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Yarimizu K, Mardones JI, Paredes-Mella J, Perera IU, Fujiyoshi S, Fuenzalida G, Acuña JJ, Ruiz-Gil T, Campos M, Rilling JI, Calabrano Miranda P, Vilugrón J, Espinoza-González O, Guzmán L, Nagai S, Jorquera MA, Maruyama F. Identification of bacteria in potential mutualism with toxic Alexandrium catenella in Chilean Patagonian fjords by in vitro and field monitoring. PLoS One 2024; 19:e0301343. [PMID: 38833478 PMCID: PMC11149857 DOI: 10.1371/journal.pone.0301343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 03/13/2024] [Indexed: 06/06/2024] Open
Abstract
The dinoflagellate Alexandrium catenella is a well-known paralytic shellfish toxin producer that forms harmful algal blooms, repeatedly causing damage to Chilean coastal waters. The causes and behavior of algal blooms are complex and vary across different regions. As bacterial interactions with algal species are increasingly recognized as a key factor driving algal blooms, the present study identifies several bacterial candidates potentially associated with Chilean Alexandrium catenella. This research narrowed down the selection of bacteria from the Chilean A. catenella culture using antibiotic treatment and 16S rRNA metabarcoding analysis. Subsequently, seawater from two Chilean coastal stations, Isla Julia and Isla San Pedro, was monitored for two years to detect Alexandrium species and the selected bacteria, utilizing 16S and 18S rRNA gene metabarcoding analyses. The results suggested a potential association between Alexandrium species and Spongiibacteraceae at both stations. The proposed candidate bacteria within the Spongiibacteraceae family, potentially engaging in mutualistic relationships with Alexandrium species, included the genus of BD1-7 clade, Spongiibbacter, and Zhongshania.
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Affiliation(s)
- Kyoko Yarimizu
- Microbial Genomics and Ecology, The IDEC Institute, Hiroshima University, Higashi-Hiroshima City, Hiroshima, Japan
| | - Jorge I. Mardones
- Centro de Estudios de Algas Nocivas (CREAN), Instituto de Fomento Pesquero (IFOP), Puerto Montt, Chile
- Centro de Investigación en Recursos Naturales y Sustentabilidad (CIRENYS), Universidad Bernardo O’Higgins, Santiago, Chile
| | - Javier Paredes-Mella
- Centro de Estudios de Algas Nocivas (CREAN), Instituto de Fomento Pesquero (IFOP), Puerto Montt, Chile
| | - Ishara Uhanie Perera
- Microbial Genomics and Ecology, The IDEC Institute, Hiroshima University, Higashi-Hiroshima City, Hiroshima, Japan
| | - So Fujiyoshi
- Microbial Genomics and Ecology, The IDEC Institute, Hiroshima University, Higashi-Hiroshima City, Hiroshima, Japan
| | - Gonzalo Fuenzalida
- Centro de Estudios de Algas Nocivas (CREAN), Instituto de Fomento Pesquero (IFOP), Puerto Montt, Chile
| | - Jacquelinne J. Acuña
- Laboratorio Ecología Microbiana Aplicada (EMALAB), Scientific and Biotechnological Bioresource Nucleus (BIOREN-UFRO), Universidad de La Frontera, Temuco, Chile
| | - Tay Ruiz-Gil
- Laboratorio Ecología Microbiana Aplicada (EMALAB), Scientific and Biotechnological Bioresource Nucleus (BIOREN-UFRO), Universidad de La Frontera, Temuco, Chile
| | - Marco Campos
- Laboratorio Ecología Microbiana Aplicada (EMALAB), Scientific and Biotechnological Bioresource Nucleus (BIOREN-UFRO), Universidad de La Frontera, Temuco, Chile
- Laboratorio de Investigación en Salud de Precisión, Departamento de Procesos Diagnósticos y Evaluación, Facultad de Ciencias de la Salud, Universidad Católica de Temuco, Temuco, Chile
| | - Joaquin-Ignacio Rilling
- Laboratorio Ecología Microbiana Aplicada (EMALAB), Scientific and Biotechnological Bioresource Nucleus (BIOREN-UFRO), Universidad de La Frontera, Temuco, Chile
| | - Pedro Calabrano Miranda
- Centro de Estudios de Algas Nocivas (CREAN), Instituto de Fomento Pesquero (IFOP), Puerto Montt, Chile
| | - Jonnathan Vilugrón
- Centro de Estudios de Algas Nocivas (CREAN), Instituto de Fomento Pesquero (IFOP), Puerto Montt, Chile
| | - Oscar Espinoza-González
- Centro de Estudios de Algas Nocivas (CREAN), Instituto de Fomento Pesquero (IFOP), Puerto Montt, Chile
| | - Leonardo Guzmán
- Centro de Estudios de Algas Nocivas (CREAN), Instituto de Fomento Pesquero (IFOP), Puerto Montt, Chile
| | - Satoshi Nagai
- Japan Coastal and Inland Fisheries Ecosystems Division, Fisheries Technology Institute, Japan Fisheries Research and Education Agency, Yokohama, Kanagawa, Japan
| | - Milko A. Jorquera
- Laboratorio Ecología Microbiana Aplicada (EMALAB), Scientific and Biotechnological Bioresource Nucleus (BIOREN-UFRO), Universidad de La Frontera, Temuco, Chile
| | - Fumito Maruyama
- Microbial Genomics and Ecology, The IDEC Institute, Hiroshima University, Higashi-Hiroshima City, Hiroshima, Japan
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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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Kezlya E, Tseplik N, Kulikovskiy M. Genetic Markers for Metabarcoding of Freshwater Microalgae: Review. BIOLOGY 2023; 12:1038. [PMID: 37508467 PMCID: PMC10376359 DOI: 10.3390/biology12071038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 07/14/2023] [Accepted: 07/18/2023] [Indexed: 07/30/2023]
Abstract
The metabarcoding methods for studying the diversity of freshwater microalgae and routine biomonitoring are actively used in modern research. A lot of experience has been accumulated already, and many methodological questions have been solved (such as the influence of the methods and time of sample conservation, DNA extraction and bioinformatical processing). The reproducibility of the method has been tested and confirmed. However, one of the main problems-choosing a genetic marker for the study-still lacks a clear answer. We analyzed 70 publications and found out that studies on eukaryotic freshwater microalgae use 12 markers (different nuclear regions 18S and ITS and plastids rbcL, 23S and 16S). Each marker has its peculiarities; they amplify differently and have various levels of efficiency (variability) in different groups of algae. The V4 and V9 18S and rbcL regions are used most often. We concentrated especially on the studies that compare the results of using different markers and microscopy. We summarize the data on the primers for each region and on how the choice of a marker affects the taxonomic composition of a community.
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Affiliation(s)
- Elena Kezlya
- Laboratory of Molecular Systematics of Aquatic Plants, K.A. Timiryazev Institute of Plant Physiology RAS, IPP RAS, 127276 Moscow, Russia
| | - Natalia Tseplik
- Laboratory of Molecular Systematics of Aquatic Plants, K.A. Timiryazev Institute of Plant Physiology RAS, IPP RAS, 127276 Moscow, Russia
| | - Maxim Kulikovskiy
- Laboratory of Molecular Systematics of Aquatic Plants, K.A. Timiryazev Institute of Plant Physiology RAS, IPP RAS, 127276 Moscow, Russia
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Nham Q, Mattsson L, Legrand C, Lindehoff E. Whey permeate as a phosphorus source for algal cultivation. WATER ENVIRONMENT RESEARCH : A RESEARCH PUBLICATION OF THE WATER ENVIRONMENT FEDERATION 2023; 95:e10865. [PMID: 37032530 DOI: 10.1002/wer.10865] [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: 01/17/2023] [Revised: 03/22/2023] [Accepted: 03/31/2023] [Indexed: 06/19/2023]
Abstract
Microalgal cultivation for biodiesel and feed requires recycled nutrient resources for a sustainable long-term operation. Whey permeate (WP) from dairy processing contains high organic load (lactose, oils, and proteins) and nitrogen (resources tested for microalgal cultivation) and organic phosphorus (P) that has not yet been tested as a P source for microalgal cultivation. We explored the potential of green algae strains (brackish) and polyculture (freshwater) in exploiting P from WP added to a medium based on either seawater (7 psu) or landfill leachate. Both strains showed a capacity of using organic P in WP with equal growth rates (0.94-1.12 d-1 ) compared with chemical phosphate treatments (0.88-1.07 d-1 ). The polyculture had comparable growth rate (0.25-0.57 d-1 ) and biomass yield (152.1-357.5 mg L-1 ) and similar or higher nutrient removal rate in the leachate-WP medium (1.3-6.4 mg L-1 day-1 nitrogen, 0.2-1.1 mg L-1 day-1 P) compared with the leachate-chemical phosphate medium (1.2-4.7 mg L-1 day-1 nitrogen, 0.3-1.4 mg L-1 day-1 P). This study showed that WP is a suitable P source for microalgal cultivation over a range of salinities. To date, this is the first study demonstrating that raw WP can replace mineral P fertilizer for algal cultivation. PRACTITIONERS POINTS: Whey permeate is a comparable phosphorus source to standard fertilizers used in algal cultivation. Green algae removed phosphorus effectively from whey permeate. Microalgal cultivation is a good approach for treatment of whey permeate in combination with a nitrogen-rich wastewater.
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Affiliation(s)
- Quyen Nham
- Department of Biology and Environmental Science, Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, Kalmar, Sweden
| | - Lina Mattsson
- Department of Biology and Environmental Science, Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, Kalmar, Sweden
| | - Catherine Legrand
- Department of Biology and Environmental Science, Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, Kalmar, Sweden
| | - Elin Lindehoff
- Department of Biology and Environmental Science, Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, Kalmar, Sweden
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Huang H, Xu S, Li S, Wang X, Guo K, Yan R, Xie W, Yin K, Hou S, Jiang H. Diversity and Distribution of Harmful Algal Bloom Species from Seamount to Coastal Waters in the South China Sea. Microbiol Spectr 2023; 11:e0416922. [PMID: 36815795 PMCID: PMC10100961 DOI: 10.1128/spectrum.04169-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 01/26/2023] [Indexed: 02/24/2023] Open
Abstract
Mount Xianbei is one of the largest shallow seamounts located in the middle of the South China Sea (SCS), which might play a role in shaping the biodiversity of surrounding continental coastal waters, particularly the diversity of phytoplankton species causing frequent harmful algal blooms (HABs) in northern SCS. However, the diversity, composition, and distribution of phytoplankton species in the seamount regions of Xianbei remain largely unexplored. In this study, samples around and outside the seamount regions were collected during a late summer cruise of 2021 to test whether seamounts play a role in HAB species propagation. In total, we identified 19 HAB species across all samples using the ASV-based DNA metabarcoding approach, 6 of which had not been reported previously in the SCS, suggesting a diverse HAB species in the SCS. Specifically, 16 HAB species were found in the seamount region of Xianbei, and 5 of them were also found in the coastal waters, indicating a close connection between seamount and coastal waters. This study was the first attempt to explore HAB species' spatial diversity and vertical distribution in the seamount region of Xianbei at single-nucleotide resolution, which provides a novel explanation for the coastal HAB occurrence in the northern SCS. IMPORTANCE There are a number of seamounts under the water of the South China Sea (SCS). The seamounts might play a role in shaping the biodiversity of surrounding continental coastal waters. However, there is no direct evidence revealing the relationship of the biodiversity of phytoplankton between seamounts and coastal waters in the SCS, especially those species having the potential to form harmful algal blooms (HABs). Some HAB species might proliferate in certain geographic locations, while others may be broadly distributed across oceanic provinces. In this study, we provided a detailed analysis of phytoplankton composition and molecular detection of HAB species from seamount to coastal waters in the SCS, which suggested a strong interaction in the HAB species between the two areas. This finding provides new insights into the diversity and distribution of HABs in seamounts and their role in shaping the composition and the occurrence of HABs in coastal water.
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Affiliation(s)
- Hailong Huang
- School of Marine Sciences, Ningbo University, Ningbo, Zhejiang, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), China
| | - Shuaishuai Xu
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China
- College of Life Science and Technology, Jinan University, Guangzhou, China
| | - Shuangqing Li
- School of Marine Sciences, Ningbo University, Ningbo, Zhejiang, China
| | - Xinwei Wang
- School of Marine Sciences, Ningbo University, Ningbo, Zhejiang, China
| | - Kangli Guo
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Rongman Yan
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Wei Xie
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), China
- School of Marine Sciences, Sun Yat-sen University, Guangzhou, China
| | - Kedong Yin
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), China
- School of Marine Sciences, Sun Yat-sen University, Guangzhou, China
| | - Shengwei Hou
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, China
| | - Haibo Jiang
- School of Marine Sciences, Ningbo University, Ningbo, Zhejiang, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), China
- School of Marine Sciences, Sun Yat-sen University, Guangzhou, China
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Kulaš A, Žutinić P, Gulin Beljak V, Kepčija RM, Perić MS, Orlić S, Petrić IS, Marković T, Gligora Udovič M. Diversity of protist genera in periphyton of tufa-depositing karstic river. ANN MICROBIOL 2023. [DOI: 10.1186/s13213-023-01712-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/20/2023] Open
Abstract
Abstract
Purpose
In aquatic ecosystems, protists play a crucial role and cover numerous ecological functions. The karstic Krka River (Croatia) is a unique hotspot for high diversity of aquatic organisms, especially protists. The main objective of the present study was to obtain a detailed overview of the protist community structure in the periphyton of the Krka River and to determine the differences in protist diversity along the river.
Methods
Protist diversity was detected by amplicon sequencing of the hypervariable region V9 of the 18S rRNA gene, using the universal eukaryotic primer pair.
Results
The three main groups of protists were as follows: Ciliophora, Cercozoa, and Bacillariophyta. In terms of abundance of protist OTUs, the shade plot revealed an evident difference from the upstream to downstream river section, which increased between locations from Krka spring to Skradinski buk. Diversity was explored using measures of alpha and beta diversity. Alpha diversity showed an increasing trend in the downstream direction of the river. The location effect, or clustering/grouping of samples by location, was confirmed by the PERMANOVA permutation test of beta diversity.
Conclusion
The combination of alpha and beta diversity can help provide deeper insight into the study of diversity patterns, but also point out to decline in species diversity and allow for effective ways to protect aquatic karst habitats in future management.
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Dzhembekova N, Moncheva S, Slabakova N, Zlateva I, Nagai S, Wietkamp S, Wellkamp M, Tillmann U, Krock B. New Knowledge on Distribution and Abundance of Toxic Microalgal Species and Related Toxins in the Northwestern Black Sea. Toxins (Basel) 2022; 14:685. [PMID: 36287954 PMCID: PMC9610735 DOI: 10.3390/toxins14100685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 09/19/2022] [Accepted: 10/03/2022] [Indexed: 06/16/2023] Open
Abstract
Numerous potentially toxic plankton species commonly occur in the Black Sea, and phycotoxins have been reported. However, the taxonomy, phycotoxin profiles, and distribution of harmful microalgae in the basin are still understudied. An integrated microscopic (light microscopy) and molecular (18S rRNA gene metabarcoding and qPCR) approach complemented with toxin analysis was applied at 41 stations in the northwestern part of the Black Sea for better taxonomic coverage and toxin profiling in natural populations. The combined dataset included 20 potentially toxic species, some of which (Dinophysis acuminata, Dinophysis acuta, Gonyaulax spinifera, and Karlodinium veneficum) were detected in over 95% of the stations. In parallel, pectenotoxins (PTX-2 as a major toxin) were registered in all samples, and yessotoxins were present at most of the sampling points. PTX-1 and PTX-13, as well as some YTX variants, were recorded for the first time in the basin. A positive correlation was found between the cell abundance of Dinophysis acuta and pectenotoxins, and between Lingulodinium polyedra and Protoceratium reticulatum and yessotoxins. Toxic microalgae and toxin variant abundance and spatial distribution was associated with environmental parameters. Despite the low levels of the identified phycotoxins and their low oral toxicity, chronic toxic exposure could represent an ecosystem and human health hazard.
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Affiliation(s)
- Nina Dzhembekova
- Institute of Oceanology “Fridtjof Nansen”—Bulgarian Academy of Sciences, 9000 Varna, Bulgaria
| | - Snejana Moncheva
- Institute of Oceanology “Fridtjof Nansen”—Bulgarian Academy of Sciences, 9000 Varna, Bulgaria
| | - Nataliya Slabakova
- Institute of Oceanology “Fridtjof Nansen”—Bulgarian Academy of Sciences, 9000 Varna, Bulgaria
| | - Ivelina Zlateva
- Institute of Oceanology “Fridtjof Nansen”—Bulgarian Academy of Sciences, 9000 Varna, Bulgaria
| | - Satoshi Nagai
- Fisheries Research and Education Agency, Fisheries Technology Institute, Yokohama 236-8648, Kanagawa, Japan
| | - Stephan Wietkamp
- Alfred Wegener Institut-Helmholtz Zentrum für Polar- und Meeresforschung, Ökologische Chemie, 0471 Bremerhaven, Germany
| | - Marvin Wellkamp
- Alfred Wegener Institut-Helmholtz Zentrum für Polar- und Meeresforschung, Ökologische Chemie, 0471 Bremerhaven, Germany
| | - Urban Tillmann
- Alfred Wegener Institut-Helmholtz Zentrum für Polar- und Meeresforschung, Ökologische Chemie, 0471 Bremerhaven, Germany
| | - Bernd Krock
- Alfred Wegener Institut-Helmholtz Zentrum für Polar- und Meeresforschung, Ökologische Chemie, 0471 Bremerhaven, Germany
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Stuart J, Smith KF, Rhodes L, Murray JS, Viallon J, Henry K, Darius HT, Murray SA, De Azevedo CD, Argyle P, Chinain M. Geographical distribution, molecular and toxin diversity of the dinoflagellate species Gambierdiscus honu in the Pacific region. HARMFUL ALGAE 2022; 118:102308. [PMID: 36195424 DOI: 10.1016/j.hal.2022.102308] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Revised: 06/29/2022] [Accepted: 08/07/2022] [Indexed: 06/16/2023]
Abstract
An increase in cases of ciguatera poisoning (CP) and expansion of the causative species in the South Pacific region highlight the need for baseline data on toxic microalgal species to help identify new areas of risk and manage known hot spots. Gambierdiscus honu is a toxin producing and potential CP causing dinoflagellate species, first described in 2017. Currently no high-resolution geographical distribution, intraspecific genetic variation or toxin production diversity data is available for G. honu. This research aimed to further characterize G. honu by investigating its distribution using species-specific real-time polymerase chain reaction assays at 25 sites in an area spanning ∼8000 km of the Coral Sea/Pacific Ocean, and assessing intraspecific genetic variation, toxicity and toxin production of isolated strains. Assessment of genetic variation of the partial rRNA operon of isolates demonstrated no significant intraspecific population structure, in addition to a lack of adherence to isolation by distance (IBD) model of evolution. The detected distribution of G. honu in the Pacific region was within the expected tropical to temperate latitudinal ranges of 10° to -30° and extended from Australia to French Polynesia. In the lipophilic fractions, the neuroblastoma cell-based assay (CBA-N2a) showed no ciguatoxin (CTX)-like activity for nine of the 10 isolates, and an atypical pattern for CAWD233 isolate which showed cytotoxic activity in OV- and OV+ conditions. In the same way, liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis confirmed no Pacific-CTXs (CTX-3B, CTX-3C, CTX-4A, CTX-4B) were produced by the ten strains. The CBA-N2a assessment of the hydrophilic fractions showed moderate to high cytotoxicity in both OV- and OV+ condition for all the strains showing a cytotoxic profile similar to that of gambierone. Indeed, this study is the first to show the cytotoxic activity of gambierone on mouse neuroblastoma cells while no cytotoxicity was observed when 44-MG was analysed at the same concentrations using the CBA-N2a. Analysis of the hydrophilic via LC-MS/MS confirmed production of gambierone in all isolates, ranging from 2.1 to 38.1 pg/cell, with 44-methylgambierone (44-MG) also produced by eight of the isolates, ranging from 0.3 to 42.9 pg/cell. No maitotoxin-1 was detected in any of the isolates. Classification of the G. honu strains according to the quantities of gambierone produced aligned with the classification of their cytotoxicity using the CBA-N2a. Finally, no maitotoxin-1 (MTX) was detected in any of the isolates. This study shows G. honu is widely distributed within the Pacific region with no significant intraspecific population structure present. This aligns with the view of microalgal populations as global metapopulations, however more in-depth assessment with other genetic markers could detect further structure. Toxicity diversity across 10 isolates assessed did not display any geographical patterns.
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Affiliation(s)
- Jacqui Stuart
- Cawthron Institute, Private Bag 2, Nelson 7042, New Zealand.
| | - Kirsty F Smith
- Cawthron Institute, Private Bag 2, Nelson 7042, New Zealand; School of Biological Sciences, University of Auckland, Auckland 1142, New Zealand
| | - Lesley Rhodes
- Cawthron Institute, Private Bag 2, Nelson 7042, New Zealand
| | - J Sam Murray
- Cawthron Institute, Private Bag 2, Nelson 7042, New Zealand
| | - Jérôme Viallon
- Institut Louis Malardé - UMR EIO, Laboratoire des Biotoxines Marines, Papeete, Tahiti, French Polynesia
| | - Kevin Henry
- Institut Louis Malardé - UMR EIO, Laboratoire des Biotoxines Marines, Papeete, Tahiti, French Polynesia
| | - H Taiana Darius
- Institut Louis Malardé - UMR EIO, Laboratoire des Biotoxines Marines, Papeete, Tahiti, French Polynesia
| | | | | | - Phoebe Argyle
- University of Technology Sydney, New South Wales, Australia
| | - Mireille Chinain
- Institut Louis Malardé - UMR EIO, Laboratoire des Biotoxines Marines, Papeete, Tahiti, French Polynesia
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Sogawa S, Tsuchiya K, Nagai S, Shimode S, Kuwahara VS. Annual dynamics of eukaryotic and bacterial communities revealed by 18S and 16S rRNA metabarcoding in the coastal ecosystem of Sagami Bay, Japan. METABARCODING AND METAGENOMICS 2022. [DOI: 10.3897/mbmg.6.78181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Sagami Bay, Japan is influenced by both the warm Kuroshio Current and the cold Oyashio Current and rich nutrients are supplied from multiple river sources and the deep-sea, forming a dynamic ecosystem. The aim of the present study was to investigate eukaryotic and bacterial communities in the coastal waters of Sagami Bay, using 16S rRNA and 18S rRNA sequencing and to assess the seasonal and vertical dynamics in relation to physicochemical and biological conditions. Eukaryotic and bacterial communities showed synchronous seasonal and vertical changes along with environmental variability. Diversity of plankton community suspended in the surface was lower than those at the subsurface layers in both the eukaryotes and bacteria communities; however, community diversity showed different characteristics in the subsurface where the eukaryotic community at the deeper layer (100 m) was as low as the surface and highest in intermediate depth layers (10–50 m), while that of bacterial community was highest in the deeper layer (100 m). The annual variability of the coastal microbial communities was driven, not only by the seasonal changes of abiotic and biotic factors and short-term rapid changes by river water inflow and phytoplankton blooms, but also largely influenced by deep-seawater upwellings due to the unique seafloor topography.
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Nagai S, Sildever S, Nishi N, Tazawa S, Basti L, Kobayashi T, Ishino Y. Comparing PCR-generated artifacts of different polymerases for improved accuracy of DNA metabarcoding. METABARCODING AND METAGENOMICS 2022. [DOI: 10.3897/mbmg.6.77704] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Accuracy of PCR amplification is vital for obtaining reliable amplicon-sequencing results by metabarcoding. Here, we performed a comparative analysis of error profiles in the PCR products by 14 different PCR kits using a mock eukaryotic community DNA sample mimicking metabarcoding analysis. To prepare a mock eukaryotic community from the marine environment, equal amounts of plasmid DNA from 40 microalgal species were mixed and used for amplicon-sequencing by a high-throughput sequencing approach. To compare the differences in PCR kits used for this experiment, we focused on the following seven parameters: 1) Quality, 2) Chimera, 3) Blast top hit accuracy, 4) Deletion, 5) Insertion, 6) Base substitution and 7) Amplification bias amongst species. The results showed statistically significant differences (p < 0.05) for all of the seven parameters depending on the PCR kits used. These differences may result from the different DNA polymerases included in each kit, although the result can also be influenced by PCR reaction conditions. Simultaneous analysis of several parameters suggested that kits containing KOD plus Neo (TOYOBO) and HotStart Taq DNA polymerase (BiONEER, CA, US) at the annealing temperature of 65 °C displayed better results in terms of parameters associated with chimeras, top hit similarity and deletions.
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11
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Frantal D, Agatha S, Beisser D, Boenigk J, Darienko T, Dirren-Pitsch G, Filker S, Gruber M, Kammerlander B, Nachbaur L, Scheffel U, Stoeck T, Qian K, Weißenbacher B, Pröschold T, Sonntag B. Molecular Data Reveal a Cryptic Diversity in the Genus Urotricha (Alveolata, Ciliophora, Prostomatida), a Key Player in Freshwater Lakes, With Remarks on Morphology, Food Preferences, and Distribution. Front Microbiol 2022; 12:787290. [PMID: 35185817 PMCID: PMC8854374 DOI: 10.3389/fmicb.2021.787290] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 12/07/2021] [Indexed: 11/13/2022] Open
Abstract
Species of the ciliate genus Urotricha are key players in freshwater plankton communities. In the pelagial of lakes, about 20 urotrich species occur throughout an annual cycle, some of which play a pivotal role in aquatic food webs. For example, during the phytoplankton spring bloom, they consume a remarkable proportion of the algal production. In ecological studies, urotrich ciliates are usually merely identified to genus rank and grouped into size classes. This is unsatisfying considering the distinct autecological properties of individual species and their specific spatial and temporal distribution patterns. As a basis for future research, we characterized in detail four common urotrich morphotypes, i.e., specimens identified as U. furcata and tentatively as U. agilis, U. pseudofurcata, and U. castalia, using state-of-the-art methods. We used an integrative polyphasic approach, in which morphological studies (in vivo observation, silver staining methods, scanning electron microscopy) were linked with a molecular approach exploiting four different gene fragments as taxonomic DNA barcodes with different resolution potential (SSU rDNA, ITS-1, ITS-2, hypervariable V4 and V9 regions of the SSU rDNA). We shed light on the diversity of urotrich ciliates as well as on their global distribution patterns, and annual cycles. Additionally, we coupled individual species occurrences and environmental parameters, and subsequently modeled the distribution and occurrence, using logistic regressions. Furthermore, for one strain putatively identified as U. castalia, we ascertained the optimal cultivation media and food preferences. Thereby, our comprehensive view on these important freshwater ciliates that frequently occur in environmental high throughput sequencing datasets worldwide will allow future studies to better exploit protistan plankton data from lakes.
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Affiliation(s)
- Daniela Frantal
- Research Department for Limnology, Mondsee, University of Innsbruck, Mondsee, Austria
| | - Sabine Agatha
- Department of Biosciences, Paris Lodron University of Salzburg, Salzburg, Austria
| | - Daniela Beisser
- Department of Biodiversity, University of Duisburg-Essen, Essen, Germany
| | - Jens Boenigk
- Department of Biodiversity, University of Duisburg-Essen, Essen, Germany
| | - Tatyana Darienko
- Research Department for Limnology, Mondsee, University of Innsbruck, Mondsee, Austria
- Experimental Phycology and Culture Collection of Algae, University of Göttingen, Göttingen, Germany
| | - Gianna Dirren-Pitsch
- Limnological Station, Department of Plant and Microbial Biology, University of Zurich, Kilchberg, Switzerland
| | - Sabine Filker
- Molecular Ecology Group, Technische Universität Kaiserslautern, Kaiserslautern, Germany
| | | | - Barbara Kammerlander
- Research Department for Limnology, Mondsee, University of Innsbruck, Mondsee, Austria
- Federal Agency for Water Management, Institute for Aquatic Ecology and Fisheries Management, Mondsee, Austria
| | - Laura Nachbaur
- Research Department for Limnology, Mondsee, University of Innsbruck, Mondsee, Austria
| | - Ulrike Scheffel
- Research Department for Limnology, Mondsee, University of Innsbruck, Mondsee, Austria
| | - Thorsten Stoeck
- Ecology Group, Technische Universität Kaiserslautern, Kaiserslautern, Germany
| | - Kuimei Qian
- Research Department for Limnology, Mondsee, University of Innsbruck, Mondsee, Austria
- College of Environmental Engineering, Xuzhou University of Technology, Xuzhou, China
| | - Birgit Weißenbacher
- Department of Biosciences, Paris Lodron University of Salzburg, Salzburg, Austria
| | - Thomas Pröschold
- Research Department for Limnology, Mondsee, University of Innsbruck, Mondsee, Austria
| | - Bettina Sonntag
- Research Department for Limnology, Mondsee, University of Innsbruck, Mondsee, Austria
- *Correspondence: Bettina Sonntag,
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Funaki H, Gaonkar CC, Kataoka T, Nishimura T, Tanaka K, Yanagida I, Abe S, Yamaguchi H, Nagasaki K, Adachi M. Horizontal and vertical distribution of Gambierdiscus spp. (Dinophyceae) including novel phylotypes in Japan identified by 18S rDNA metabarcoding. HARMFUL ALGAE 2022; 111:102163. [PMID: 35016767 DOI: 10.1016/j.hal.2021.102163] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Revised: 11/30/2021] [Accepted: 12/05/2021] [Indexed: 06/14/2023]
Abstract
The genus Gambierdiscus is a marine benthic/epiphytic dinoflagellate considered the causative agent of ciguatera poisoning (CP). Clarifying the geographical distribution of this genus to understand the potential risk of CP is important. Many studies have focused only on the species/phylotype composition of Gambierdiscus in shallow waters, but no study has investigated the species/phylotype composition of the genus in deep waters. In the present study, the distributions of Gambierdiscus species/phylotypes at two depths (2-8 and 30 m) and two sampling sites (temperate and subtropical) in Japan was investigated using high throughput sequencing (HTS) with a newly developed primer set that preferentially amplifies the 18S rDNA V8-V9 region of Alveolata. A phylogenetic analysis using 89 samples collected over three years revealed of ten Gambierdiscus species/phylotypes including not only two species that have not been reported in Japan (G. caribaeus and G. silvae) but also four novel phylotypes (Gambierdiscus spp. Clade II_1, Clade II_2, Clade II_3, and Clade VI_1). Uncorrected genetic distances also supported that these new phylotypes clearly diverged from other Gambierdiscus species. All four new phylotypes, G. caribaeus, and G. silvae were distributed in the subtropical region. Among them, Clade II_2, Clade VI_1, and G. silvae were also distributed in the temperate region. Four species/phylotypes previously reported from Japan showed a similar distribution as reported previously. Among the ten species/phylotypes, Gambierdiscus sp. type 3 and Clade VI_1 were found only in deep waters, whereas five species/phylotypes were observed only in shallow waters. The other three species/phylotypes were found in both deep and shallow waters. The results of the horizontal and vertical distribution suggest that the growth characteristics of each species/phylotypes found in Japan might adapt to the ambient environmental conditions. This study revealed an inclusive assemblage of Gambierdiscus species/phylotypes in Japan through metabarcoding using the Alveolata primer set. In the future, the abundance and toxicities/toxin productions of the newly reported species/phylotypes need to be clarified to understand the mechanism of CP outbreaks in Japan.
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Affiliation(s)
- Hiroshi Funaki
- Laboratory of Aquatic Environmental Science (LAQUES), Faculty of Agriculture and Marine Science, Kochi University, 200 Otsu, Monobe, Nankoku, Kochi, 783-8502, Japan; The United Graduate School of Agricultural Sciences, Ehime University, 3-5-7 Tarumi, Matsuyama, Ehime, 790-8566, Japan.
| | - Chetan Chandrakant Gaonkar
- Laboratory of Aquatic Environmental Science (LAQUES), Faculty of Agriculture and Marine Science, Kochi University, 200 Otsu, Monobe, Nankoku, Kochi, 783-8502, Japan.
| | - Takafumi Kataoka
- Faculty of Marine Science and Technology, Fukui Prefectural University, 1-1 Gakuen-cho, Obama, Fukui, 917-0003, Japan.
| | - Tomohiro Nishimura
- Laboratory of Aquatic Environmental Science (LAQUES), Faculty of Agriculture and Marine Science, Kochi University, 200 Otsu, Monobe, Nankoku, Kochi, 783-8502, Japan.
| | - Kouki Tanaka
- Usa Marine Biological Institute, Kochi University, 194 Inoshiri, Usa, Tosa, Kochi, 781-1164, Japan.
| | | | - Shouta Abe
- Laboratory of Aquatic Environmental Science (LAQUES), Faculty of Agriculture and Marine Science, Kochi University, 200 Otsu, Monobe, Nankoku, Kochi, 783-8502, Japan.
| | - Haruo Yamaguchi
- Laboratory of Aquatic Environmental Science (LAQUES), Faculty of Agriculture and Marine Science, Kochi University, 200 Otsu, Monobe, Nankoku, Kochi, 783-8502, Japan; The United Graduate School of Agricultural Sciences, Ehime University, 3-5-7 Tarumi, Matsuyama, Ehime, 790-8566, Japan.
| | - Keizo Nagasaki
- Faculty of Agriculture and Marine Science, Kochi University, 200 Otsu, Monobe, Nankoku, Kochi, 783-8502, Japan.
| | - Masao Adachi
- Laboratory of Aquatic Environmental Science (LAQUES), Faculty of Agriculture and Marine Science, Kochi University, 200 Otsu, Monobe, Nankoku, Kochi, 783-8502, Japan; The United Graduate School of Agricultural Sciences, Ehime University, 3-5-7 Tarumi, Matsuyama, Ehime, 790-8566, Japan.
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13
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de Medeiros Azevedo T, Aburjaile FF, Ferreira-Neto JRC, Pandolfi V, Benko-Iseppon AM. The endophytome (plant-associated microbiome): methodological approaches, biological aspects, and biotech applications. World J Microbiol Biotechnol 2021; 37:206. [PMID: 34708327 DOI: 10.1007/s11274-021-03168-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 10/05/2021] [Indexed: 11/25/2022]
Abstract
Similar to other organisms, plants establish interactions with a variety of microorganisms in their natural environment. The plant microbiome occupies the host plant's tissues, either internally or on its surfaces, showing interactions that can assist in its growth, development, and adaptation to face environmental stresses. The advance of metagenomics and metatranscriptomics approaches has strongly driven the study and recognition of plant microbiome impacts. Research in this regard provides comprehensive information about the taxonomic and functional aspects of microbial plant communities, contributing to a better understanding of their dynamics. Evidence of the plant microbiome's functional potential has boosted its exploitation to develop more ecological and sustainable agricultural practices that impact human health. Although microbial inoculants' development and use are promising to revolutionize crop production, interdisciplinary studies are needed to identify new candidates and promote effective practical applications. On the other hand, there are challenges in understanding and analyzing complex data generated within a plant microbiome project's scope. This review presents aspects about the complex structuring and assembly of the microbiome in the host plant's tissues, metagenomics, and metatranscriptomics approaches for its understanding, covering descriptions of recent studies concerning metagenomics to characterize the microbiome of non-model plants under different aspects. Studies involving bio-inoculants, isolated from plant microbial communities, capable of assisting in crops' productivity, are also reviewed.
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Affiliation(s)
- Thamara de Medeiros Azevedo
- Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco (UFPE), Av. Prof. Moraes Rego, 1235 - Cidade Universitária, Recife, PE, CEP: 50670-901, Brazil
| | - Flávia Figueira Aburjaile
- Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco (UFPE), Av. Prof. Moraes Rego, 1235 - Cidade Universitária, Recife, PE, CEP: 50670-901, Brazil
| | - José Ribamar Costa Ferreira-Neto
- Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco (UFPE), Av. Prof. Moraes Rego, 1235 - Cidade Universitária, Recife, PE, CEP: 50670-901, Brazil
| | - Valesca Pandolfi
- Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco (UFPE), Av. Prof. Moraes Rego, 1235 - Cidade Universitária, Recife, PE, CEP: 50670-901, Brazil
| | - Ana Maria Benko-Iseppon
- Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco (UFPE), Av. Prof. Moraes Rego, 1235 - Cidade Universitária, Recife, PE, CEP: 50670-901, Brazil.
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14
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Hii KS, Mohd-Din M, Luo Z, Tan SN, Lim ZF, Lee LK, Leong SCY, Teng ST, Gu H, Cao X, Lim PT, Leaw CP. Diverse harmful microalgal community assemblages in the Johor Strait and the environmental effects on its community dynamics. HARMFUL ALGAE 2021; 107:102077. [PMID: 34456026 DOI: 10.1016/j.hal.2021.102077] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 06/15/2021] [Accepted: 06/27/2021] [Indexed: 06/13/2023]
Abstract
Coastal ecosystems are often subjected to anthropogenic disturbances that lead to water quality deterioration and an increase in harmful algal bloom (HAB) events. Using the next-generation molecular tool of 18S rDNA metabarcoding, we examined the community assemblages of HAB species in the Johor Strait, Malaysia between May 2018 and September 2019, covering 19 stations across the strait. The molecular operational taxonomic units (OTUs) of HAB taxa retrieved from the dataset (n = 194) revealed a much higher number of HAB taxa (26 OTUs) than before, with 12 taxa belong to new records in the strait. As revealed in the findings of this study, the diversity and community structure of HAB taxa varied significantly over time and space. The most common and abundant HAB taxa in the strait (frequency of occurrence >70%) comprised Heterosigma akashiwo, Fibrocapsa japonica, Pseudo-nitzschia pungens, Dinophysis spp., Gymnodinium catenatum, Alexandrium leei, and A. tamiyavanichii. Also, our results demonstrated that the HAB community assemblages in the strait were dependent on the interplay of environmental variables that influence by the monsoonal effects. Different HAB taxa, constitute various functional types, occupied and prevailed in different environmental niches across space and time, leading to diverse community assemblages and population density. This study adds to the current understandings of HAB dynamics and provides a robust overview of temporal-spatial changes in HAB community assemblages along the environmental gradients in a tropical eutrophic coastal ecosystem.
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Affiliation(s)
- Kieng Soon Hii
- Bachok Marine Research Station, Institute of Ocean and Earth Sciences, University of Malaya, 16310 Bachok, Kelantan, Malaysia
| | - Monaliza Mohd-Din
- Bachok Marine Research Station, Institute of Ocean and Earth Sciences, University of Malaya, 16310 Bachok, Kelantan, Malaysia; Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, 81310 Skudai, Johor, Malaysia
| | - Zhaohe Luo
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005, China
| | - Suh Nih Tan
- Bachok Marine Research Station, Institute of Ocean and Earth Sciences, University of Malaya, 16310 Bachok, Kelantan, Malaysia
| | - Zhen Fei Lim
- Bachok Marine Research Station, Institute of Ocean and Earth Sciences, University of Malaya, 16310 Bachok, Kelantan, Malaysia
| | - Li Keat Lee
- Bachok Marine Research Station, Institute of Ocean and Earth Sciences, University of Malaya, 16310 Bachok, Kelantan, Malaysia
| | - Sandric Chee Yew Leong
- Tropical Marine Science Institute, National University of Singapore, 18 Kent Ridge Road, S2S Building, Singapore, 119227 Singapore
| | - Sing Tung Teng
- Faculty of Resource Science and Technology, Universiti Malaysia Sarawak, 94300 Kota Samarahan, Sarawak, Malaysia
| | - Haifeng Gu
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005, China
| | - Xiuyun Cao
- Institute of Hydrobiologia, Chinese Academic of Science, Wuhan, China
| | - Po Teen Lim
- Bachok Marine Research Station, Institute of Ocean and Earth Sciences, University of Malaya, 16310 Bachok, Kelantan, Malaysia.
| | - Chui Pin Leaw
- Bachok Marine Research Station, Institute of Ocean and Earth Sciences, University of Malaya, 16310 Bachok, Kelantan, Malaysia.
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15
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Gao B, Chi L, Zhu Y, Shi X, Tu P, Li B, Yin J, Gao N, Shen W, Schnabl B. An Introduction to Next Generation Sequencing Bioinformatic Analysis in Gut Microbiome Studies. Biomolecules 2021; 11:530. [PMID: 33918473 PMCID: PMC8066849 DOI: 10.3390/biom11040530] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 03/28/2021] [Accepted: 03/29/2021] [Indexed: 12/12/2022] Open
Abstract
The gut microbiome is a microbial ecosystem which expresses 100 times more genes than the human host and plays an essential role in human health and disease pathogenesis. Since most intestinal microbial species are difficult to culture, next generation sequencing technologies have been widely applied to study the gut microbiome, including 16S rRNA, 18S rRNA, internal transcribed spacer (ITS) sequencing, shotgun metagenomic sequencing, metatranscriptomic sequencing and viromic sequencing. Various software tools were developed to analyze different sequencing data. In this review, we summarize commonly used computational tools for gut microbiome data analysis, which extended our understanding of the gut microbiome in health and diseases.
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Affiliation(s)
- Bei Gao
- Department of Marine Science, School of Marine Sciences, Nanjing University of Information Science and Technology, Nanjing 210044, China;
| | - Liang Chi
- Metaorganism Immunity Section, Laboratory of Immune Systems Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA;
| | - Yixin Zhu
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA;
| | - Xiaochun Shi
- Department of Environmental Ecological Engineering, School of Environmental Science and Engineering, Nanjing University of Information Science and Technology, Nanjing 210044, China; (X.S.); (W.S.)
| | - Pengcheng Tu
- Department of Food Science and Nutrition, College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China;
| | - Bing Li
- Suzhou Industrial Park Environmental Law Enforcement Brigade (Environmental Monitoring Station), Suzhou 215021, China;
| | - Jun Yin
- Department of Hydrometeorology, School of Hydrology and Water Resources, Nanjing University of Information Science and Technology, Nanjing 210044, China;
| | - Nan Gao
- Department of Biotechnology, School of Biological and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China;
| | - Weishou Shen
- Department of Environmental Ecological Engineering, School of Environmental Science and Engineering, Nanjing University of Information Science and Technology, Nanjing 210044, China; (X.S.); (W.S.)
- Jiangsu Key Laboratory of Atmospheric Environment Monitoring and Pollution Control, Collaborative Innovation Center of Atmospheric Environment and Equipment Technology, Nanjing 210044, China
| | - Bernd Schnabl
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA;
- Department of Medicine, VA San Diego Healthcare System, San Diego, CA 92161, USA
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16
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18S rRNA gene sequences of leptocephalus gut contents, particulate organic matter, and biological oceanographic conditions in the western North Pacific. Sci Rep 2021; 11:5488. [PMID: 33658626 PMCID: PMC7930194 DOI: 10.1038/s41598-021-84532-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 02/15/2021] [Indexed: 11/09/2022] Open
Abstract
Eel larvae apparently feed on marine snow, but many aspects of their feeding ecology remain unknown. The eukaryotic 18S rRNA gene sequence compositions in the gut contents of four taxa of anguilliform eel larvae were compared with the sequence compositions of vertically sampled seawater particulate organic matter (POM) in the oligotrophic western North Pacific Ocean. Both gut contents and POM were mainly composed of dinoflagellates as well as other phytoplankton (cryptophytes and diatoms) and zooplankton (ciliophoran and copepod) sequences. Gut contents also contained cryptophyte and ciliophoran genera and a few other taxa. Dinoflagellates (family Gymnodiniaceae) may be an important food source and these phytoplankton were predominant in gut contents and POM as evidenced by DNA analysis and phytoplankton cell counting. The compositions of the gut contents were not specific to the species of eel larvae or the different sampling areas, and they were most similar to POM at the chlorophyll maximum in the upper part of the thermocline (mean depth: 112 m). Our results are consistent with eel larvae feeding on marine snow at a low trophic level, and feeding may frequently occur in the chlorophyll maximum in the western North Pacific.
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Yu RC, Zhang QC, Liu Y, Chen ZF, Geng HX, Dai L, Lin ZR, Tang WJ, Kong FZ, Yan T, Zhou MJ. The dinoflagellate Alexandrium catenella producing only carbamate toxins may account for the seafood poisonings in Qinhuangdao, China. HARMFUL ALGAE 2021; 103:101980. [PMID: 33980430 DOI: 10.1016/j.hal.2021.101980] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 12/25/2020] [Accepted: 01/21/2021] [Indexed: 06/12/2023]
Abstract
An outbreak of paralytic shellfish poisoning, recorded in April 2016 in Qinhuangdao China, was suspected to be caused by a toxic species in genus Alexandrium. Shortly after the poisoning outbreak, shellfish and net-concentrated phytoplankton samples were collected from the Bohai Sea, and analysed using high performance liquid chromatography coupled with fluorescence detection. Paralytic shellfish toxins (PSTs) were detected in both phytoplankton and shellfish samples, with similar toxin profiles dominated by carbamate toxins. High throughput sequencing data for phytoplankton samples collected previously in the coastal waters of Qinhuangdao were then analysed, and 8 operational taxonomic units (OTUs) were assigned to Alexandrium affine, A. andersonii/A. ostenfeldii, A. catenella, A. fraterculus, A. hiranoi/A. pseudogonyaulax, A. margalefii, A. pacificum and A. pohangense, among which A. catenella, A. pacificum and A. ostenfeldii could be potential producers of PSTs. During a cruise in 2019, three isolates of Alexandrium were established by cyst germination, and identified as A. catenella based on the sequences of the 28S ribosomal RNA gene (28S rDNA) D1-D2 region. Interestingly, all the three strains had the same toxin profile consisting of gonyautoxins 1, 3, 4 (GTX1, 3, 4) and neosaxitoxin (NEO). The toxin profile is similar to those of phytoplankton samples collected previously in the coastal waters of Qinhuangdao, but remarkably different from the general toxin profile of A. catenella dominated by N-sulfocarbamoyl toxins C1-2 in the Bohai Sea and the Yellow Sea. The results suggest that A. catenella is most likely to be the causative species of the poisoning outbreak in Qinhuangdao. As far as we know, this is the first report of A. catenella in the Bohai Sea producing PSTs dominated by high potent gonyautoxins GTX1-4. Occurrence of the highly toxic A. catenella will increase the risk of paralytic shellfish poisoning, which necessitates in-depth mechanism studies and increasing monitoring efforts.
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Affiliation(s)
- Ren-Cheng Yu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Key Laboratory for Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266071, China; University of Chinese Academy of Sciences, Beijing 100049, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China.
| | - Qing-Chun Zhang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Key Laboratory for Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266071, China
| | - Yang Liu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Zhen-Fan Chen
- College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Hui-Xia Geng
- Changjiang River Estuary Ecosystem Research Station, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Li Dai
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhuo-Ru Lin
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wen-Jiao Tang
- College of Marine Life Science, Ocean University of China, Qingdao 266003, China
| | - Fan-Zhou Kong
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Key Laboratory for Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266071, China
| | - Tian Yan
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Key Laboratory for Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266071, China
| | - Ming-Jiang Zhou
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
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Yarimizu K, Sildever S, Hamamoto Y, Tazawa S, Oikawa H, Yamaguchi H, Basti L, Mardones JI, Paredes-Mella J, Nagai S. Development of an absolute quantification method for ribosomal RNA gene copy numbers per eukaryotic single cell by digital PCR. HARMFUL ALGAE 2021; 103:102008. [PMID: 33980448 DOI: 10.1016/j.hal.2021.102008] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 03/04/2021] [Accepted: 03/04/2021] [Indexed: 06/12/2023]
Abstract
Recent increase of Harmful Algal Blooms (HAB) causes world-wide ecological, economical, and health issues, and more attention is paid to frequent coastal monitoring for the early detection of HAB species to prevent or reduce such impacts. Use of molecular tools in addition to traditional microscopy-based observation has become one of the promising methodologies for coastal monitoring. However, as ribosomal RNA (rRNA) genes are commonly targeted in molecular studies, variability in the rRNA gene copy number within and between species must be considered to provide quantitative information in quantitative PCR (qPCR), digital PCR (dPCR), and metabarcoding analyses. Currently, this information is only available for a limited number of species. The present study utilized a dPCR technology to quantify copy numbers of rRNA genes per single cell in 16 phytoplankton species, the majority of which are toxin-producers, using a newly developed universal primer set accompanied by a labeled probe with a fluorophore and a double-quencher. In silico PCR using the newly developed primers allowed the detection of taxa from 8 supergroups, demonstrating universality and broad coverage of the primer set. Chelex buffer was found to be suitable for DNA extraction to obtain DNA fragments with suitable size to avoid underestimation of the copy numbers. The study successfully demonstrated the first comparison of absolute quantification of 18S rRNA copy numbers per cell from 16 phytoplankton species by the dPCR technology.
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Affiliation(s)
- Kyoko Yarimizu
- Japan Fisheries Research and Education Agency, Fisheries Resources Institute, Fisheries Stock Assessment Center, 2-12-4 Fukuura, Kanazawa-ku, Yokohama, Kanagawa 236-8648, Japan; Office of Industry-Academia-Government and Community Collaboration, Hiroshima University, 1-3-2 22 Kagamiyama, Higashi-Hiroshima City, Hiroshima 739-8511, Japan
| | - Sirje Sildever
- Japan Fisheries Research and Education Agency, Fisheries Resources Institute, Fisheries Stock Assessment Center, 2-12-4 Fukuura, Kanazawa-ku, Yokohama, Kanagawa 236-8648, Japan; Department of Marine Systems, Tallinn University of Technology, Akadeemia tee 15A, 12618 Tallinn, Estonia
| | - Yoko Hamamoto
- Japan Fisheries Research and Education Agency, Fisheries Resources Institute, Fisheries Stock Assessment Center, 2-12-4 Fukuura, Kanazawa-ku, Yokohama, Kanagawa 236-8648, Japan
| | - Satoshi Tazawa
- AXIOHELIX Co. Ltd, 12-17 Kandaizumicho, Chiyoda-ku, Tokyo 101-0024, Japan
| | - Hiroshi Oikawa
- Japan Fisheries Research and Education Agency, Fisheries Resources Institute, Fisheries Stock Assessment Center, 2-12-4 Fukuura, Kanazawa-ku, Yokohama, Kanagawa 236-8648, Japan
| | - Haruo Yamaguchi
- Faculty of Agriculture and Marine Sciences, Kochi University, Nankoku, Kochi 783-8502, Japan
| | - Leila Basti
- Department of Ocean Sciences, Tokyo University of Marine Science and Technology, Minato, Tokyo 108-8477, Japan
| | - Jorge I Mardones
- Instituto de Fomento Pesquero, Centro de Estudios de Algas Nocivas (IFOP-CREAN), Padre Harter 574, Puerto Montt 5501679, Chile; Centro FONDAP de Investigación en Dinámica de Ecosistemas Marinos de Altas Latitudes (IDEAL), Valdivia, Chile
| | - Javier Paredes-Mella
- Instituto de Fomento Pesquero, Centro de Estudios de Algas Nocivas (IFOP-CREAN), Padre Harter 574, Puerto Montt 5501679, Chile
| | - Satoshi Nagai
- Japan Fisheries Research and Education Agency, Fisheries Resources Institute, Fisheries Stock Assessment Center, 2-12-4 Fukuura, Kanazawa-ku, Yokohama, Kanagawa 236-8648, Japan.
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19
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Lee FCH, Muthu V. From 18S to 28S rRNA Gene: An Improved Targeted Sarcocystidae PCR Amplification, Species Identification with Long DNA Sequences. Am J Trop Med Hyg 2021; 104:1388-1393. [PMID: 33617472 PMCID: PMC8045662 DOI: 10.4269/ajtmh.20-0767] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 10/26/2020] [Indexed: 11/30/2022] Open
Abstract
Sarcocystosis outbreaks in Tioman and Pangkor islands of Malaysia between 2011 and 2014 have raised the need to improve Sarcocystis species detection from environmental samples. In-house works found that published primers amplifying the 18S rRNA gene of Sarcocystis either could not produce the target from environmental samples or produced Sarcocystis DNA sequence that was insufficient for species identification. Using the primer pair of 18S S5 F (published) and 28S R6 R (new), this study improved the PCR amplification of Sarcocystidae to overcome these two difficulties. The PCR product spanned from the 18S to 28S rRNA genes, providing more information for species identification. The long DNA sequence allowed comparison between the “Ident” and “Query Cover” sorting in GenBank identity matching. This revealed the ambiguity in identity matching caused by different lengths of reference DNA sequences, which is seldom discussed in the literature. Using the disparity index test, a measurement of homogeneity in nucleotide substitution pattern, it is shown that the internal transcribed spacer (ITS)1-5.8S-ITS2 and 28S genes are better than the 18S gene in indicating nucleotide variations, implying better potentials for species identification. The example given by the handful of Sarcocystidae long DNA sequences reported herein calls for the need to report DNA sequence from the 18S to the 28S rRNA genes for species identification, especially among emerging pathogens. DNA sequence reporting should include the hypervariable 5.8S and ITS2 regions where applicable, and not be limited to single gene, per the current general trend.
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Affiliation(s)
- Florence C H Lee
- 1Environmental Health Research Centre, Institute for Medical Research (IMR), National Institutes of Health, Ministry of Health Malaysia, Setia Alam, Malaysia
| | - Vickneshwaran Muthu
- 2Zoonosis Sector, Disease Control Division, Ministry of Health Malaysia, Putrajaya, Malaysia
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20
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Consistent patterns in 16S and 18S microbial diversity from the shells of the common and widespread red-eared slider turtle (Trachemys scripta). PLoS One 2020; 15:e0244489. [PMID: 33370423 PMCID: PMC7769255 DOI: 10.1371/journal.pone.0244489] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 12/10/2020] [Indexed: 01/04/2023] Open
Abstract
Microbial communities associated with freshwater aquatic habitats and resident species are both critical to and indicative of ecosystem status and organismal health. External surfaces of turtle shells readily accumulate microbial growth and could carry representation of habitat-wide microbial diversity, since they are in regular contact with multiple elements of freshwater environments. Yet, microbial diversity residing on freshwater turtle shells is poorly understood. We applied 16S and 18S metabarcoding to characterize microbiota associated with external shell surfaces of 20 red-eared slider (Trachemys scripta) turtles collected from varied habitats in central and western Oklahoma, and ranging to southeast Iowa. Shell-associated microbial communities were highly diverse, with samples dominated by Bacteroidia and alpha-/gamma-proteobacteria, and ciliophoran alveolates. Alpha diversity was lower on turtle shells compared to shallow-water-associated environmental samples, likely resulting from basking-drying behavior and seasonal scute shedding, while alpha diversity was higher on carapace than plastron surfaces. Beta diversity of turtle shells was similarly differentiated from environmental samples, although sampling site was consistently a significant factor. Deinococcus-Thermus bacteria and ciliophoran alveolates were recovered with significantly higher abundance on turtle shells versus environmental samples, while bacterial taxa known to include human-pathogenic species were variably more abundant between shell and environmental samples. Microbial communities from a single, shared-site collection of the ecologically similar river cooter (P. concinna) largely overlapped with those of T. scripta. These data add to a foundation for further characterization of turtle shell microbial communities across species and habitats, with implications for freshwater habitat assessment, microbial ecology and wildlife conservation efforts.
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21
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Yarimizu K, Fujiyoshi S, Kawai M, Norambuena-Subiabre L, Cascales EK, Rilling JI, Vilugrón J, Cameron H, Vergara K, Morón-López J, Acuña JJ, Gajardo G, Espinoza-González O, Guzmán L, Jorquera MA, Nagai S, Pizarro G, Riquelme C, Ueki S, Maruyama F. Protocols for Monitoring Harmful Algal Blooms for Sustainable Aquaculture and Coastal Fisheries in Chile. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2020; 17:ijerph17207642. [PMID: 33092111 PMCID: PMC7589761 DOI: 10.3390/ijerph17207642] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Revised: 10/14/2020] [Accepted: 10/18/2020] [Indexed: 11/16/2022]
Abstract
Harmful algae blooms (HABs) cause acute effects on marine ecosystems due to their production of endogenous toxins or their enormous biomass, leading to significant impacts on local economies and public health. Although HAB monitoring has been intensively performed at spatiotemporal scales in coastal areas of the world over the last decades, procedures have not yet been standardized. HAB monitoring procedures are complicated and consist of many methodologies, including physical, chemical, and biological water sample measurements. Each monitoring program currently uses different combinations of methodologies depending on site specific purposes, and many prior programs refer to the procedures in quotations. HAB monitoring programs in Chile have adopted the traditional microscopic and toxin analyses but not molecular biology and bacterial assemblage approaches. Here we select and optimize the HAB monitoring methodologies suitable for Chilean geography, emphasizing on metabarcoding analyses accompanied by the classical tools with considerations including cost, materials and instrument availability, and easiness and efficiency of performance. We present results from a pilot study using the standardized stepwise protocols, demonstrating feasibility and plausibility for sampling and analysis for the HAB monitoring. Such specific instructions in the standardized protocol are critical obtaining quality data under various research environments involving multiple stations, different analysts, various time-points, and long HAB monitoring duration.
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Affiliation(s)
- Kyoko Yarimizu
- Office of Industry-Academia-Government and Community Collaboration, Hiroshima University, 1-3-2 Kagamiyama, Higashi-Hiroshima City, Hiroshima 739-8511, Japan;
- Correspondence: (K.Y.); (F.M.); Tel.: +81-082-424-7048 (K.Y. & F.M.)
| | - So Fujiyoshi
- Office of Industry-Academia-Government and Community Collaboration, Hiroshima University, 1-3-2 Kagamiyama, Higashi-Hiroshima City, Hiroshima 739-8511, Japan;
| | - Mikihiko Kawai
- Graduate School of Human and Environmental Studies, Kyoto University, Yoshidanihonmatsu-cho, Kyoto 606-8501, Japan;
| | - Luis Norambuena-Subiabre
- Centro de Estudios de Algas Nocivas (CREAN), Instituto de Fomento Pesquero (IFOP), Padre Harter 547, Puerto Montt 5480000, Chile; (L.N.-S.); (E.-K.C.); (J.V.); (O.E.-G.); (L.G.)
| | - Emma-Karin Cascales
- Centro de Estudios de Algas Nocivas (CREAN), Instituto de Fomento Pesquero (IFOP), Padre Harter 547, Puerto Montt 5480000, Chile; (L.N.-S.); (E.-K.C.); (J.V.); (O.E.-G.); (L.G.)
| | - Joaquin-Ignacio Rilling
- Scientific and Biotechnological Bioresource Nucleus (BIOREN-UFRO), Universidad de La Frontera, Ave. Francisco Salazar 01145, Temuco 4811230, Chile; (J.-I.R.); (J.J.A.); (M.A.J.)
| | - Jonnathan Vilugrón
- Centro de Estudios de Algas Nocivas (CREAN), Instituto de Fomento Pesquero (IFOP), Padre Harter 547, Puerto Montt 5480000, Chile; (L.N.-S.); (E.-K.C.); (J.V.); (O.E.-G.); (L.G.)
| | - Henry Cameron
- Centro de Bioinnovacion, Facultad de Ciencias del Mar y Recursos Biologicos, Universidad de Antofagasta, Av. Angamos 601, Antofagasta 1270300, Chile; (H.C.); (C.R.)
| | - Karen Vergara
- Laboratorio de Genética, Acuicultura & Biodiversidad, Departamento de Ciencias Biológicas y Biodiversidad, Universidad de Los Lagos, Osorno 5290000, Chile; (K.V.); (G.G.)
| | - Jesus Morón-López
- Institute of Plant Science and Resources, Okayama University, 2-20-1 Chuo, Kurashiki, Okayama 710-0046, Japan; (J.M.-L.); (S.U.)
| | - Jacquelinne J. Acuña
- Scientific and Biotechnological Bioresource Nucleus (BIOREN-UFRO), Universidad de La Frontera, Ave. Francisco Salazar 01145, Temuco 4811230, Chile; (J.-I.R.); (J.J.A.); (M.A.J.)
| | - Gonzalo Gajardo
- Laboratorio de Genética, Acuicultura & Biodiversidad, Departamento de Ciencias Biológicas y Biodiversidad, Universidad de Los Lagos, Osorno 5290000, Chile; (K.V.); (G.G.)
| | - Oscar Espinoza-González
- Centro de Estudios de Algas Nocivas (CREAN), Instituto de Fomento Pesquero (IFOP), Padre Harter 547, Puerto Montt 5480000, Chile; (L.N.-S.); (E.-K.C.); (J.V.); (O.E.-G.); (L.G.)
| | - Leonardo Guzmán
- Centro de Estudios de Algas Nocivas (CREAN), Instituto de Fomento Pesquero (IFOP), Padre Harter 547, Puerto Montt 5480000, Chile; (L.N.-S.); (E.-K.C.); (J.V.); (O.E.-G.); (L.G.)
| | - Milko A. Jorquera
- Scientific and Biotechnological Bioresource Nucleus (BIOREN-UFRO), Universidad de La Frontera, Ave. Francisco Salazar 01145, Temuco 4811230, Chile; (J.-I.R.); (J.J.A.); (M.A.J.)
| | - Satoshi Nagai
- Japan Fisheries Research and Education Agency, Fisheries Resources Institute, Fisheries Stock Assessment Center, 2-12-4 Fukuura, Kanazawa-ku, Yokohama, Kanagawa 236-8648, Japan;
| | - Gemita Pizarro
- Laboratorio de toxinas y fitoplancton, IFOP, Enrique Abello 0552, Punta Arenas 6200000, Chile;
| | - Carlos Riquelme
- Centro de Bioinnovacion, Facultad de Ciencias del Mar y Recursos Biologicos, Universidad de Antofagasta, Av. Angamos 601, Antofagasta 1270300, Chile; (H.C.); (C.R.)
| | - Shoko Ueki
- Institute of Plant Science and Resources, Okayama University, 2-20-1 Chuo, Kurashiki, Okayama 710-0046, Japan; (J.M.-L.); (S.U.)
| | - Fumito Maruyama
- Office of Industry-Academia-Government and Community Collaboration, Hiroshima University, 1-3-2 Kagamiyama, Higashi-Hiroshima City, Hiroshima 739-8511, Japan;
- Correspondence: (K.Y.); (F.M.); Tel.: +81-082-424-7048 (K.Y. & F.M.)
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22
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Dzhembekova N, Rubino F, Nagai S, Zlateva I, Slabakova N, Ivanova P, Slabakova V, Moncheva S. Comparative analysis of morphological and molecular approaches integrated into the study of the dinoflagellate biodiversity within the recently deposited Black Sea sediments - benefits and drawbacks. Biodivers Data J 2020; 8:e55172. [PMID: 32903988 PMCID: PMC7447646 DOI: 10.3897/bdj.8.e55172] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Accepted: 07/27/2020] [Indexed: 11/23/2022] Open
Abstract
One of the assets, assigned to the phytoplankton resting stages, is that of serving as the “memory” of the aquatic ecosystems and preserved biodiversity in the course of time. However, an accurate cyst identification proves to be a more difficult and extremely challenging process, even today. In order to gain a better taxonomic coverage of cyst assemblages in the Black Sea, an integrated approach of the classical morphological identification with metabarcoding methods (MySeq sequencing of V7-V9 regions of the 18S rDNA) was applied on thirteen surface sediment samples collected from different sites. A total number of 112 dinoflagellate taxa was detected at the species level and ascribed to 51 genera. In general, it is the molecular analysis that yields a higher number of taxa as compared to those obtained through the morphological taxonomy (66 taxa based on the DNA sequences versus 56 morphologically-identified taxa). Besides, it should be pointed out that the integrated dataset includes 14 potentially toxic dinoflagellate species. Discerned, subsequently, was a good dataset consistency for ten species, followed by some discrepancies as to a number of taxa, identified with one of the methods only, due to specific methodological biases. On the whole, it could be concluded that the combination of morphological and molecular methods is likely to increase the potential for a more reliable taxonomic assessment of phytoplankton diversity in marine sediments which, in turn, proves conclusively the utmost importance of the integrated approach.
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Affiliation(s)
- Nina Dzhembekova
- Institute of Oceanology "Fridtjof Nansen", Marine Biology and Ecology Department, Bulgarian Academy of Sciences, Varna, Bulgaria Institute of Oceanology "Fridtjof Nansen", Marine Biology and Ecology Department, Bulgarian Academy of Sciences Varna Bulgaria
| | - Fernando Rubino
- Water Research Institute, Unit Talassografico "A. Cerruti", National Research Council CNR-IRSA, Taranto, Italy Water Research Institute, Unit Talassografico "A. Cerruti", National Research Council CNR-IRSA Taranto Italy
| | - Satoshi Nagai
- National Research Institute of Fisheries Science, Research Center for Aquatic Genomics, Fisheries Research and Education Agency, Yokohama Kanagawa, Japan National Research Institute of Fisheries Science, Research Center for Aquatic Genomics, Fisheries Research and Education Agency Yokohama Kanagawa Japan
| | - Ivelina Zlateva
- Institute of Oceanology "Fridtjof Nansen", Marine Biology and Ecology Department, Bulgarian Academy of Sciences, Varna, Bulgaria Institute of Oceanology "Fridtjof Nansen", Marine Biology and Ecology Department, Bulgarian Academy of Sciences Varna Bulgaria
| | - Nataliya Slabakova
- Institute of Oceanology "Fridtjof Nansen", Marine Biology and Ecology Department, Bulgarian Academy of Sciences, Varna, Bulgaria Institute of Oceanology "Fridtjof Nansen", Marine Biology and Ecology Department, Bulgarian Academy of Sciences Varna Bulgaria
| | - Petya Ivanova
- Institute of Oceanology "Fridtjof Nansen", Marine Biology and Ecology Department, Bulgarian Academy of Sciences, Varna, Bulgaria Institute of Oceanology "Fridtjof Nansen", Marine Biology and Ecology Department, Bulgarian Academy of Sciences Varna Bulgaria
| | - Violeta Slabakova
- Institute of Oceanology "Fridtjof Nansen", Ocean Technologies Department, Bulgarian Academy of Sciences, Varna, Bulgaria Institute of Oceanology "Fridtjof Nansen", Ocean Technologies Department, Bulgarian Academy of Sciences Varna Bulgaria
| | - Snejana Moncheva
- Institute of Oceanology "Fridtjof Nansen", Marine Biology and Ecology Department, Bulgarian Academy of Sciences, Varna, Bulgaria Institute of Oceanology "Fridtjof Nansen", Marine Biology and Ecology Department, Bulgarian Academy of Sciences Varna Bulgaria
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23
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Lin S, Hu Z, Deng Y, Shang L, Gobler CJ, Tang YZ. An assessment on the intrapopulational and intraindividual genetic diversity in LSU rDNA in the harmful algal blooms-forming dinoflagellate Margalefidinium (= Cochlodinium) fulvescens based on clonal cultures and bloom samples from Jiaozhou Bay, China. HARMFUL ALGAE 2020; 96:101821. [PMID: 32560829 DOI: 10.1016/j.hal.2020.101821] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 04/20/2020] [Accepted: 04/30/2020] [Indexed: 06/11/2023]
Abstract
Large subunit ribosomal DNA (LSU rDNA) sequences have been increasingly used to infer the phylogeny and species identity of organisms, a few previous studies, however, have observed high intraspecific and even intraindividual variability in LSU rDNA in some dinoflagellate species due to, assumably, large copy numbers of rDNA in dinoflagellates. Since the copy number of LSU rDNA varies tremendously among dinoflagellate species, the intraspecific and intraindividual diversity for a species of particular interest thus needs to be investigated individually. As a toxic and HABs-forming dinoflagellate, Margalefidinium (= Cochlodinium) fulvescens has been observed to approach blooming density in Jiaozhou Bay, China since 2015 after numerous blooms having been reported from other countries. In trying to identify the source of this newly observed HABs-forming species in China by sequencing the LSU rDNA for both field samples and clonal cultures, we noticed and thus further investigated high intrapopulational and intraindividual genetic diversities of the dinoflagellate. The D1-D6 region of the LSU rDNA (1,435 bases) was amplified from 7 field samples (pooled cells) and 11 clonal cultures, cloned, sequenced, and analyzed phylogenetically for 2,341 sequences obtained. All the numbers of sequences obtained from each clonal culture were far less than the estimated rDNA copy number in M. fulvescens. In the clone library, only one unique sequence was contained in all samples as the most dominant sequence. We found high intrapopulational and intraindividual genetic diversity in M. fulvescens as reflected in the number of polymorphic sites and unique sequences in the clone library for different field samples and clonal cultures in comparison to other species. The mean number of nucleotide differences of each sequence from different field samples and clonal cultures were 6.43 and 4.42 bases, respectively, with the highest being 132 bases, nearly 10%. The sequences with highest variability may be easily annotated as different species if they were obtained from environmental genomic studies because sequence-based species identification in meta-barcoding studies often use "97% identity" threshold. Based on that the mean and overall intrapopulational genetic diversity calculated for 7 field samples was equivalent to the mean and overall intraindividual variability for 11 clonal cultures in indices of genetic diversity, together with the result of AMOVA analysis, we infer that the variability within individual cells (i.e. variability among LSU rDNA polymorphic copies) caused both the intraindividual and intrapopulational genetic diversities observed in the M. fulvescens population, and a higher interpopulational diversity may exist among different geographic populations. The results provide an insightful basis for such a comprehensive interpopulational comparison and important implications for identifying species and establishing new taxa based on the similarity comparison to reference sequences deposited in databases.
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Affiliation(s)
- Siheng Lin
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao 266071, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhangxi Hu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, 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, 7 Nanhai Road, 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, 7 Nanhai Road, 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
| | - Christopher J Gobler
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY 11790, USA
| | - Ying Zhong Tang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, 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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24
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Kumar M, Singh P, Murugesan S, Vetizou M, McCulloch J, Badger JH, Trinchieri G, Al Khodor S. Microbiome as an Immunological Modifier. Methods Mol Biol 2020; 2055:595-638. [PMID: 31502171 PMCID: PMC8276114 DOI: 10.1007/978-1-4939-9773-2_27] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Humans are living ecosystems composed of human cells and microbes. The microbiome is the collection of microbes (microbiota) and their genes. Recent breakthroughs in the high-throughput sequencing technologies have made it possible for us to understand the composition of the human microbiome. Launched by the National Institutes of Health in USA, the human microbiome project indicated that our bodies harbor a wide array of microbes, specific to each body site with interpersonal and intrapersonal variabilities. Numerous studies have indicated that several factors influence the development of the microbiome including genetics, diet, use of antibiotics, and lifestyle, among others. The microbiome and its mediators are in a continuous cross talk with the host immune system; hence, any imbalance on one side is reflected on the other. Dysbiosis (microbiota imbalance) was shown in many diseases and pathological conditions such as inflammatory bowel disease, celiac disease, multiple sclerosis, rheumatoid arthritis, asthma, diabetes, and cancer. The microbial composition mirrors inflammation variations in certain disease conditions, within various stages of the same disease; hence, it has the potential to be used as a biomarker.
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Affiliation(s)
- Manoj Kumar
- Division of Translational Medicine, Research Department, Sidra Medicine, Doha, Qatar
| | - Parul Singh
- Division of Translational Medicine, Research Department, Sidra Medicine, Doha, Qatar
| | - Selvasankar Murugesan
- Division of Translational Medicine, Research Department, Sidra Medicine, Doha, Qatar
| | - Marie Vetizou
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - John McCulloch
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jonathan H Badger
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Giorgio Trinchieri
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Souhaila Al Khodor
- Division of Translational Medicine, Research Department, Sidra Medicine, Doha, Qatar.
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25
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Nagai S, Chen H, Kawakami Y, Yamamoto K, Sildever S, Kanno N, Oikawa H, Yasuike M, Nakamura Y, Hongo Y, Fujiwara A, Kobayashi T, Gojobori T. Monitoring of the toxic dinoflagellate Alexandrium catenella in Osaka Bay, Japan using a massively parallel sequencing (MPS)-based technique. HARMFUL ALGAE 2019; 89:101660. [PMID: 31672234 DOI: 10.1016/j.hal.2019.101660] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 08/10/2019] [Accepted: 08/28/2019] [Indexed: 06/10/2023]
Abstract
Since 2002, blooms of Alexandrium catenella sensu Fraga et al. (2015) and paralytic shellfish toxicity events have occurred almost yearly in Osaka Bay, Japan. To better understand the triggers for reoccurring A. catenella blooms in Osaka Bay, phytoplankton community was monitored during the spring seasons of 2012-2015. Monitoring was performed using massively parallel sequencing (MPS)-based technique on amplicon sequences of the 18S rRNA gene. Dense blooms of A. catenella occurred every year except in 2012, however, there was no significant correlation with the environmental parameters investigated. Plankton community diversity decreased before and middle of the A. catenella blooms, suggesting that the decline in diversity could be an indicator for the bloom occurrence. The yearly abundance pattern of A. catenella cells obtained by morphology-based counting coincided with the relative sequence abundances, which supports the effectiveness of MPS-based phytoplankton monitoring.
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Affiliation(s)
- Satoshi Nagai
- National Research Institute of Fisheries Science, 2-12-4 Fukuura, Kanazawa-ku, Yokohama, Kanagawa, 236-8648, Japan.
| | - Hungyen Chen
- Department of Agronomy, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei, 10617, Taiwan
| | - Yoko Kawakami
- AXIOHELIX Co. Ltd, -12-17 Kandaizumicho, Chiyoda-ku, Tokyo, 101-0024, Japan
| | - Keigo Yamamoto
- Research Institute of Environment, Agriculture and Fisheries, Osaka Prefecture, 2926-1 Tanigawa, Misaki, Sen-Nan, Osaka, 599-0311, Japan
| | - Sirje Sildever
- National Research Institute of Fisheries Science, 2-12-4 Fukuura, Kanazawa-ku, Yokohama, Kanagawa, 236-8648, Japan
| | - Nanako Kanno
- National Research Institute of Fisheries Science, 2-12-4 Fukuura, Kanazawa-ku, Yokohama, Kanagawa, 236-8648, Japan
| | - Hiroshi Oikawa
- National Research Institute of Fisheries Science, 2-12-4 Fukuura, Kanazawa-ku, Yokohama, Kanagawa, 236-8648, Japan
| | - Motoshige Yasuike
- National Research Institute of Fisheries Science, 2-12-4 Fukuura, Kanazawa-ku, Yokohama, Kanagawa, 236-8648, Japan
| | - Yoji Nakamura
- National Research Institute of Fisheries Science, 2-12-4 Fukuura, Kanazawa-ku, Yokohama, Kanagawa, 236-8648, Japan
| | - Yuki Hongo
- National Research Institute of Fisheries Science, 2-12-4 Fukuura, Kanazawa-ku, Yokohama, Kanagawa, 236-8648, Japan
| | - Atushi Fujiwara
- National Research Institute of Fisheries Science, 2-12-4 Fukuura, Kanazawa-ku, Yokohama, Kanagawa, 236-8648, Japan
| | - Takanori Kobayashi
- National Research Institute of Fisheries Science, 2-12-4 Fukuura, Kanazawa-ku, Yokohama, Kanagawa, 236-8648, Japan
| | - Takashi Gojobori
- Computational Bioscience Research Center, King Abdullah University of Science and Technology, 4700 KAUST, Thuwal, 23955-6900, Saudi Arabia
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26
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Tang YZ, Ma Z, Hu Z, Deng Y, Yang A, Lin S, Yi L, Chai Z, Gobler CJ. 3,000 km and 1,500‐year presence of
Aureococcus anophagefferens
reveals indigenous origin of brown tides in China. Mol Ecol 2019; 28:4065-4076. [DOI: 10.1111/mec.15196] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 06/29/2019] [Accepted: 07/08/2019] [Indexed: 02/01/2023]
Affiliation(s)
- Ying Zhong Tang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences Institute of Oceanology Chinese Academy of Sciences Qingdao China
- Laboratory for Marine Ecology and Environmental Science Qingdao National Laboratory for Marine Science and Technology Qingdao China
| | - Zhaopeng Ma
- CAS Key Laboratory of Marine Ecology and Environmental Sciences Institute of Oceanology Chinese Academy of Sciences Qingdao China
- University of Chinese Academy of Sciences Beijing China
| | - Zhangxi Hu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences Institute of Oceanology Chinese Academy of Sciences Qingdao China
| | - Yunyan Deng
- CAS Key Laboratory of Marine Ecology and Environmental Sciences Institute of Oceanology Chinese Academy of Sciences Qingdao China
| | - Aoao Yang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences Institute of Oceanology Chinese Academy of Sciences Qingdao China
- University of Chinese Academy of Sciences Beijing China
| | - Siheng Lin
- CAS Key Laboratory of Marine Ecology and Environmental Sciences Institute of Oceanology Chinese Academy of Sciences Qingdao China
- University of Chinese Academy of Sciences Beijing China
| | - Liang Yi
- State Key Laboratory of Marine Geology Tongji University Shanghai China
| | - Zhaoyang Chai
- CAS Key Laboratory of Marine Ecology and Environmental Sciences Institute of Oceanology Chinese Academy of Sciences Qingdao China
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Sildever S, Kawakami Y, Kanno N, Kasai H, Shiomoto A, Katakura S, Nagai S. Toxic HAB species from the Sea of Okhotsk detected by a metagenetic approach, seasonality and environmental drivers. HARMFUL ALGAE 2019; 87:101631. [PMID: 31349888 DOI: 10.1016/j.hal.2019.101631] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 05/30/2019] [Accepted: 06/10/2019] [Indexed: 06/10/2023]
Abstract
During recent decades, the distribution of harmful algal bloom (HAB) species has expanded worldwide together with the increase of blooms and toxicity events. In this study, the presence of toxic HAB species in the Sea of Okhotsk was investigated based on metagenetic data collected during 6 years of weekly monitoring. Operational taxonomic units (OTUs) associated with the toxic HAB species were detected based on amplifying 18S V7-V9 and 28S D1 rRNA gene regions. In total, 43 unique OTUs associated with toxic HAB species were revealed, with 26 of those previously not reported from the Sea of Okhotsk. More OTUs belonging to dinoflagellates were detected by 18S, whereas a similar number of OTUs associated with dinoflagellates and diatoms were detected by targeting the 28S region. Species belonging to genera Alexandrium, Karenia and Karlodinium were mainly associated with OTUs under Dinophyceae, whereas Bacillariophyceae was represented by the species belonging to genus Pseudo-nitzschia. From the detected OTUs, 22 showed a clear seasonal pattern with the majority of those appearing during summer-autumn. For Alexandrium pacificum, Aureococcus anophagefferens, and Pseudo-nitzschia pungens, the seasonal pattern was detected based on both rRNA regions. Additionally, 14 OTUs were detected during all seasons and two OTUs appeared sporadically. OTUs associated with the toxic species had low relative read abundances, which together with other factors such as similar and variable morphology as well as usage of fixatives, may explain why those species have previously not been detected by light microscopy. Environmental parameters, especially water temperature, significantly (<0.05) influenced the variability in OTU relative abundances and displayed significant (<0.05) correlations with the unique OTUs. The results of this study demonstrate the usefulness of the metagenetic approach for phytoplankton monitoring, which is especially relevant for detecting toxic HAB species.
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Affiliation(s)
- Sirje Sildever
- National Research Institute of Fisheries Science, Yokohama Kanagawa, 236-8648, Japan
| | - Yoko Kawakami
- AXIOHELIX Co. Ltd, Chiyoda-ku, Tokyo, 101-0024, Japan
| | - Nanako Kanno
- National Research Institute of Fisheries Science, Yokohama Kanagawa, 236-8648, Japan
| | - Hiromi Kasai
- Hokkaido National Fisheries Research Institute, Kushiro, Hokkaido, 085-0802, Japan
| | | | | | - Satoshi Nagai
- National Research Institute of Fisheries Science, Yokohama Kanagawa, 236-8648, Japan.
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28
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Pitsch G, Bruni EP, Forster D, Qu Z, Sonntag B, Stoeck T, Posch T. Seasonality of Planktonic Freshwater Ciliates: Are Analyses Based on V9 Regions of the 18S rRNA Gene Correlated With Morphospecies Counts? Front Microbiol 2019; 10:248. [PMID: 30837972 PMCID: PMC6389714 DOI: 10.3389/fmicb.2019.00248] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 01/30/2019] [Indexed: 12/23/2022] Open
Abstract
Ciliates represent central nodes in freshwater planktonic food webs, and many species show pronounced seasonality, with short-lived maxima of a few dominant taxa while many being rare or ephemeral. These observations are primarily based on morphospecies counting methods, which, however, have limitations concerning the amount and volume of samples that can be processed. For high sampling frequencies at large scales, high throughput sequencing (HTS) of freshwater ciliates seems to be a promising tool. However, several studies reported large discrepancy between species abundance determinations by molecular compared to morphological means. Therefore, we compared ciliate DNA metabarcodes (V9 regions of the 18S rRNA gene) with morphospecies counts for a 3-year study (Lake Zurich, Switzerland; biweekly sampling, n = 74). In addition, we isolated, cultivated and sequenced the 18S rRNA gene of twelve selected ciliate species that served as seeds for HTS analyses. This workflow allowed for a detailed comparison of V9 data with microscopic analyses by quantitative protargol staining (QPS). The dynamics of V9 read abundances over the seasonal cycle corroborated well with morphospecies population patterns. Annual successions of rare and ephemeral species were more adequately characterized by V9 reads than by QPS. However, numbers of species specific sequence reads only partly reflected rank orders seen by counts. In contrast, biomass-based assemblage compositions showed higher similarity to V9 read numbers, probably indicating a relation between cell sizes and numbers / sizes of macronuclei (or 18S rRNA operons). Full-length 18S rRNA sequences of ciliates assigned to certain morphospecies are urgently needed for barcoding approaches as planktonic taxa are still poorly represented in public databases and the interpretation of HTS data depends on profound reference sequences. Through linking operational taxonomic units (OTUs) with known morphospecies, we can use the deep knowledge about the autecology of these species.
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Affiliation(s)
- Gianna Pitsch
- Limnological Station, Department of Plant and Microbial Biology, University of Zurich, Kilchberg, Switzerland
| | - Estelle Patricia Bruni
- Limnological Station, Department of Plant and Microbial Biology, University of Zurich, Kilchberg, Switzerland
| | - Dominik Forster
- Ecology Group, Technical University of Kaiserslautern, Kaiserslautern, Germany
| | - Zhishuai Qu
- Ecology Group, Technical University of Kaiserslautern, Kaiserslautern, Germany
| | - Bettina Sonntag
- Research Department for Limnology, Mondsee, University of Innsbruck, Mondsee, Austria
| | - Thorsten Stoeck
- Ecology Group, Technical University of Kaiserslautern, Kaiserslautern, Germany
| | - Thomas Posch
- Limnological Station, Department of Plant and Microbial Biology, University of Zurich, Kilchberg, Switzerland
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29
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Dzhembekova N, Moncheva S, Ivanova P, Slabakova N, Nagai S. Biodiversity of phytoplankton cyst assemblages in surface sediments of the Black Sea based on metabarcoding. BIOTECHNOL BIOTEC EQ 2018. [DOI: 10.1080/13102818.2018.1532816] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Affiliation(s)
- Nina Dzhembekova
- Marine Biology and Ecology Department, Institute of Oceanology, Bulgarian Academy of Sciences, Varna, Bulgaria
| | - Snejana Moncheva
- Marine Biology and Ecology Department, Institute of Oceanology, Bulgarian Academy of Sciences, Varna, Bulgaria
| | - Petya Ivanova
- Marine Biology and Ecology Department, Institute of Oceanology, Bulgarian Academy of Sciences, Varna, Bulgaria
| | - Nataliya Slabakova
- Marine Biology and Ecology Department, Institute of Oceanology, Bulgarian Academy of Sciences, Varna, Bulgaria
| | - Satoshi Nagai
- Research Center for Aquatic Genomics, National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, Yokohama, Kanagawa, Japan
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30
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Mars Brisbin M, Mesrop LY, Grossmann MM, Mitarai S. Intra-host Symbiont Diversity and Extended Symbiont Maintenance in Photosymbiotic Acantharea (Clade F). Front Microbiol 2018; 9:1998. [PMID: 30210473 PMCID: PMC6120437 DOI: 10.3389/fmicb.2018.01998] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 08/08/2018] [Indexed: 11/15/2022] Open
Abstract
Photosymbiotic protists contribute to surface primary production in low-nutrient, open-ocean ecosystems and constitute model systems for studying plastid acquisition via endosymbiosis. Little is known, however, about host-symbiont dynamics in these important relationships, and whether these symbioses are mutualistic is debated. In this study, we applied single-cell sequencing methods and advanced fluorescent microscopy to investigate host-symbiont dynamics in clade F acantharians, a major group of photosymbiotic protists in oligotrophic subtropical gyres. We amplified the 18S rRNA gene from single acantharian hosts and environmental samples to assess intra-host symbiont diversity and to determine whether intra-host symbiont community composition directly reflects the available symbiont community in the surrounding environment. Our results demonstrate that clade F acantharians simultaneously host multiple species from the haptophyte genera Phaeocystis and Chrysochromulina. The intra-host symbiont community composition was distinct from the external free-living symbiont community, suggesting that these acantharians maintain symbionts for extended periods of time. After selectively staining digestive organelles, fluorescent confocal microscopy showed that symbionts were not being systematically digested, which is consistent with extended symbiont maintenance within hosts. Extended maintenance within hosts may benefit symbionts through protection from grazing or viral lysis, and therefore could enhance dispersal, provided that symbionts retain reproductive capacity. The evidence for extended symbiont maintenance therefore allows that Phaeocystis could glean some advantage from the symbiosis and leaves the possibility of mutualism.
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Affiliation(s)
- Margaret Mars Brisbin
- Marine Biophysics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Lisa Y Mesrop
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, United States
| | - Mary M Grossmann
- Marine Biophysics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Satoshi Mitarai
- Marine Biophysics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
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31
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Arroyo AS, López-Escardó D, Kim E, Ruiz-Trillo I, Najle SR. Novel Diversity of Deeply Branching Holomycota and Unicellular Holozoans Revealed by Metabarcoding in Middle Paraná River, Argentina. Front Ecol Evol 2018. [DOI: 10.3389/fevo.2018.00099] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
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32
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Wangensteen OS, Cebrian E, Palacín C, Turon X. Under the canopy: Community-wide effects of invasive algae in Marine Protected Areas revealed by metabarcoding. MARINE POLLUTION BULLETIN 2018; 127:54-66. [PMID: 29475694 DOI: 10.1016/j.marpolbul.2017.11.033] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Revised: 11/12/2017] [Accepted: 11/15/2017] [Indexed: 06/08/2023]
Abstract
We analysed with multigene (18S and COI) metabarcoding the effects of the proliferation of invasive seaweeds on rocky littoral communities in two Spanish Marine Protected Areas. The invasive algae studied were Caulerpa cylindracea, Lophocladia lallemandii and Asparagopsis armata. They are canopy-forming, landscape-dominant seaweeds, and we were interested in their effects on the underlying communities of meiobenthos and macrobenthos, separated in two size fractions through sieving. A new semiquantitative treatment of metabarcoding data is introduced. The results for both markers showed that the presence of the invasive seaweed had a significant effect on the understory communities for Lophocladia lallemandii and Asparagopsis armata but not for Caulerpa cylindracea. Likewise, changes in MOTU richness and diversity with invasion status varied in magnitude and direction depending on the alga considered. Our results showed that metabarcoding allows monitoring of the less conspicuous, but not least important, effects of the presence of dominant invasive seaweeds.
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Affiliation(s)
- Owen S Wangensteen
- Ecosystems and Environment Research Centre, School of Environment and Life Sciences, University of Salford, Salford, UK
| | - Emma Cebrian
- Aquatic Ecology Institute, University of Girona, Campus Montilivi, Girona, Spain
| | - Creu Palacín
- Department of Evolutionary Biology, Ecology and Environmental Sciences, Biodiversity Research Institute (IRBio), University of Barcelona, Barcelona, Spain
| | - Xavier Turon
- Center for Advanced Studies of Blanes (CEAB-CSIC), Blanes (Girona), Spain.
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33
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Reich M, Labes A. How to boost marine fungal research: A first step towards a multidisciplinary approach by combining molecular fungal ecology and natural products chemistry. Mar Genomics 2017; 36:57-75. [PMID: 29031541 DOI: 10.1016/j.margen.2017.09.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Revised: 09/22/2017] [Accepted: 09/23/2017] [Indexed: 12/30/2022]
Abstract
Marine fungi have attracted attention in recent years due to increased appreciation of their functional role in ecosystems and as important sources of new natural products. The concomitant development of various "omic" technologies has boosted fungal research in the fields of biodiversity, physiological ecology and natural product biosynthesis. Each of these research areas has its own research agenda, scientific language and quality standards, which have so far hindered an interdisciplinary exchange. Inter- and transdisciplinary interactions are, however, vital for: (i) a detailed understanding of the ecological role of marine fungi, (ii) unlocking their hidden potential for natural product discovery, and (iii) designing access routes for biotechnological production. In this review and opinion paper, we describe the two different "worlds" of marine fungal natural product chemists and marine fungal molecular ecologists. The individual scientific approaches and tools employed are summarised and explained, and enriched with a first common glossary. We propose a strategy to find a multidisciplinary approach towards a comprehensive view on marine fungi and their chemical potential.
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Affiliation(s)
- Marlis Reich
- University of Bremen, BreMarE, NW2 B3320, Leobener Str. 5, D-28359 Bremen, Germany.
| | - Antje Labes
- Flensburg University of Applied Sciences, Kanzleistr. 91-93, D-24943 Flensburg, Germany.
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34
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Arrigoni R, Vacherie B, Benzoni F, Stefani F, Karsenti E, Jaillon O, Not F, Nunes F, Payri C, Wincker P, Barbe V. A new sequence data set of SSU rRNA gene for Scleractinia and its phylogenetic and ecological applications. Mol Ecol Resour 2017; 17:1054-1071. [DOI: 10.1111/1755-0998.12640] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Revised: 11/01/2016] [Accepted: 11/15/2016] [Indexed: 11/29/2022]
Affiliation(s)
- Roberto Arrigoni
- Red Sea Research Center; Division of Biological and Environmental Science and Engineering; King Abdullah University of Science and Technology; Thuwal 23955-6900 Saudi Arabia
- Department of Biotechnology and Biosciences; University of Milano-Bicocca; Piazza della Scienza 2 Milan 20126 Italy
| | | | - Francesca Benzoni
- Department of Biotechnology and Biosciences; University of Milano-Bicocca; Piazza della Scienza 2 Milan 20126 Italy
- Institut de Recherche pour le Développement; UMR227 Coreus2; 101 Promenade Roger Laroque BP A5 Noumea Cedex 98848 New Caledonia
| | - Fabrizio Stefani
- Water Research Institute-National Research Council (IRSA-CNR); Via del Mulino 19 Brugherio I-20861 Italy
| | - Eric Karsenti
- Ecole Normale Supérieure; Institut de Biologie de l'ENS (IBENS), and Inserm U1024, and CNRS UMR 8197; Paris F-75005 France
- Directors’ Research; European Molecular Biology Laboratory; Meyerhofstr. 1 Heidelberg 69117 Germany
| | - Olivier Jaillon
- CEA/DSV/IG/Genoscope; Evry Cedex France
- Université d'Evry; UMR 8030; Evry CP5706 France
| | - Fabrice Not
- UPMC-CNRS; UMR 7144; Station Biologique de Roscoff; Place Georges Teissier Roscoff 29680 France
| | - Flavia Nunes
- Ifremer Centre Bretagne; DYNECO; Laboratoire d’Écologie Benthique Côtière (LEBCO); 29280 Plouzané France
| | - Claude Payri
- Institut de Recherche pour le Développement; UMR227 Coreus2; 101 Promenade Roger Laroque BP A5 Noumea Cedex 98848 New Caledonia
| | - Patrick Wincker
- CEA/DSV/IG/Genoscope; Evry Cedex France
- Université d'Evry; UMR 8030; Evry CP5706 France
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35
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Freeland JR. The importance of molecular markers and primer design when characterizing biodiversity from environmental DNA. Genome 2016; 60:358-374. [PMID: 28177833 DOI: 10.1139/gen-2016-0100] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Environmental DNA (eDNA) comprises DNA fragments that have been shed into the environment by organisms, and which can be extracted from environmental samples such as water or soil. Characterization of eDNA can allow researchers to infer the presence or absence of species from a particular site without the need to locate and identify individuals, and therefore may provide an extremely valuable tool for quantifying biodiversity. However, as is often the case with relatively new protocols, methodological challenges remain. A number of earlier reviews have discussed these challenges, but none have provided extensive treatment of the critical decisions surrounding molecular markers and primer development for use in eDNA assays. This review discusses a number of options and approaches that can be used when determining which primers and gene regions are most appropriate for either targeted species detection or metabarcoding macro-organisms from eDNA. The latter represents a new field that is growing rapidly, and which has the potential to revolutionize future assessments of community and ecosystem diversity.
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Affiliation(s)
- Joanna R Freeland
- Department of Biology, Trent University, Peterborough, ON K9J 7B8, Canada.,Department of Biology, Trent University, Peterborough, ON K9J 7B8, Canada
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36
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Design and Evaluation of Illumina MiSeq-Compatible, 18S rRNA Gene-Specific Primers for Improved Characterization of Mixed Phototrophic Communities. Appl Environ Microbiol 2016; 82:5878-91. [PMID: 27451454 DOI: 10.1128/aem.01630-16] [Citation(s) in RCA: 117] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Accepted: 07/20/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED The use of high-throughput sequencing technologies with the 16S rRNA gene for characterization of bacterial and archaeal communities has become routine. However, the adoption of sequencing methods for eukaryotes has been slow, despite their significance to natural and engineered systems. There are large variations among the target genes used for amplicon sequencing, and for the 18S rRNA gene, there is no consensus on which hypervariable region provides the most suitable representation of diversity. Additionally, it is unclear how much PCR/sequencing bias affects the depiction of community structure using current primers. The present study amplified the V4 and V8-V9 regions from seven microalgal mock communities as well as eukaryotic communities from freshwater, coastal, and wastewater samples to examine the effect of PCR/sequencing bias on community structure and membership. We found that degeneracies on the 3' end of the current V4-specific primers impact read length and mean relative abundance. Furthermore, the PCR/sequencing error is markedly higher for GC-rich members than for communities with balanced GC content. Importantly, the V4 region failed to reliably capture 2 of the 12 mock community members, and the V8-V9 hypervariable region more accurately represents mean relative abundance and alpha and beta diversity. Overall, the V4 and V8-V9 regions show similar community representations over freshwater, coastal, and wastewater environments, but specific samples show markedly different communities. These results indicate that multiple primer sets may be advantageous for gaining a more complete understanding of community structure and highlight the importance of including mock communities composed of species of interest. IMPORTANCE The quantification of error associated with community representation by amplicon sequencing is a critical challenge that is often ignored. When target genes are amplified using currently available primers, differential amplification efficiencies result in inaccurate estimates of community structure. The extent to which amplification bias affects community representation and the accuracy with which different gene targets represent community structure are not known. As a result, there is no consensus on which region provides the most suitable representation of diversity for eukaryotes. This study determined the accuracy with which commonly used 18S rRNA gene primer sets represent community structure and identified particular biases related to PCR amplification and Illumina MiSeq sequencing in order to more accurately study eukaryotic microbial communities.
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