Prorocentrum concavum and P. malayense from Broome in north Western Australia using light and scanning electron microscopy as well as molecular sequences of large subunit regions of ribosomal DNA, marking the first record of these species from Australian waters. The morphology of the motile cells of P. malayense was similar to P. concavum in the light microscopy, but differed by the smooth thecal surface, the pore pattern and the production of mucous stalk-like structures and a hyaline sheath around the non-motile cells. P. malayense could also be differentiated from other closely related species, P. leve and P. foraminosum, despite the similarity in thecal surface and pore pattern, by its platelet formula and morphologies. We tested the production of OA and DTXs from both species, but found that they did not produce detectable levels of these toxins in the given culturing conditions. This study aids in establishing more effective monitoring of potential harmful algal taxa in Australian waters for aquaculture and recreational purposes.
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Affiliation(s)
- Arjun Verma
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW 2007, Australia.
| | - Aniuska Kazandjian
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW 2007, Australia.
- Laboratorio de Sistemática Molecular, Centro de Biodiversidad Marina, Universidad Simón Bolívar, Caracas 89000, Venezuela.
| | | | - D Tim Harwood
- Seafood Safety Research Programme, Cawthron Institute, Nelson 7010, New Zealand.
| | - J Sam Murray
- Seafood Safety Research Programme, Cawthron Institute, Nelson 7010, New Zealand.
| | - Insa Pargmann
- Institut für Biologie und Umweltwissenschaften, Carl von Ossietzky Universität Oldenburg, D-26129 Oldenburg; Germany.
| | - Mona Hoppenrath
- Institut für Biologie und Umweltwissenschaften, Carl von Ossietzky Universität Oldenburg, D-26129 Oldenburg; Germany.
- Senckenberg am Meer, German Centre for Marine Biodiversity Research (DZMB), D-26382 Wilhelmshaven, Germany.
| | - Shauna A Murray
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW 2007, Australia.
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34
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Verma A, Barua A, Ruvindy R, Savela H, Ajani PA, Murray SA. The Genetic Basis of Toxin Biosynthesis in Dinoflagellates. Microorganisms 2019; 7:E222. [PMID: 31362398 PMCID: PMC6722697 DOI: 10.3390/microorganisms7080222] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2019] [Revised: 07/23/2019] [Accepted: 07/27/2019] [Indexed: 02/07/2023] Open
Abstract
In marine ecosystems, dinoflagellates can become highly abundant and even dominant at times, despite their comparatively slow growth rates. One factor that may play a role in their ecological success is the production of complex secondary metabolite compounds that can have anti-predator, allelopathic, or other toxic effects on marine organisms, and also cause seafood poisoning in humans. Our knowledge about the genes involved in toxin biosynthesis in dinoflagellates is currently limited due to the complex genomic features of these organisms. Most recently, the sequencing of dinoflagellate transcriptomes has provided us with valuable insights into the biosynthesis of polyketide and alkaloid-based toxin molecules in dinoflagellate species. This review synthesizes the recent progress that has been made in understanding the evolution, biosynthetic pathways, and gene regulation in dinoflagellates with the aid of transcriptomic and other molecular genetic tools, and provides a pathway for future studies of dinoflagellates in this exciting omics era.
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Affiliation(s)
- Arjun Verma
- Climate Change Cluster, University of Technology Sydney, Sydney 2007, Australia.
| | - Abanti Barua
- Climate Change Cluster, University of Technology Sydney, Sydney 2007, Australia
- Department of Microbiology, Noakhali Science and Technology University, Chittagong 3814, Bangladesh
| | - Rendy Ruvindy
- Climate Change Cluster, University of Technology Sydney, Sydney 2007, Australia
| | - Henna Savela
- Finnish Environment Institute, Marine Research Centre, 00790 Helsinki, Finland
| | - Penelope A Ajani
- Climate Change Cluster, University of Technology Sydney, Sydney 2007, Australia
| | - Shauna A Murray
- Climate Change Cluster, University of Technology Sydney, Sydney 2007, Australia
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Flegontova O, Flegontov P, Malviya S, Poulain J, de Vargas C, Bowler C, Lukeš J, Horák A. Neobodonids are dominant kinetoplastids in the global ocean. Environ Microbiol 2019; 20:878-889. [PMID: 29266706 DOI: 10.1111/1462-2920.14034] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 12/01/2017] [Accepted: 12/17/2017] [Indexed: 11/29/2022]
Abstract
Kinetoplastid flagellates comprise basal mostly free-living bodonids and derived obligatory parasitic trypanosomatids, which belong to the best-studied protists. Due to their omnipresence in aquatic environments and soil, the bodonids are of ecological significance. Here, we present the first global survey of marine kinetoplastids and compare it with the strikingly different patterns of abundance and diversity in their sister clade, the diplonemids. Based on analysis of 18S rDNA V9 ribotypes obtained from 124 sites sampled during the Tara Oceans expedition, our results show generally low to moderate abundance and diversity of planktonic kinetoplastids. Although we have identified all major kinetoplastid lineages, 98% of kinetoplastid reads are represented by neobodonids, namely specimens of the Neobodo and Rhynchomonas genera, which make up 59% and 18% of all reads, respectively. Most kinetoplastids have small cell size (0.8-5 µm) and tend to be more abundant in the mesopelagic as compared to the euphotic zone. Some of the most abundant operational taxonomic units have distinct geographical distributions, and three novel putatively parasitic neobodonids were identified, along with their potential hosts.
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Affiliation(s)
- Olga Flegontova
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic.,Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Pavel Flegontov
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic.,Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Shruti Malviya
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India.,Ecole Normale Supérieure, PSL Research University, Institut de Biologie de l'Ecole Normale Supérieure (IBENS), CNRS UMR 8197, INSERM U1024, 46 rue d'Ulm, Paris F-75005, France
| | - Julie Poulain
- CEA - GENOSCOPE - Institut François Jacob, 2 rue Gaston Crémieux, 91057 Evry, France.,CNRS, UMR 8030, CP5706, Evry, France.,Université d'Evry, UMR 8030, CP5706, Evry, France
| | - Colomban de Vargas
- Station Biologique de Roscoff, Roscoff, France.,Sorbonne Universités, Paris, France
| | - Chris Bowler
- Ecole Normale Supérieure, PSL Research University, Institut de Biologie de l'Ecole Normale Supérieure (IBENS), CNRS UMR 8197, INSERM U1024, 46 rue d'Ulm, Paris F-75005, France
| | - Julius Lukeš
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic.,Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Aleš Horák
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic.,Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
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36
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Gao Y, Chen Y, Xiong W, Li S, Zhan A. Distribution patterns of dinoflagellate communities along the Songhua River. PeerJ 2019; 7:e6733. [PMID: 30993050 PMCID: PMC6461062 DOI: 10.7717/peerj.6733] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 03/07/2019] [Indexed: 12/04/2022] Open
Abstract
Background Dinoflagellates have the potential to pose severe ecological and economic damages to aquatic ecosystems. It is therefore largely needed to understand the causes and consequences of distribution patterns of dinoflagellate communities in order to manage potential environmental problems. However, a majority of studies have focused on marine ecosystems, while the geographical distribution patterns of dinoflagellate communities and associated determinants in freshwater ecosystems remain unexplored, particularly in running water ecosystems such as rivers and streams. Methods Here we utilized multiple linear regression analysis and combined information on species composition recovered by high-throughput sequencing and spatial and environmental variables to analyze the distribution patterns of dinoflagellate communities along the Songhua River. Results After high-throughput sequencing, a total of 490 operational taxonomic units (OTUs) were assigned to dinoflagellates, covering seven orders, 13 families and 22 genera. Although the sample sites were grouped into three distinctive clusters with significant difference (p < 0.05) in environmental variables, OTUs-based dinoflagellate communities among the three clusters showed no significant difference (p > 0.05). Among all 24 environmental factors, two environmental variables, including NO3-N and total dissolved solids (TDS), were selected as the significantly influential factors (p < 0.05) on the distribution patterns of dinoflagellate communities based on forward selection. The redundancy analysis (RDA) model showed that only a small proportion of community variation (6.1%) could be explained by both environmental (NO3-N and TDS) and dispersal predictors (watercourse distance) along the River. Variance partitioning revealed a larger contribution of local environmental factors (5.85%) than dispersal (0.50%) to the total variation of dinoflagellate communities. Discussion Our findings indicated that in addition to the two quantifiable processes in this study (species sorting and dispersal), more unquantifiable stochastic processes such as temporal extinction and colonization events due to rainfall may be responsible for the observed geographical distribution of the dinoflagellate community along the Songhua River. Results obtained in this study suggested that deeper investigations covering different seasons are needed to understand the causes and consequences of geographical distribution patterns of dinoflagellate biodiversity in river ecosystems.
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Affiliation(s)
- Yangchun Gao
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
| | - Yiyong Chen
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
| | - Wei Xiong
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Shiguo Li
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
| | - Aibin Zhan
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
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37
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Prabowo DA, Agusti S. Free-living dinoflagellates of the central Red Sea, Saudi Arabia: Variability, new records and potentially harmful species. MARINE POLLUTION BULLETIN 2019; 141:629-648. [PMID: 30955778 DOI: 10.1016/j.marpolbul.2019.03.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 03/06/2019] [Indexed: 06/09/2023]
Abstract
The diversity of free-living dinoflagellates in the coastal areas of the central Red Sea, Saudi Arabia, was studied from April 2016 to March 2017. A total of 106 dinoflagellates belonging to 36 genera, 20 families and 7 orders were identified and characterized using light microscopy. Of these, 47 taxa were potentially harmful, and 60 taxa were recorded for the first time from the Red Sea. The unexpectedly high species diversity, including new records, was due to the benthic species. The monthly variability of planktonic species records exhibited negative correlations with temperature and salinity, although in most cases, the links between them were insignificant. Subsequently, the dinoflagellates checklist for the entire Red Sea was updated and showed that there were currently 395 taxa and 66 genera. The results of this study provide a solid foundation for future studies of dinoflagellate biodiversity in the Red Sea, particularly for benthic and harmful species.
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Affiliation(s)
- Danang Ambar Prabowo
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Jeddah 23955, Saudi Arabia.
| | - Susana Agusti
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Jeddah 23955, Saudi Arabia
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38
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Ramond P, Sourisseau M, Simon N, Romac S, Schmitt S, Rigaut-Jalabert F, Henry N, de Vargas C, Siano R. Coupling between taxonomic and functional diversity in protistan coastal communities. Environ Microbiol 2019; 21:730-749. [PMID: 30672084 DOI: 10.1111/1462-2920.14537] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 01/19/2019] [Indexed: 01/11/2023]
Abstract
The study of protistan functional diversity is crucial to understand the dynamics of oceanic ecological processes. We combined the metabarcoding data of various coastal ecosystems and a newly developed trait-based approach to study the link between taxonomic and functional diversity across marine protistan communities of different size-classes. Environmental DNA was extracted and the V4 18S rDNA genomic region was amplified and sequenced. In parallel, we tried to annotate the operational taxonomic units (OTUs) from our metabarcoding dataset to 30 biological traits using published and accessible information on protists. We then developed a method to study trait correlations across protists (i.e. trade-offs) in order to build the best functional groups. Based on the annotated OTUs and our functional groups, we demonstrated that the functional diversity of marine protist communities varied in parallel with their taxonomic diversity. The coupling between functional and taxonomic diversity was conserved across different protist size classes. However, the smallest size-fraction was characterized by wider taxonomic and functional groups diversity, corroborating the idea that nanoplankton and picoplankton are part of a more stable ecological background on which larger protists and metazoans might develop.
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Affiliation(s)
- Pierre Ramond
- IFREMER, Dyneco Pelagos, BP 70, 29280 Plouzané, France.,Sorbonne University, CNRS, Station Biologique de Roscoff, UMR7144, ECOMAP, 29688 Roscoff, France
| | | | - Nathalie Simon
- Sorbonne University, CNRS, Station Biologique de Roscoff, UMR7144, ECOMAP, 29688 Roscoff, France
| | - Sarah Romac
- Sorbonne University, CNRS, Station Biologique de Roscoff, UMR7144, ECOMAP, 29688 Roscoff, France.,Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/GOSEE, 3 rue Michel-Ange, 75016 Paris, France
| | | | - Fabienne Rigaut-Jalabert
- Sorbonne Université, CNRS - FR2424, Station Biologique de Roscoff, Place Georges Teissier, 29688 Roscoff, France
| | - Nicolas Henry
- Sorbonne University, CNRS, Station Biologique de Roscoff, UMR7144, ECOMAP, 29688 Roscoff, France.,Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/GOSEE, 3 rue Michel-Ange, 75016 Paris, France
| | - Colomban de Vargas
- Sorbonne University, CNRS, Station Biologique de Roscoff, UMR7144, ECOMAP, 29688 Roscoff, France.,Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/GOSEE, 3 rue Michel-Ange, 75016 Paris, France
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39
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Wang H, Zhang B, Song X, Jian X, Tang C, Campbell DA, Lin Q, Li G. High antioxidant capability interacts with respiration to mediate two Alexandrium species growth exploitation of photoperiods and light intensities. HARMFUL ALGAE 2019; 82:26-34. [PMID: 30928008 DOI: 10.1016/j.hal.2018.12.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 12/26/2018] [Accepted: 12/26/2018] [Indexed: 06/09/2023]
Abstract
Light drives phytoplankton photosynthesis, so phytoplankton in their living habitats must exploit variable light levels and exposure durations, depending upon seasons, latitudes, depths and mixing events. Comparative growth, physiology and biochemical compositions were explored for the small Alexnadrium minutum (˜40 μm3 biovolume) and large Alexandrium catenella (˜9300 μm3 biovolume), globally wide spread coastal toxic red tide dinoflagellates, responding to a matrix of photoperiods (Light:Dark, 8:16, 16:8 and 24:0) and growth light irradiances. Smaller A. minutum grew faster under shorter photoperiods across growth light levels, while larger A. catenella grew fastest under longer photoperiods at the lowest applied light level. Photosystem II function responded largely to the instantaneous growth light level across photoperiod lengths, while the cell biovolume-based respiration, antioxidant capacity as well as cell composition responded more to photoperiod duration than to light level. These complex photophysiological responses resolved into linear correlations between growth rate versus cellular antioxidant activity and versus dark respiration, indicating that respiration energizes cellular antioxidant systems to benefit the growth of the cells. These results show the growth responses of Alexandrium species to light levels across photoperiods vary with species, and possibly with cell size. Together with previous results this puts a note of caution on meta-analytical extrapolations of physiological responses to light intensity derived from studies applying different photoperiods to different taxa, because different taxa show differential, even opposite growth responses to photoperiods and light intensities.
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Affiliation(s)
- Hui Wang
- Department of Biology, College of Sciences, Shantou University, Shantou 515063, Guangdong, China; STU-UNIVPM Joint Algal Research Center, College of Sciences, Shantou University, Shantou 515063, Guangdong, China
| | - Bowen Zhang
- Department of Biology, College of Sciences, Shantou University, Shantou 515063, Guangdong, China; STU-UNIVPM Joint Algal Research Center, College of Sciences, Shantou University, Shantou 515063, Guangdong, China
| | - Xingyu Song
- Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Xiaohui Jian
- Department of Biology, College of Sciences, Shantou University, Shantou 515063, Guangdong, China
| | - Chengxi Tang
- Department of Biology, College of Sciences, Shantou University, Shantou 515063, Guangdong, China
| | - Douglas A Campbell
- Department of Biology, Mount Allison University, Sackville NB, E4L 1G7, Canada
| | - Qiang Lin
- Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Gang Li
- Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510530, China.
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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.
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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
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41
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Klinger CM, Paoli L, Newby RJ, Wang MYW, Carroll HD, Leblond JD, Howe CJ, Dacks JB, Bowler C, Cahoon AB, Dorrell RG, Richardson E. Plastid Transcript Editing across Dinoflagellate Lineages Shows Lineage-Specific Application but Conserved Trends. Genome Biol Evol 2018; 10:1019-1038. [PMID: 29617800 PMCID: PMC5888634 DOI: 10.1093/gbe/evy057] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/09/2018] [Indexed: 11/24/2022] Open
Abstract
Dinoflagellates are a group of unicellular protists with immense ecological and evolutionary significance and cell biological diversity. Of the photosynthetic dinoflagellates, the majority possess a plastid containing the pigment peridinin, whereas some lineages have replaced this plastid by serial endosymbiosis with plastids of distinct evolutionary affiliations, including a fucoxanthin pigment-containing plastid of haptophyte origin. Previous studies have described the presence of widespread substitutional RNA editing in peridinin and fucoxanthin plastid genes. Because reports of this process have been limited to manual assessment of individual lineages, global trends concerning this RNA editing and its effect on the biological function of the plastid are largely unknown. Using novel bioinformatic methods, we examine the dynamics and evolution of RNA editing over a large multispecies data set of dinoflagellates, including novel sequence data from the peridinin dinoflagellate Pyrocystis lunula and the fucoxanthin dinoflagellate Karenia mikimotoi. We demonstrate that while most individual RNA editing events in dinoflagellate plastids are restricted to single species, global patterns, and functional consequences of editing are broadly conserved. We find that editing is biased toward specific codon positions and regions of genes, and generally corrects otherwise deleterious changes in the genome prior to translation, though this effect is more prevalent in peridinin than fucoxanthin lineages. Our results support a model for promiscuous editing application subsequently shaped by purifying selection, and suggest the presence of an underlying editing mechanism transferred from the peridinin-containing ancestor into fucoxanthin plastids postendosymbiosis, with remarkably conserved functional consequences in the new lineage.
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Affiliation(s)
- Christen M Klinger
- Department of Cell Biology, University of Alberta, Edmonton, Alberta, Canada
| | - Lucas Paoli
- Department of Cell Biology, University of Alberta, Edmonton, Alberta, Canada.,Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL Research University, Paris, France
| | - Robert J Newby
- Department of Biology, Middle Tennessee State University
| | - Matthew Yu-Wei Wang
- Center for Computational Science and Department of Computer Science, Columbus State University, Columbus, GA 31907
| | - Hyrum D Carroll
- Center for Computational Science and Department of Computer Science, Columbus State University, Columbus, GA 31907
| | | | | | - Joel B Dacks
- Department of Cell Biology, University of Alberta, Edmonton, Alberta, Canada
| | - Chris Bowler
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL Research University, Paris, France
| | - Aubery Bruce Cahoon
- Department of Natural Sciences, The University of Virginia's College at Wise
| | - Richard G Dorrell
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL Research University, Paris, France
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42
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Meng A, Marchet C, Corre E, Peterlongo P, Alberti A, Da Silva C, Wincker P, Pelletier E, Probert I, Decelle J, Le Crom S, Not F, Bittner L. A de novo approach to disentangle partner identity and function in holobiont systems. MICROBIOME 2018; 6:105. [PMID: 29885666 PMCID: PMC5994019 DOI: 10.1186/s40168-018-0481-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 05/13/2018] [Indexed: 05/27/2023]
Abstract
BACKGROUND Study of meta-transcriptomic datasets involving non-model organisms represents bioinformatic challenges. The production of chimeric sequences and our inability to distinguish the taxonomic origins of the sequences produced are inherent and recurrent difficulties in de novo assembly analyses. As the study of holobiont meta-transcriptomes is affected by challenges invoked above, we propose an innovative bioinformatic approach to tackle such difficulties and tested it on marine models as a proof of concept. RESULTS We considered three holobiont models, of which two transcriptomes were previously published and a yet unpublished transcriptome, to analyze and sort their raw reads using Short Read Connector, a k-mer based similarity method. Before assembly, we thus defined four distinct categories for each holobiont meta-transcriptome: host reads, symbiont reads, shared reads, and unassigned reads. Afterwards, we observed that independent de novo assemblies for each category led to a diminution of the number of chimeras compared to classical assembly methods. Moreover, the separation of each partner's transcriptome offered the independent and comparative exploration of their functional diversity in the holobiont. Finally, our strategy allowed to propose new functional annotations for two well-studied holobionts (a Cnidaria-Dinophyta, a Porifera-Bacteria) and a first meta-transcriptome from a planktonic Radiolaria-Dinophyta system forming widespread symbiotic association for which our knowledge is considerably limited. CONCLUSIONS In contrast to classical assembly approaches, our bioinformatic strategy generates less de novo assembled chimera and allows biologists to study separately host and symbiont data from a holobiont mixture. The pre-assembly separation of reads using an efficient tool as Short Read Connector is an effective way to tackle meta-transcriptomic challenges and offers bright perpectives to study holobiont systems composed of either well-studied or poorly characterized symbiotic lineages and ultimately expand our knowledge about these associations.
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Affiliation(s)
- Arnaud Meng
- Sorbonne Université, Univ Antilles, CNRS, Evolution Paris Seine - Institut de Biologie Paris Seine (EPS - IBPS), F-75005 Paris, France
| | - Camille Marchet
- Univ Rennes, CNRS, Inria, IRISA - UMR 6074, F-35000 Rennes, France
| | - Erwan Corre
- Sorbonne Universités, CNRS - FR2424, ABiMS, Station biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France
| | | | - Adriana Alberti
- Institut de biologie François Jacob, GENOSCOPE, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Corinne Da Silva
- Institut de biologie François Jacob, GENOSCOPE, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Patrick Wincker
- Institut de biologie François Jacob, GENOSCOPE, 2 rue Gaston Crémieux, 91057 Evry, France
- UMR8030, CNRS, Evry, France
| | - Eric Pelletier
- Institut de biologie François Jacob, GENOSCOPE, 2 rue Gaston Crémieux, 91057 Evry, France
- UMR8030, CNRS, Evry, France
| | - Ian Probert
- Sorbonne Université, CNRS - FR2424, Roscoff Culture Collection, Station Biologique de Roscoff, Place Georges Teissier, 29682 Roscoff, France
| | - Johan Decelle
- Helmholtz Centre for Environmental Research – UFZ, Department of Isotope Biogeochemistry, Permoserstraße 15, 04318 Leipzig, Germany
| | - Stéphane Le Crom
- Sorbonne Université, Univ Antilles, CNRS, Evolution Paris Seine - Institut de Biologie Paris Seine (EPS - IBPS), F-75005 Paris, France
| | - Fabrice Not
- Sorbonne Université, CNRS - UMR7144 - Ecology of Marine Plankton Group, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France
| | - Lucie Bittner
- Sorbonne Université, Univ Antilles, CNRS, Evolution Paris Seine - Institut de Biologie Paris Seine (EPS - IBPS), F-75005 Paris, France
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43
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Sze Y, Miranda LN, Sin TM, Huang D. Characterising planktonic dinoflagellate diversity in Singapore using DNA metabarcoding. METABARCODING AND METAGENOMICS 2018. [DOI: 10.3897/mbmg.2.25136] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Dinoflagellates are traditionally identified morphologically using microscopy, which is a time-consuming and labour-intensive process. Hence, we explored DNA metabarcoding using high-throughput sequencing as a more efficient way to study planktonic dinoflagellate diversity in Singapore’s waters. From 29 minimally pre-sorted water samples collected at four locations in western Singapore, DNA was extracted, amplified and sequenced for a 313-bp fragment of the V4–V5 region in the 18S ribosomal RNA gene. Two sequencing runs generated 2,847,170 assembled paired-end reads, corresponding to 573,176 unique sequences. Sequences were clustered at 97% similarity and analysed with stringent thresholds (≥150 bp, ≥20 reads, ≥95% match to dinoflagellates), recovering 28 dinoflagellate taxa. Dinoflagellate diversity captured includes parasitic and symbiotic groups which are difficult to identify morphologically. Richness is similar between the inner and outer West Johor Strait, but variations in community structure are apparent, likely driven by environmental differences. None of the taxa detected in a recent phytoplankton bloom along the West Johor Strait have been recovered in our samples, suggesting that background communities are distinct from bloom communities. The voluminous data obtained in this study contribute baseline information for Singapore’s phytoplankton communities and prompt future research and monitoring to adopt the approach established here.
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44
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Meng A, Corre E, Probert I, Gutierrez-Rodriguez A, Siano R, Annamale A, Alberti A, Da Silva C, Wincker P, Le Crom S, Not F, Bittner L. Analysis of the genomic basis of functional diversity in dinoflagellates using a transcriptome-based sequence similarity network. Mol Ecol 2018; 27:2365-2380. [PMID: 29624751 DOI: 10.1111/mec.14579] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 02/23/2018] [Accepted: 03/21/2018] [Indexed: 02/06/2023]
Abstract
Dinoflagellates are one of the most abundant and functionally diverse groups of eukaryotes. Despite an overall scarcity of genomic information for dinoflagellates, constantly emerging high-throughput sequencing resources can be used to characterize and compare these organisms. We assembled de novo and processed 46 dinoflagellate transcriptomes and used a sequence similarity network (SSN) to compare the underlying genomic basis of functional features within the group. This approach constitutes the most comprehensive picture to date of the genomic potential of dinoflagellates. A core-predicted proteome composed of 252 connected components (CCs) of putative conserved protein domains (pCDs) was identified. Of these, 206 were novel and 16 lacked any functional annotation in public databases. Integration of functional information in our network analyses allowed investigation of pCDs specifically associated with functional traits. With respect to toxicity, sequences homologous to those of proteins found in species with toxicity potential (e.g., sxtA4 and sxtG) were not specific to known toxin-producing species. Although not fully specific to symbiosis, the most represented functions associated with proteins involved in the symbiotic trait were related to membrane processes and ion transport. Overall, our SSN approach led to identification of 45,207 and 90,794 specific and constitutive pCDs of, respectively, the toxic and symbiotic species represented in our analyses. Of these, 56% and 57%, respectively (i.e., 25,393 and 52,193 pCDs), completely lacked annotation in public databases. This stresses the extent of our lack of knowledge, while emphasizing the potential of SSNs to identify candidate pCDs for further functional genomic characterization.
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Affiliation(s)
- Arnaud Meng
- Sorbonne Universités, UPMC Univ Paris 06, Univ Antilles Guyane, Univ Nice Sophia Antipolis, CNRS, Evolution Paris Seine - Institut de Biologie Paris Seine (EPS - IBPS), Paris, France
| | - Erwan Corre
- CNRS, UPMC, FR2424, ABiMS, Station Biologique, Roscoff, France
| | - Ian Probert
- UPMC-CNRS, FR2424, Roscoff Culture Collection, Station Biologique de Roscoff, Place Georges Teissier, Roscoff, France
| | | | - Raffaele Siano
- Ifremer - Centre de Brest, DYNECO PELAGOS, Plouzané, France
| | - Anita Annamale
- CEA - Institut de Génomique, GENOSCOPE, Evry, France.,CNRS, UMR8030, Evry, France.,Université d'Evry Val d'Essonne, Evry, France
| | - Adriana Alberti
- CEA - Institut de Génomique, GENOSCOPE, Evry, France.,CNRS, UMR8030, Evry, France.,Université d'Evry Val d'Essonne, Evry, France
| | - Corinne Da Silva
- CEA - Institut de Génomique, GENOSCOPE, Evry, France.,CNRS, UMR8030, Evry, France.,Université d'Evry Val d'Essonne, Evry, France
| | - Patrick Wincker
- CEA - Institut de Génomique, GENOSCOPE, Evry, France.,CNRS, UMR8030, Evry, France.,Université d'Evry Val d'Essonne, Evry, France
| | - Stéphane Le Crom
- Sorbonne Universités, UPMC Univ Paris 06, Univ Antilles Guyane, Univ Nice Sophia Antipolis, CNRS, Evolution Paris Seine - Institut de Biologie Paris Seine (EPS - IBPS), Paris, France
| | - Fabrice Not
- CNRS, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, Roscoff, France
| | - Lucie Bittner
- Sorbonne Universités, UPMC Univ Paris 06, Univ Antilles Guyane, Univ Nice Sophia Antipolis, CNRS, Evolution Paris Seine - Institut de Biologie Paris Seine (EPS - IBPS), Paris, France
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45
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Mordret S, Piredda R, Vaulot D, Montresor M, Kooistra WHCF, Sarno D. dinoref: A curated dinoflagellate (Dinophyceae) reference database for the 18S rRNA gene. Mol Ecol Resour 2018; 18:974-987. [PMID: 29603631 DOI: 10.1111/1755-0998.12781] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 02/15/2018] [Accepted: 02/24/2018] [Indexed: 01/28/2023]
Abstract
Dinoflagellates are a heterogeneous group of protists present in all aquatic ecosystems where they occupy various ecological niches. They play a major role as primary producers, but many species are mixotrophic or heterotrophic. Environmental metabarcoding based on high-throughput sequencing is increasingly applied to assess diversity and abundance of planktonic organisms, and reference databases are definitely needed to taxonomically assign the huge number of sequences. We provide an updated 18S rRNA reference database of dinoflagellates: dinoref. Sequences were downloaded from genbank and filtered based on stringent quality criteria. All sequences were taxonomically curated, classified taking into account classical morphotaxonomic studies and molecular phylogenies, and linked to a series of metadata. dinoref includes 1,671 sequences representing 149 genera and 422 species. The taxonomic assignation of 468 sequences was revised. The largest number of sequences belongs to Gonyaulacales and Suessiales that include toxic and symbiotic species. dinoref provides an opportunity to test the level of taxonomic resolution of different 18S barcode markers based on a large number of sequences and species. As an example, when only the V4 region is considered, 374 of the 422 species included in dinoref can still be unambiguously identified. Clustering the V4 sequences at 98% similarity, a threshold that is commonly applied in metabarcoding studies, resulted in a considerable underestimation of species diversity.
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Affiliation(s)
- Solenn Mordret
- Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Roberta Piredda
- Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Daniel Vaulot
- Sorbonne Université, CNRS, UMR Adaptation et Diversité en Milieu Marin, Station Biologique, Roscoff, France
| | - Marina Montresor
- Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Naples, Italy
| | | | - Diana Sarno
- Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Naples, Italy
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46
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Vader A, Laughinghouse HD, Griffiths C, Jakobsen KS, Gabrielsen TM. Proton-pumping rhodopsins are abundantly expressed by microbial eukaryotes in a high-Arctic fjord. Environ Microbiol 2018; 20:890-902. [PMID: 29266690 DOI: 10.1111/1462-2920.14035] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2017] [Revised: 11/21/2017] [Accepted: 12/18/2017] [Indexed: 01/07/2023]
Abstract
Proton-pumping rhodopsins provide an alternative pathway to photosynthesis by which solar energy can enter the marine food web. Rhodopsin genes are widely found in marine bacteria, also in the Arctic, and were recently reported from several eukaryotic lineages. So far, little is known about rhodopsin expression in Arctic eukaryotes. In this study, we used metatranscriptomics and 18S rDNA tag sequencing to examine the mid-summer function and composition of marine protists (size 0.45-10 µm) in the high-Arctic Billefjorden (Spitsbergen), especially focussing on the expression of microbial proton-pumping rhodopsins. Rhodopsin transcripts were highly abundant, at a level similar to that of genes involved in photosynthesis. Phylogenetic analyses placed the environmental rhodopsins within disparate eukaryotic lineages, including dinoflagellates, stramenopiles, haptophytes and cryptophytes. Sequence comparison indicated the presence of several functional types, including xanthorhodopsins and a eukaryotic clade of proteorhodopsin. Transcripts belonging to the proteorhodopsin clade were also abundant in published metatranscriptomes from other oceanic regions, suggesting a global distribution. The diversity and abundance of rhodopsins show that these light-driven proton pumps play an important role in Arctic microbial eukaryotes. Understanding this role is imperative to predicting the future of the Arctic marine ecosystem faced by a changing light climate due to diminishing sea-ice.
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Affiliation(s)
- Anna Vader
- University Centre in Svalbard, Longyearbyen, Norway
| | | | | | - Kjetill S Jakobsen
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis, University of Oslo, Norway
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47
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Tan S, Liu H. Unravel the hidden protistan diversity: application of blocking primers to suppress PCR amplification of metazoan DNA. Appl Microbiol Biotechnol 2017; 102:389-401. [PMID: 29080999 DOI: 10.1007/s00253-017-8565-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Revised: 08/08/2017] [Accepted: 09/28/2017] [Indexed: 11/28/2022]
Abstract
Planktonic protists, including both autotroph and heterotroph, have been recognized as a major contributor to primary production and consumers of bacteria, archaea and picophytoplankton. However, the understanding of protistan diversity is typically impeded by the large amount of metazoans when employing universal primers to environmental samples. In this study, we developed 3 blocking primers to inhibit the amplification of metazoan DNA in PCR. First, we optimized the design and concentration of blocking primers by using 2 metazoans and 3 protists in quantitative PCR. No significant difference (q > 0.05) was found in protistan community structure at phylum, family or OTU levels and genetic diversity between samples amplified with and without adding blocking primers, indicating that the blocking primer does not alter the composition of protistan community. An application to samples with a high abundance of metazoans showed that the blocking primer can reduce 42.1-72.4% of metazoan sequences, resulting the retrieval of a higher protistan richness and diversity. The use of the blocking primer helped to identify protistan community composition from a large size fraction, which is usually dominated by metazoans. Protistan community from the small (0.2-10 μm) and large (> 10 μm) size fractions exhibited a low similarity of 36.6% and shared 14.7% OTUs. About 63.8% of the OTUs were unique to the large fraction. Species from groups, such as Lepidodinium, Warnowia, Kareniaceae, Torodiniales, Phaeocystis, Chrysochromulina and Chrysophyceae, were enriched in the large fraction, indicating that they could be largely underestimated in studies that exclude the large-sized cells. Blocking primers are a promising tool to increase the efficiency for the characterization of protistan diversity in aquatic planktonic ecosystems.
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Affiliation(s)
- Shangjin Tan
- Division of Life Science, The Hong Kong University of Science and Technology, CYT5004, Clear Water Bay, Kowloon, Hong Kong, SAR, China
| | - Hongbin Liu
- Division of Life Science, The Hong Kong University of Science and Technology, CYT5004, Clear Water Bay, Kowloon, Hong Kong, SAR, China.
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48
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Reñé A, Alacid E, Ferrera I, Garcés E. Evolutionary Trends of Perkinsozoa (Alveolata) Characters Based on Observations of Two New Genera of Parasitoids of dinoflagellates, Dinovorax gen. nov. and Snorkelia gen. nov. Front Microbiol 2017; 8:1594. [PMID: 28970818 PMCID: PMC5609580 DOI: 10.3389/fmicb.2017.01594] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 08/04/2017] [Indexed: 11/13/2022] Open
Abstract
Parasites are one of the ecologically most relevant groups of marine food webs, but their taxonomic and biological complexity hampers the assessment of their diversity and evolutionary trends. Moreover, the within-host processes that govern parasitoid infection, development and reproduction are often unknown. In this study, we describe a new species of a perkinsozoan endoparasitoid that infects the toxic dinoflagellate Dinophysis sacculus, by including observations of its morphology, ultrastructure, life-cycle development and phylogeny. The SSU rDNA sequence and main morphological features were also obtained for a second parasitoid species infecting the bloom-forming dinoflagellate Levanderina fissa. Phylogenetic analyses including the sequences obtained show that all known Perkinsozoa species infecting dinoflagellates cluster together. However, sequences of Parvilucifera prorocentri and those obtained in this study cluster at the base of the clade, while the rest of Parvilucifera representatives form a separated highly-supported cluster. These results, together with differing morphological characters like the formation of a germ-tube, the presence of trichocysts, or the heterochromatin presence in zoospores nucleus justify the erection of Dinovorax pyriformis gen. nov. et sp. nov., and Snorkelia prorocentri gen. nov. et comb. nov. (=Parvilucifera prorocentri). The morphological features and phylogenetic position of these parasitoids represent ancestral characters for the Perkinsozoa phylum, and also for Dinozoa clade, allowing the inference of the evolutionary framework of these Alveolata members.
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Affiliation(s)
- Albert Reñé
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar (CSIC)Barcelona, Spain
| | - Elisabet Alacid
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar (CSIC)Barcelona, Spain
| | - Isabel Ferrera
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar (CSIC)Barcelona, Spain
| | - Esther Garcés
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar (CSIC)Barcelona, Spain
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49
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Smith KF, Biessy L, Argyle PA, Trnski T, Halafihi T, Rhodes LL. Molecular Identification of Gambierdiscus and Fukuyoa (Dinophyceae) from Environmental Samples. Mar Drugs 2017; 15:md15080243. [PMID: 28767092 PMCID: PMC5577598 DOI: 10.3390/md15080243] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Revised: 07/11/2017] [Accepted: 07/28/2017] [Indexed: 12/03/2022] Open
Abstract
Ciguatera Fish Poisoning (CFP) is increasing across the Pacific and the distribution of the causative dinoflagellates appears to be expanding. Subtle differences in thecal plate morphology are used to distinguish dinoflagellate species, which are difficult to determine using light microscopy. For these reasons we sought to develop a Quantitative PCR assay that would detect all species from both Gambierdiscus and Fukuyoa genera in order to rapidly screen environmental samples for potentially toxic species. Additionally, a specific assay for F. paulensis was developed as this species is of concern in New Zealand coastal waters. Using the assays we analyzed 31 samples from three locations around New Zealand and the Kingdom of Tonga. Fourteen samples in total were positive for Gambierdiscus/Fukuyoa and two samples were also positive using the F. paulensis assay. Samples from the Kermadec Islands were further characterized using high-throughput sequencing metabarcoding. The majority of reads corresponded to Gambierdiscus species with three species identified at all sites (G. australes, G. honu and G. polynesiensis). This is the first confirmed identification of G. polynesiensis, a known ciguatoxin producer, in New Zealand waters. Other known toxin-producing genera were also detected, included Alexandrium, Amphidinium, Azadinium, Dinophysis, Ostreopsis, and Prorocentrum.
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Affiliation(s)
- Kirsty F Smith
- Coastal & Freshwater Group, Cawthron Institute, Private Bag 2, 98 Halifax Street East, Nelson 7042, New Zealand.
| | - Laura Biessy
- Coastal & Freshwater Group, Cawthron Institute, Private Bag 2, 98 Halifax Street East, Nelson 7042, New Zealand.
| | - Phoebe A Argyle
- Coastal & Freshwater Group, Cawthron Institute, Private Bag 2, 98 Halifax Street East, Nelson 7042, New Zealand.
- School of Biological Sciences, University of Canterbury, Private Bag 4800, 20 Kirkwood Avenue, Christchurch 8041, New Zealand.
| | - Tom Trnski
- Auckland War Memorial Museum, Private Bag 92018, Victoria Street West, Auckland 1142, New Zealand.
| | | | - Lesley L Rhodes
- Coastal & Freshwater Group, Cawthron Institute, Private Bag 2, 98 Halifax Street East, Nelson 7042, New Zealand.
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50
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Price DC, Bhattacharya D. Robust Dinoflagellata phylogeny inferred from public transcriptome databases. JOURNAL OF PHYCOLOGY 2017; 53:725-729. [PMID: 28273342 DOI: 10.1111/jpy.12529] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Accepted: 02/24/2017] [Indexed: 05/13/2023]
Abstract
Dinoflagellates are dominant members of the plankton and play key roles in ocean ecosystems as primary producers, predators, parasites, coral photobionts, and causative agents of algal blooms that produce toxins harmful to humans and commercial fisheries. These unicellular protists exhibit remarkable trophic and morphological diversity and include species with some of the largest reported nuclear genomes. Despite their high ecological and economic importance, comprehensive genome (or transcriptome) based dinoflagellate trees of life are few in number. To address this issue, we used recently generated public sequencing data, including from the Moore Microbial Eukaryote Transcriptome Sequencing Project, to identify dinoflagellate-specific ortholog groups. These orthologs were combined to create a broadly sampled and highly resolved phylogeny of dinoflagellates. Our results emphasize the scope and utility of public sequencing databases in creating broad and robust phylogenies for large and complex taxonomic lineages, while also providing unique insights into the evolution of thecate dinoflagellates.
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Affiliation(s)
- Dana C Price
- Department of Plant Biology, Rutgers University, New Brunswick, New Jersey, 08901, USA
| | - Debashish Bhattacharya
- Department of Ecology, Evolution and Natural Resources, Rutgers University, New Brunswick, New Jersey, 08901, USA
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