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Hiltunen Thorén M, Onuț-Brännström I, Alfjorden A, Pecková H, Swords F, Hooper C, Holzer AS, Bass D, Burki F. Comparative genomics of Ascetosporea gives new insight into the evolutionary basis for animal parasitism in Rhizaria. BMC Biol 2024; 22:103. [PMID: 38702750 PMCID: PMC11069148 DOI: 10.1186/s12915-024-01898-x] [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: 12/21/2023] [Accepted: 04/22/2024] [Indexed: 05/06/2024] Open
Abstract
BACKGROUND Ascetosporea (Endomyxa, Rhizaria) is a group of unicellular parasites infecting aquatic invertebrates. They are increasingly being recognized as widespread and important in marine environments, causing large annual losses in invertebrate aquaculture. Despite their importance, little molecular data of Ascetosporea exist, with only two genome assemblies published to date. Accordingly, the evolutionary origin of these parasites is unclear, including their phylogenetic position and the genomic adaptations that accompanied the transition from a free-living lifestyle to parasitism. Here, we sequenced and assembled three new ascetosporean genomes, as well as the genome of a closely related amphizoic species, to investigate the phylogeny, origin, and genomic adaptations to parasitism in Ascetosporea. RESULTS Using a phylogenomic approach, we confirm the monophyly of Ascetosporea and show that Paramyxida group with Mikrocytida, with Haplosporida being sister to both groups. We report that the genomes of these parasites are relatively small (12-36 Mb) and gene-sparse (~ 2300-5200 genes), while containing surprisingly high amounts of non-coding sequence (~ 70-90% of the genomes). Performing gene-tree aware ancestral reconstruction of gene families, we demonstrate extensive gene losses at the origin of parasitism in Ascetosporea, primarily of metabolic functions, and little gene gain except on terminal branches. Finally, we highlight some functional gene classes that have undergone expansions during evolution of the group. CONCLUSIONS We present important new genomic information from a lineage of enigmatic but important parasites of invertebrates and illuminate some of the genomic innovations accompanying the evolutionary transition to parasitism in this lineage. Our results and data provide a genetic basis for the development of control measures against these parasites.
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Affiliation(s)
- Markus Hiltunen Thorén
- Department of Organismal Biology, Uppsala University, Norbyv. 18D, Uppsala, SE-752 36, Sweden.
- Present Address: Department of Ecology, Environment and Plant Sciences, Stockholm University, Svante Arrhenius V. 20 A, Stockholm, SE-114 18, Sweden.
- Present Address: The Royal Swedish Academy of Sciences, Stockholm, SE-114 18, Sweden.
| | - Ioana Onuț-Brännström
- Present Address: Department of Ecology and Genetics, Uppsala University, Norbyv. 18D, Uppsala, SE-752 36, Sweden
- Present Address: Natural History Museum, Oslo University, Oslo, 0562, Norway
| | - Anders Alfjorden
- Department of Organismal Biology, Uppsala University, Norbyv. 18D, Uppsala, SE-752 36, Sweden
| | - Hana Pecková
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, Branišovská 31, České Budějovice, 370 05, Czech Republic
| | - Fiona Swords
- Marine Institute, Rinville, Oranmore, H91R673, Ireland
| | - Chantelle Hooper
- Centre for Environment, Fisheries and Aquaculture Science (Cefas), Weymouth Laboratory, Weymouth, Dorset, DT4 8UB, UK
- Sustainable Aquaculture Futures, Biosciences, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK
| | - Astrid S Holzer
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, Branišovská 31, České Budějovice, 370 05, Czech Republic
- Division of Fish Health, University of Veterinary Medicine, Veterinärplatz 1, Vienna, 1210, Austria
| | - David Bass
- Centre for Environment, Fisheries and Aquaculture Science (Cefas), Weymouth Laboratory, Weymouth, Dorset, DT4 8UB, UK
- Sustainable Aquaculture Futures, Biosciences, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK
- Natural History Museum (NHM), Science, London, SW7 5BD, UK
| | - Fabien Burki
- Department of Organismal Biology, Uppsala University, Norbyv. 18D, Uppsala, SE-752 36, Sweden.
- Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
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Lourenço L, Ellegaard Bager S, Ng DYK, Sheikh S, Lunding Kindtler N, Broman Nielsen I, Guldberg Frøslev T, Ekelund F. DNA metabarcoding reveals the impact of Cu 2+ on soil cercozoan diversity. Protist 2024; 175:126016. [PMID: 38350284 DOI: 10.1016/j.protis.2024.126016] [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: 02/12/2023] [Revised: 01/12/2024] [Accepted: 01/26/2024] [Indexed: 02/15/2024]
Abstract
Although copper (Cu2+) is a micronutrient, the metal may be toxic if present in high concentrations in soil ecosystems and subsequently affect various organisms, ranging from microorganisms to earthworms. We performed a microcosm study with an array of Cu2+ concentrations, with a specific focus on Cercozoa, an important protozoan group in most soil food webs. Research on Cercozoa is still scarce in terms of both diversity and ecology; hence, to explore this group in more depth, we used high-throughput sequencing to detect Cu2+ induced community changes. Increased levels of Cu2+ caused a shift in the cercozoan community, and we observed decreased cercozoan relative abundance across the majority of orders, families and genera. Due to their key role in soil food webs, especially as bacterial predators and providers of nutrients to plants, the reduction of cercozoan abundance and diversity may seriously affect soil functionality. Our results indicate that the increase of Cu2+ concentrations in the soil could potentially have this effect and the consequences need exploration.
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Affiliation(s)
- Leah Lourenço
- Terrestrial Ecology Section, Department of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen Ø, Denmark.
| | - Sara Ellegaard Bager
- Terrestrial Ecology Section, Department of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen Ø, Denmark
| | - Duncan Y K Ng
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Sanea Sheikh
- Terrestrial Ecology Section, Department of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen Ø, Denmark
| | - Nikolaj Lunding Kindtler
- Terrestrial Ecology Section, Department of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen Ø, Denmark
| | - Ida Broman Nielsen
- Section for Evolutionary Genomics, GLOBE Institute, University of Copenhagen, Øster Farimagsgade 5, 1353 Copenhagen K, Denmark
| | - Tobias Guldberg Frøslev
- Section for Geogenetics, GLOBE Institute, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen K, Denmark
| | - Flemming Ekelund
- Terrestrial Ecology Section, Department of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen Ø, Denmark
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3
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Kaushik T, Dixit V, Murugan T. Morphology and molecular phylogeny of two new species of Psammophaga (Rhizaria, Foraminifera) from the west coast of India. Eur J Protistol 2024; 92:126035. [PMID: 38100884 DOI: 10.1016/j.ejop.2023.126035] [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: 07/17/2023] [Revised: 11/17/2023] [Accepted: 11/18/2023] [Indexed: 12/17/2023]
Abstract
Benthic foraminifera are unicellular eukaryotic protists that construct an organic, agglutinated, or calcareous test wall. Although single-chambered (monothalamous) foraminifera are ubiquitous in marine habitats worldwide, they are poorly known compared to their multi-chambered relatives, notably from the tropical marine environments of India. In this study, we describe two new species of marine monothalamid genus Psammophaga Arnold, 1982, from the Rajapuri Creek, coastal Maharashtra, India (Arabian Sea). Psammophaga holzmannae sp. nov. is ovoid to spherical shaped, 103-246 µm in length, single aperture, translucent to orange color cytoplasm, outer surface is composed of agglutinated fine clay particles, and ingested mineral grains are concentrated near its aperture. Psammophaga sinhai sp. nov. is oblong, elliptical, or droplet-shaped, 279-448 µm in length, single aperture, yellow olive color cytoplasm, the exterior surface formed of agglutinated fine clay particles, and the ingested mineral grains are dispersed throughout the body. Phylogenetic analyses based on partial small subunit rRNA gene sequences position new species within the Clade E of monothalamids and are genetically distinct from other Psammophaga. Elemental (SEM-EDS) analysis of engulfed mineral grains revealed preferential selection and uptake of heavy opaque titaniferous minerals from the ambient environment in the cytoplasm.
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Affiliation(s)
- Tushar Kaushik
- Biodiversity and Palaeobiology Group, Agharkar Research Institute, G. G. Agarkar Road, Pune 411004, Maharashtra, India; Savitribai Phule Pune University, Pune 411007, Maharashtra, India.
| | - Vaishnavi Dixit
- Biodiversity and Palaeobiology Group, Agharkar Research Institute, G. G. Agarkar Road, Pune 411004, Maharashtra, India
| | - Thirumalai Murugan
- Biodiversity and Palaeobiology Group, Agharkar Research Institute, G. G. Agarkar Road, Pune 411004, Maharashtra, India
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Lamża Ł. Diversity of 'simple' multicellular eukaryotes: 45 independent cases and six types of multicellularity. Biol Rev Camb Philos Soc 2023; 98:2188-2209. [PMID: 37475165 DOI: 10.1111/brv.13001] [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: 03/16/2023] [Revised: 07/10/2023] [Accepted: 07/13/2023] [Indexed: 07/22/2023]
Abstract
Multicellularity evolved multiple times in the history of life, with most reviewers agreeing that it appeared at least 20 times in eukaryotes. However, a specific list of multicellular eukaryotes with clear criteria for inclusion has not yet been published. Herein, an updated critical review of eukaryotic multicellularity is presented, based on current understanding of eukaryotic phylogeny and new discoveries in microbiology, phycology and mycology. As a result, 45 independent multicellular lineages are identified that fall into six distinct types. Functional criteria, as distinct from a purely topological definition of a cell, are introduced to bring uniformity and clarity to the existing definitions of terms such as colony, multicellularity, thallus or plasmodium. The category of clonal multicellularity is expanded to include: (i) septated multinucleated thalli found in Pseudofungi and early-branching Fungi such as Chytridiomycota and Blastocladiomycota; and (ii) multicellular reproductive structures formed by plasmotomy in intracellular parasites such as Phytomyxea. Furthermore, (iii) endogeneous budding, as found in Paramyxida, is described as a form of multicellularity. The best-known case of clonal multicellularity, i.e. (iv) non-separation of cells after cell division, as known from Metazoa and Ochrophyta, is also discussed. The category of aggregative multicellularity is expanded to include not only (v) pseudoplasmodial forms, such a sorocarp-forming Acrasida, but also (vi) meroplasmodial organisms, such as members of Variosea or Filoreta. A common set of topological, geometric, genetic and life-cycle criteria are presented that form a coherent, philosophically sound framework for discussing multicellularity. A possibility of a seventh type of multicellularity is discussed, that of multi-species superorganisms formed by protists with obligatory bacterial symbionts, such as some members of Oxymonada or Parabasalia. Its inclusion is dependent on the philosophical stance taken towards the concepts of individuality and organism in biology. Taxa that merit special attention are identified, such as colonial Centrohelea, and a new speculative form of multicellularity, possibly present in some reticulopodial amoebae, is briefly described. Because of insufficient phylogenetic and morphological data, not all lineages could be unequivocally identified, and the true total number of all multicellular eukaryotic lineages is therefore higher, likely close to a hundred.
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Affiliation(s)
- Łukasz Lamża
- Copernicus Center for Interdisciplinary Studies, Jagiellonian University, Szczepanska 1, Kraków, 31-011, Poland
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5
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Xi DD, Gao L, Miao LM, Ge LA, Zhang DY, Zhang ZH, Li XF, Zhu YY, Shen HB, Zhu HF. Changes in Diversity and Composition of Rhizosphere Bacterial and Fungal Community between Resistant and Susceptible Pakchoi under Plasmodiophora brassicae. Int J Mol Sci 2023; 24:16779. [PMID: 38069101 PMCID: PMC10706474 DOI: 10.3390/ijms242316779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 11/23/2023] [Accepted: 11/24/2023] [Indexed: 12/18/2023] Open
Abstract
Plasmodiophora brassicae (P. brassicae) is a soil-born pathogen worldwide and can infect most cruciferous plants, which causes great yield decline and economic losses. It is not well known how microbial diversity and community composition change during P. brassicae infecting plant roots. Here, we employed a resistant and a susceptible pakchoi cultivar with and without inoculation with P. brassicae to analyze bacterial and fungal diversity using 16S rRNA V3-V4 and ITS_V1 regions, respectively. 16S rRNA V3-V4 and ITS_V1 regions were amplified and sequenced separately. Results revealed that both fungal and bacterial diversity increased, and composition was changed in the rhizosphere soil of the susceptible pakchoi compared with the resistant cultivar. In the four groups of R_mock, S_mock, R_10d, and S_10d, the most relatively abundant bacterium and fungus was Proteobacteria, accounting for 61.92%, 58.17%, 48.64%, and 50.00%, respectively, and Ascomycota, accounting for 75.11%, 63.69%, 72.10%, and 90.31%, respectively. A total of 9488 and 11,914 bacteria were observed uniquely in the rhizosphere soil of resistant and susceptible pakchoi, respectively, while only 80 and 103 fungi were observed uniquely in the correlated soil. LefSe analysis showed that 107 and 49 differentially abundant taxa were observed in bacteria and fungi. Overall, we concluded that different pakchoi cultivars affect microbial diversity and community composition, and microorganisms prefer to gather around the rhizosphere of susceptible pakchoi. These findings provide a new insight into plant-microorganism interactions.
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Affiliation(s)
- Dan-Dan Xi
- Shanghai Key Laboratory of Protected Horticultural Technology, Horticultural Research Institute, Zhuanghang Comprehensive Experiment Station, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China; (D.-D.X.); (L.G.); (L.-M.M.); (D.-Y.Z.); (Z.-H.Z.); (X.-F.L.); (Y.-Y.Z.); (H.-B.S.)
| | - Lu Gao
- Shanghai Key Laboratory of Protected Horticultural Technology, Horticultural Research Institute, Zhuanghang Comprehensive Experiment Station, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China; (D.-D.X.); (L.G.); (L.-M.M.); (D.-Y.Z.); (Z.-H.Z.); (X.-F.L.); (Y.-Y.Z.); (H.-B.S.)
| | - Li-Ming Miao
- Shanghai Key Laboratory of Protected Horticultural Technology, Horticultural Research Institute, Zhuanghang Comprehensive Experiment Station, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China; (D.-D.X.); (L.G.); (L.-M.M.); (D.-Y.Z.); (Z.-H.Z.); (X.-F.L.); (Y.-Y.Z.); (H.-B.S.)
| | - Li-Ao Ge
- Jinshan Agricultural Technology Extension Center, Shanghai 201599, China;
| | - Ding-Yu Zhang
- Shanghai Key Laboratory of Protected Horticultural Technology, Horticultural Research Institute, Zhuanghang Comprehensive Experiment Station, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China; (D.-D.X.); (L.G.); (L.-M.M.); (D.-Y.Z.); (Z.-H.Z.); (X.-F.L.); (Y.-Y.Z.); (H.-B.S.)
| | - Zhao-Hui Zhang
- Shanghai Key Laboratory of Protected Horticultural Technology, Horticultural Research Institute, Zhuanghang Comprehensive Experiment Station, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China; (D.-D.X.); (L.G.); (L.-M.M.); (D.-Y.Z.); (Z.-H.Z.); (X.-F.L.); (Y.-Y.Z.); (H.-B.S.)
| | - Xiao-Feng Li
- Shanghai Key Laboratory of Protected Horticultural Technology, Horticultural Research Institute, Zhuanghang Comprehensive Experiment Station, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China; (D.-D.X.); (L.G.); (L.-M.M.); (D.-Y.Z.); (Z.-H.Z.); (X.-F.L.); (Y.-Y.Z.); (H.-B.S.)
| | - Yu-Ying Zhu
- Shanghai Key Laboratory of Protected Horticultural Technology, Horticultural Research Institute, Zhuanghang Comprehensive Experiment Station, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China; (D.-D.X.); (L.G.); (L.-M.M.); (D.-Y.Z.); (Z.-H.Z.); (X.-F.L.); (Y.-Y.Z.); (H.-B.S.)
| | - Hai-Bin Shen
- Shanghai Key Laboratory of Protected Horticultural Technology, Horticultural Research Institute, Zhuanghang Comprehensive Experiment Station, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China; (D.-D.X.); (L.G.); (L.-M.M.); (D.-Y.Z.); (Z.-H.Z.); (X.-F.L.); (Y.-Y.Z.); (H.-B.S.)
| | - Hong-Fang Zhu
- Shanghai Key Laboratory of Protected Horticultural Technology, Horticultural Research Institute, Zhuanghang Comprehensive Experiment Station, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China; (D.-D.X.); (L.G.); (L.-M.M.); (D.-Y.Z.); (Z.-H.Z.); (X.-F.L.); (Y.-Y.Z.); (H.-B.S.)
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6
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Kreuter S, Holzmann M, Holdsworth DG, Motoc R, Pavel AB. Three new species of Gromia (Protista, Rhizaria) identified from the Romanian Black Sea shelf. Eur J Protistol 2023; 90:126004. [PMID: 37459806 DOI: 10.1016/j.ejop.2023.126004] [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: 04/07/2023] [Revised: 06/28/2023] [Accepted: 06/30/2023] [Indexed: 09/12/2023]
Abstract
The protist genus Gromia was first described in 1835 by Dujardin and while gromiids are prominent in the marine environment, Gromia oviformis was, for a long time, the only valid species regularly recorded. To date, 16 species that are morphologically and/or genetically distinct have been described. While recent studies are documenting their diversity and their ecological importance, G. oviformis has been the sole gromiid species identified in the Black Sea, although unnamed Gromia species have also been recorded. We collected sediment samples from the Romanian continental shelf at varying depths (48 - 58 m) to study the morphological and genetic diversity of gromiids in this part of the Black Sea. Three new species, Gromia bugnae sp. nov., Gromia dianae sp. nov. and Gromia fabi sp. nov., were identified based on an integrative taxonomic approach, thus bringing the total described gromiid species to 19. Analysis of partial SSU rRNA gene sequences confirms that these are distinct species. Additionally, an undescribed species is represented by a sequence from the northern part of the Black Sea (Sevastopol, Kazachya Bay). The study provides further evidence of the diversity of gromiids in the Black Sea and underlines the importance of this little-known group in marginal seas.
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Affiliation(s)
- Sylvain Kreuter
- National Institute of Marine Geology and Geo-Ecology - GeoEcoMar, 23-25 Dimitrie Onciul St., 024053 Bucharest, Romania
| | - Maria Holzmann
- Department of Genetics and Evolution, University of Geneva, Quai Ernest Ansermet 30, 1211 Geneva 4, Switzerland
| | - Diana Grace Holdsworth
- National Institute of Marine Geology and Geo-Ecology - GeoEcoMar, 23-25 Dimitrie Onciul St., 024053 Bucharest, Romania
| | - Rozalia Motoc
- Grigore Antipa National Museum of Natural History, Sos. Kiseleff No. 1, Bucharest 011341, Romania
| | - Ana Bianca Pavel
- National Institute of Marine Geology and Geo-Ecology - GeoEcoMar, 23-25 Dimitrie Onciul St., 024053 Bucharest, Romania.
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Wang K, Xu HH, Liu BC, Bai J, Wang Y, Tang P, Lu JF, Wang Y. Shallow-marine testate amoebae with internal structures from the Lower Devonian of China. iScience 2023; 26:106678. [PMID: 37182111 PMCID: PMC10173733 DOI: 10.1016/j.isci.2023.106678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 03/08/2023] [Accepted: 04/12/2023] [Indexed: 05/16/2023] Open
Abstract
Testate amoebae, a polyphyletic protist group inhabiting a wide variety of extant ecosystems, have evolved as far back as early Neoproterozoic. However, their fossil record is discontinuous and biased toward empty shells. Here, we report an arcellinid testate amoeba species, Cangwuella ampulliformis gen. nov., sp. nov., from a shallow-marine community in the Early Devonian of Guangxi, southwestern China. With the aid of scanning electron microscopy and X-ray micro-tomography, we find that the shell of our testate amoeba contains some acetabuliform structures. Although such configuration does not match exactly with the known internal structures in extant testate amoebae, our fossils highlight the potential of exploring the ecological relationships between fossil testate amoebae and their associated organisms, and increase our knowledge on the diversity of testate amoebae in Early Devonian environments.
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Affiliation(s)
- Kai Wang
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology and Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Nanjing 210008, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hong-He Xu
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology and Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Nanjing 210008, China
- Corresponding author
| | - Bing-Cai Liu
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology and Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Nanjing 210008, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiao Bai
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology and Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Nanjing 210008, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yao Wang
- School of Geography and Tourism, Qufu Normal University, Rizhao 276826, China
| | - Peng Tang
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology and Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Nanjing 210008, China
| | - Jian-Feng Lu
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology and Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Nanjing 210008, China
| | - Yi Wang
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology and Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Nanjing 210008, China
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Kan P, Zhang N, Zeng B, Yao J, Zhi S, Chen H, Yao Z, Yangyao J, Zhang Z. Satellite taxa regulated the response of constructed wetlands microeukaryotic community to changing hydraulic loading rate. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 863:160742. [PMID: 36528101 DOI: 10.1016/j.scitotenv.2022.160742] [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: 06/09/2022] [Revised: 11/20/2022] [Accepted: 12/03/2022] [Indexed: 06/17/2023]
Abstract
Revealing how species interaction and assembly processes structure the core and satellite microeukaryotic subcommunities in an engineering environment is crucial for understanding how biodiversity influences system function. By investigating the core and satellite microeukaryotic subcommunities in constructed wetlands (CWs), we depicted an integrated distribution pattern of microeukaryotic communities in the CWs with different hydraulic loading rates (HLRs). Surprisingly, our results suggested that high HLR reduced the diversity and network stability of the microeukaryote community in CW. The stochastic process becomes more important with the increased HLR. In addition, satellite and core taxa varied inconsistently under different HLRs except for niche breadth. And the changes in all taxa were consistent with those in satellite taxa. Satellite taxa, but not core taxa, was an important driver in shaping the dynamics of microeukaryotic communities and played an important role in maintaining the stability of the microeukaryotic community. Overall, our results not only fill a gap in understanding the microeukaryotic community dynamics and its basic drivers of CWs under different HLRs but also highlights the particular importance of satellite microeukaryotes in mediating biogeochemical cycles in CWs ecosystems.
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Affiliation(s)
- Peiying Kan
- School of Civil and Environmental Engineering, Ningbo University, Ningbo 315211, China; Institute of Ocean Engineering, Ningbo University, Ningbo 315211, China
| | - Nan Zhang
- School of Civil and Environmental Engineering, Ningbo University, Ningbo 315211, China; Institute of Ocean Engineering, Ningbo University, Ningbo 315211, China
| | - Bianhao Zeng
- School of Civil and Environmental Engineering, Ningbo University, Ningbo 315211, China
| | - Jiafeng Yao
- School of Civil and Environmental Engineering, Ningbo University, Ningbo 315211, China
| | - Shuai Zhi
- School of Medicine, Ningbo University, Ningbo 315211, China
| | - Huaihai Chen
- School of Ecology, Sun Yat-sen University, Shenzhen 518107, China; State Key Laboratory of Biocontrol, Sun Yat-sen University, Shenzhen 518107, China
| | - Zhiyuan Yao
- School of Civil and Environmental Engineering, Ningbo University, Ningbo 315211, China; Institute of Ocean Engineering, Ningbo University, Ningbo 315211, China.
| | - Jiannan Yangyao
- School of Marine Sciences, Ningbo University, Ningbo 315211, China
| | - Zheyun Zhang
- Institute of Ocean Engineering, Ningbo University, Ningbo 315211, China
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9
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Xu H, Liu W, Zhang S, Wei J, Li Y, Pei H. Cyanobacterial bloom intensities determine planktonic eukaryote community structure and stability. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 838:156637. [PMID: 35697213 DOI: 10.1016/j.scitotenv.2022.156637] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 06/06/2022] [Accepted: 06/07/2022] [Indexed: 06/15/2023]
Abstract
The intensity of cyanobacterial blooms that predominate in the world's lakes and reservoirs is variable, which may lead to differing effects on the freshwater ecosystem. Planktonic eukaryotes play key roles in the structure and function of freshwater ecosystems; however, little is known about the influence of cyanobacterial blooms on eukaryotic plankton communities and their function. Herein, the dynamics of eukaryotic plankton communities in Hongze Lake, which is the fourth largest freshwater lake in China, with a range of bloom levels occurred, from low to high, were studied to reveal the effect of cyanobacterial blooms' spatial heterogeneity on planktonic eukaryotes. Results showed that the diversity, richness, and evenness of eukaryotic plankton community were not affected by low level of bloom; however, they were decreased obviously by high level of bloom. Metazoa, Ochrophyta, Chloroplastida, Cryptomonadales, and Ciliophora were the main planktonic eukaryotes in this lake. Metazoa relative abundance declined 25.1% and relative abundance of eukaryotic phytoplankton (mainly Ochrophyta, Chloroplastida, and Cryptomonadales) and Ciliophora increased 17.4% and 2.0%, respectively, during the period with low level of bloom; conversely, the site with the high bloom level manifested the opposite changes. The linkage density of planktonic eukaryotic network was 0.188 and 0.138 with low and high level of bloom, respectively, indicating the stability of planktonic eukaryotes was lower when a high level of bloom occurred compared to that of a low bloom level. Our findings indicate that cyanobacterial blooms should be controlled at low level to avoid their obvious negative impact on microeukaryotes in lakes or reservoirs.
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Affiliation(s)
- Hangzhou Xu
- School of Environmental Science and Engineering, Shandong University, Qingdao 266237, China; Shandong Provincial Engineering Center on Environmental Science and Technology, Jinan 250061, China
| | - Wei Liu
- Huai'an Hydrological Bureau, Huai'an 223005, China
| | - Shasha Zhang
- School of Environmental Science and Engineering, Shandong University, Qingdao 266237, China
| | - Jielin Wei
- School of Environmental Science and Engineering, Shandong University, Qingdao 266237, China
| | - Yizhen Li
- School of Environmental Science and Engineering, Shandong University, Qingdao 266237, China
| | - Haiyan Pei
- School of Environmental Science and Engineering, Shandong University, Qingdao 266237, China; Department of Environmental Science and Engineering, Fudan University, Shanghai 200433, China; Shandong Provincial Engineering Center on Environmental Science and Technology, Jinan 250061, China.
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10
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Fry MY, Najdrová V, Maggiolo AO, Saladi SM, Doležal P, Clemons WM. Structurally derived universal mechanism for the catalytic cycle of the tail-anchored targeting factor Get3. Nat Struct Mol Biol 2022; 29:820-830. [DOI: 10.1038/s41594-022-00798-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 05/26/2022] [Indexed: 11/09/2022]
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11
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Skujina I, Hooper C, Bass D, Feist SW, Bateman KS, Villalba A, Carballal MJ, Iglesias D, Cao A, Ward GM, Ryder DRG, Bignell JP, Kerr R, Ross S, Hazelgrove R, Macarie NA, Prentice M, King N, Thorpe J, Malham SK, McKeown NJ, Ironside JE. Discovery of the parasite Marteilia cocosarum sp. nov. In common cockle (Cerastoderma edule) fisheries in Wales, UK and its comparison with Marteilia cochillia. J Invertebr Pathol 2022; 192:107786. [PMID: 35700790 DOI: 10.1016/j.jip.2022.107786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 05/05/2022] [Accepted: 06/08/2022] [Indexed: 12/01/2022]
Abstract
Diseases of bivalve molluscs caused by paramyxid parasites of the genus Marteilia have been linked to mass mortalities and the collapse of commercially important shellfish populations. Until recently, no Marteilia spp. have been detected in common cockle (Cerastoderma edule) populations in the British Isles. Molecular screening of cockles from ten sites on the Welsh coast indicates that a Marteilia parasite is widespread in Welsh C. edule populations, including major fisheries. Phylogenetic analysis of ribosomal DNA (rDNA) gene sequences from this parasite indicates that it is a closely related but different species to Marteilia cochillia, a parasite linked to mass mortality of C. edule fisheries in Spain, and that both are related to Marteilia octospora, for which we provide new rDNA sequence data. Preliminary light and transmission electron microscope (TEM) observations support this conclusion, indicating that the parasite from Wales is located primarily within areas of inflammation in the gills and the connective tissue of the digestive gland, whereas M. cochillia is found mainly within the epithelium of the digestive gland. The impact of infection by the new species, here described as Marteilia cocosarum n. sp., upon Welsh fisheries is currently unknown.
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Affiliation(s)
- Ilze Skujina
- Institute of Biological, Environmental & Rural Sciences (IBERS), Aberystwyth University, Aberystwyth, Wales, UK
| | - Chantelle Hooper
- International Centre of Excellence for Aquatic Animal Health, The Centre for Environment, Fisheries and Aquaculture Science, Weymouth, UK
| | - David Bass
- International Centre of Excellence for Aquatic Animal Health, The Centre for Environment, Fisheries and Aquaculture Science, Weymouth, UK; Sustainable Aquaculture Futures, Biosciences, College of Life and Environmental Sciences, University of Exeter, Stocker Road, Exeter UK; Department of Life Sciences, Natural History Museum, London, UK
| | - Stephen W Feist
- International Centre of Excellence for Aquatic Animal Health, The Centre for Environment, Fisheries and Aquaculture Science, Weymouth, UK
| | - Kelly S Bateman
- International Centre of Excellence for Aquatic Animal Health, The Centre for Environment, Fisheries and Aquaculture Science, Weymouth, UK
| | - Antonio Villalba
- Centro de Investigacións Mariñas, Vilanova de Arousa, Spain; Departamento de Ciencias de la Vida, Universdad de Alcalá, Alcalá de Henares, Spain; Research Centre for Experimental Marine Biology and Biotechnology, University of the Basque Country, Plentzia, Spain
| | | | - David Iglesias
- Centro de Investigacións Mariñas, Vilanova de Arousa, Spain
| | - Asunción Cao
- Centro de Investigacións Mariñas, Vilanova de Arousa, Spain
| | - Georgia M Ward
- Department of Life Sciences, Natural History Museum, London, UK
| | - David R G Ryder
- International Centre of Excellence for Aquatic Animal Health, The Centre for Environment, Fisheries and Aquaculture Science, Weymouth, UK
| | - John P Bignell
- International Centre of Excellence for Aquatic Animal Health, The Centre for Environment, Fisheries and Aquaculture Science, Weymouth, UK
| | - Rose Kerr
- International Centre of Excellence for Aquatic Animal Health, The Centre for Environment, Fisheries and Aquaculture Science, Weymouth, UK
| | - Stuart Ross
- International Centre of Excellence for Aquatic Animal Health, The Centre for Environment, Fisheries and Aquaculture Science, Weymouth, UK
| | - Richard Hazelgrove
- International Centre of Excellence for Aquatic Animal Health, The Centre for Environment, Fisheries and Aquaculture Science, Weymouth, UK
| | - Nicolae A Macarie
- Institute of Biological, Environmental & Rural Sciences (IBERS), Aberystwyth University, Aberystwyth, Wales, UK
| | - Melanie Prentice
- Institute of Biological, Environmental & Rural Sciences (IBERS), Aberystwyth University, Aberystwyth, Wales, UK
| | - Nathan King
- School of Ocean Sciences, Bangor University, Menai Bridge, Anglesey, UK
| | - Jamie Thorpe
- School of Ocean Sciences, Bangor University, Menai Bridge, Anglesey, UK
| | - Shelagh K Malham
- School of Ocean Sciences, Bangor University, Menai Bridge, Anglesey, UK
| | - Niall J McKeown
- Institute of Biological, Environmental & Rural Sciences (IBERS), Aberystwyth University, Aberystwyth, Wales, UK
| | - Joseph E Ironside
- Institute of Biological, Environmental & Rural Sciences (IBERS), Aberystwyth University, Aberystwyth, Wales, UK.
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12
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Yang X, Sun L, Sun H, Hong Y, Xia Z, Pang W, Piao Z, Feng J, Liang Y. A Loop-Mediated Isothermal DNA Amplification (LAMP) Assay for Detection of the Clubroot Pathogen Plasmodiophora brassicae. PLANT DISEASE 2022; 106:1730-1735. [PMID: 34879734 DOI: 10.1094/pdis-11-21-2430-re] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Clubroot caused by Plasmodiophora brassicae is a serious threat to cruciferous crops around the world. The resting spores of P. brassicae are a primary source of infection and can survive in soil for many years. Detection of resting spores in soil is essential for forecasting clubroot prevalence. Detection of P. brassicae has been relying on plant bioassays or PCR-based methods. The loop-mediated isothermal DNA amplification (LAMP) is a promising approach for microorganism detection with the advantage of high sensitivity, accuracy, and convenience in viewing. In this study, we developed a LAMP assay for detection of P. brassicae in soil, roots, and seeds. This method can detect P. brassicae at a minimal amount of 1 fg of plasmid DNA or 10 resting spores in the soil. Compared with conventional PCR, the LAMP was more sensitive in detection of P. brassicae at the lower levels in soil samples. In conclusion, we elaborated a sensitive, accurate, and easy-to-use LAMP assay to detect P. brassicae, which will facilitate sustainable clubroot management and planning.
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Affiliation(s)
- Xinyu Yang
- College of Plant Protection, Shenyang Agricultural University, Shenyang, Liaoning 110866, China
| | - Lin Sun
- College of Plant Protection, Shenyang Agricultural University, Shenyang, Liaoning 110866, China
| | - Huiying Sun
- College of Plant Protection, Shenyang Agricultural University, Shenyang, Liaoning 110866, China
| | - Yingzhe Hong
- College of Plant Protection, Shenyang Agricultural University, Shenyang, Liaoning 110866, China
| | - Zihao Xia
- College of Plant Protection, Shenyang Agricultural University, Shenyang, Liaoning 110866, China
| | - Wenxing Pang
- College of Horticulture, Shenyang Agricultural University, Shenyang, Liaoning 110866, China
| | - Zhongyun Piao
- College of Horticulture, Shenyang Agricultural University, Shenyang, Liaoning 110866, China
| | - Jie Feng
- Alberta Plant Health Lab, Alberta Agriculture and Forestry, Edmonton, Alberta T5Y 6H3, Canada
| | - Yue Liang
- College of Plant Protection, Shenyang Agricultural University, Shenyang, Liaoning 110866, China
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13
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Hittorf M, Kirchmair M, Garvetto A, Neuhauser S. Molecular data reallocates Sorosphaerula radicalis (Plasmodiophorida, Phytomyxea, Rhizaria) to the genus Hillenburgia. J Eukaryot Microbiol 2022; 69:e12924. [PMID: 35593513 PMCID: PMC9543377 DOI: 10.1111/jeu.12924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
This study reports the first record of Sorosphaerula radicalis (Phytomyxea, Rhizaria) in continental Europe (Tirol, Austria) and provides first molecular data for this species. An 18S rRNA phylogeny placed S. radicalis into the Plasmodiophorida, although distant from other members of the genus Sorosphaerula and close to the parasite of water cress Hillenburgia nasturtii. To resolve this polyphyly, we compare morphological data and life cycles of Sorosphaerula veronicae (the type species of the genus Sorosphaerula), Hillenburgia nasturtii, and Sorosphaerula radicalis. We conclude that Sorosphaerula radicalis belongs to the recently established genus Hillenburgia.
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Affiliation(s)
- Michaela Hittorf
- Institute of Microbiology, University of Innsbruck, Innsbruck, Austria
| | - Martin Kirchmair
- Institute of Microbiology, University of Innsbruck, Innsbruck, Austria
| | - Andrea Garvetto
- Institute of Microbiology, University of Innsbruck, Innsbruck, Austria
| | - Sigrid Neuhauser
- Institute of Microbiology, University of Innsbruck, Innsbruck, Austria
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14
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Compositional Changes and Co-Occurrence Patterns of Planktonic Bacteria and Microeukaryotes in a Subtropical Estuarine Ecosystem, the Pearl River Delta. WATER 2022. [DOI: 10.3390/w14081227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Planktonic microorganisms in aquatic ecosystems form complex assemblages of highly interactive taxa and play key roles in biogeochemical cycles. However, the microbial interactions within bacterial and microeukaryotic communities, and the mechanisms underpinning the responses of abundant and rare microbial taxa to environmental disturbances in the river estuary remain unknown. Here, 16S and 18S rRNA gene sequencing were used to investigate the compositional changes and the co-occurrence patterns of bacterial and microeukaryotic communities. The results showed that the rare taxa in the bacterial communities were more prevalent than those in the microeukaryotic communities and may influence the resilience and resistance of microorganisms to environmental variations in estuarine ecosystems. The environmental variations had strong effects on the microeukaryotic communities and their assembly mechanisms but not on the bacterial communities in our studied area. However, based on co-occurrence network analyses, the bacterial communities had stronger links and more complex interactions than microeukaryotic communities, suggesting that bacterial networks may help improve the buffering capacities of the estuarine ecosystem against environmental change. The keystone taxa of bacteria mainly belonged to rare subcommunities, which further illustrates that rare taxa may play fundamental roles in network persistence. Overall, these results provide insights into the microbial responses of aquatic ecosystems to environmental heterogeneity.
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15
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Control Strategies of Clubroot Disease Caused by Plasmodiophora brassicae. Microorganisms 2022; 10:microorganisms10030620. [PMID: 35336194 PMCID: PMC8949847 DOI: 10.3390/microorganisms10030620] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 02/17/2022] [Accepted: 03/11/2022] [Indexed: 12/04/2022] Open
Abstract
The clubroot disease caused by the soil-borne pathogen Plasmodiophora brassicae is one of the most important diseases of cruciferous crops worldwide. As with many plant pathogens, the spread is closely related to the cultivation of suitable host plants. In addition, temperature and water availability are crucial determinants for the occurrence and reproduction of clubroot disease. Current global changes are contributing to the widespread incidence of clubroot disease. On the one hand, global trade and high prices are leading to an increase in the cultivation of the host plant rapeseed worldwide. On the other hand, climate change is improving the living conditions of the pathogen P. brassicae in temperate climates and leading to its increased occurrence. Well-known ways to control efficiently this disease include arable farming strategies: growing host plants in wide crop rotations, liming the contaminated soils, and using resistant host plants. Since chemical control of the clubroot disease is not possible or not ecologically compatible, more and more alternative control options are being investigated. In this review, we address the challenges for its control, with a focus on biological control options.
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16
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Lattos A, Chaligiannis I, Papadopoulos D, Giantsis IA, Petridou EI, Vafeas G, Staikou A, Michaelidis B. How Safe to Eat Are Raw Bivalves? Host Pathogenic and Public Health Concern Microbes within Mussels, Oysters, and Clams in Greek Markets. Foods 2021; 10:2793. [PMID: 34829074 PMCID: PMC8623680 DOI: 10.3390/foods10112793] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Revised: 11/07/2021] [Accepted: 11/11/2021] [Indexed: 12/27/2022] Open
Abstract
Raw-bivalves consumption is a wide trend in Mediterranean countries. Despite the unambiguous nutritional value of seafood, raw consumption of bivalves may involve risks that could pose a significant threat to consumers' health. Their filter-feeding behavior is responsible for the potential hosting of a wide variety of microorganisms, either pathogenic for the bivalves or public health threats. Under this prism, the current study was conducted in an effort to evaluate the risk of eating raw bivalves originating from the two biggest seafood markets in Thessaloniki, the largest production area of bivalves in Greece. Both microbiological and molecular methodologies were applied in order to assess the presence of various harmful microbes, including noroviruses, Bonamia, Marteilia, Esherichia coli, Salmonella, and Vibrio. Results indicated the presence of several Vibrio strains in the analyzed samples, of which the halophilic Vibrio harveyi was verified by 16S rRNA sequencing; other than this, no enteropathogenic Vibrio spp. was detected. Furthermore, although Esherichia coli was detected in several samples, it was mostly below the European Union (EU) legislation thresholds. Interestingly, the non-target Photobacterium damselae was also detected, which is associated with both wound infections in human and aquatic animals. Regarding host pathogenic microorganisms, apart from Vibrio harveyi, the protozoan parasite Marteilia refrigens was identified in oysters, highlighting the continuous infection of this bivalve in Greece. In conclusion, bivalves can be generally characterized as a safe-to-eat raw food, hosting more bivalve pathogenic microbes than those of public health concern.
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Affiliation(s)
- Athanasios Lattos
- Laboratory of Animal Physiology, Department of Zoology, Faculty of Science, School of Biology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (I.C.); (D.P.); (B.M.)
- Environmental Control and Research Laboratory, Region of Central Macedonia, 54625 Thessaloniki, Greece;
| | - Ilias Chaligiannis
- Laboratory of Animal Physiology, Department of Zoology, Faculty of Science, School of Biology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (I.C.); (D.P.); (B.M.)
- Hellenic Agricultural Organization-DEMETER, Veterinary Research Institute of Thessaloniki, Campus of Thermi, 57001 Thermi, Greece;
| | - Dimitrios Papadopoulos
- Laboratory of Animal Physiology, Department of Zoology, Faculty of Science, School of Biology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (I.C.); (D.P.); (B.M.)
- Environmental Control and Research Laboratory, Region of Central Macedonia, 54625 Thessaloniki, Greece;
| | - Ioannis A. Giantsis
- Environmental Control and Research Laboratory, Region of Central Macedonia, 54625 Thessaloniki, Greece;
- Department of Animal Science, Faculty of Agricultural Sciences, University of Western Macedonia, 53100 Florina, Greece
| | - Evanthia I. Petridou
- Laboratory of Microbiology and Infectious Diseases, Faculty of Veterinary Medicine, School of Health Science, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece;
| | - George Vafeas
- Hellenic Agricultural Organization-DEMETER, Veterinary Research Institute of Thessaloniki, Campus of Thermi, 57001 Thermi, Greece;
| | - Alexandra Staikou
- Environmental Control and Research Laboratory, Region of Central Macedonia, 54625 Thessaloniki, Greece;
- Department of Zoology, School of Biology, Faculty of Science, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Basile Michaelidis
- Laboratory of Animal Physiology, Department of Zoology, Faculty of Science, School of Biology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (I.C.); (D.P.); (B.M.)
- Environmental Control and Research Laboratory, Region of Central Macedonia, 54625 Thessaloniki, Greece;
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17
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Xing M, Guan G, Zhang X, Sun H, Wang Z, Pang W, Piao Z, Yang X, Feng J, Liang Y. Spatiotemporal Quantification of Plasmodiophora brassicae Inoculum in Relation to Clubroot Development Under Inoculated and Naturally Infested Field Conditions. PLANT DISEASE 2021; 105:3636-3642. [PMID: 34018813 DOI: 10.1094/pdis-03-21-0653-re] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Clubroot caused by Plasmodiophora brassicae is a destructive disease of cruciferous plants worldwide. A quantitative PCR (qPCR) system specific to P. brassicae was developed. Analysis of the qPCR sensitivity indicated that the lower limit of detection was 1 × 101 resting spores/ml, 1 × 102 spores/g of soil, and 1 × 103 spores/g of roots and seeds. The regression curves generated from the qPCR data of different samples had a parallel relationship. The difference between the theoretical and actual concentrations was lowest at 1 × 105 spores/g of sample, compared with other concentrations. The P. brassicae biomass in soil and plant root tissues after inoculated with different spore concentrations was correlated. A correlation analysis confirmed that the clubroot incidence and disease index at 6 weeks after inoculation increased as the spore concentration increased. Under field conditions, the natural inoculum density of the P. brassicae population decreased at the early stage and then increased, with P. brassicae mainly being detected at a soil depth of 0 to 50 cm. The horizontal distribution of P. brassicae varied in the field with occurrences of hot spots. This study established a qPCR-based method for quantitative detection of clubroot. The developed assay is useful for monitoring the spatiotemporal dynamics of P. brassicae in the field. It may also be applicable for clubroot forecasting as a part of proactive disease management.
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Affiliation(s)
- Manzhu Xing
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
- Liaoning Key Laboratory of Plant Pathology, Shenyang Agricultural University, Shenyang 110866, China
| | - Gege Guan
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
- Liaoning Key Laboratory of Plant Pathology, Shenyang Agricultural University, Shenyang 110866, China
| | - Xinyu Zhang
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
- Liaoning Key Laboratory of Plant Pathology, Shenyang Agricultural University, Shenyang 110866, China
| | - Huiying Sun
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
- Liaoning Key Laboratory of Plant Pathology, Shenyang Agricultural University, Shenyang 110866, China
| | - Zehao Wang
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
- Liaoning Key Laboratory of Plant Pathology, Shenyang Agricultural University, Shenyang 110866, China
| | - Wenxing Pang
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China
| | - Zhongyun Piao
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China
| | - Xinyu Yang
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
- Liaoning Key Laboratory of Plant Pathology, Shenyang Agricultural University, Shenyang 110866, China
| | - Jie Feng
- Alberta Plant Health Lab, Alberta Agriculture and Forestry, Edmonton, Alberta T5Y6H3, Canada
| | - Yue Liang
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
- Liaoning Key Laboratory of Plant Pathology, Shenyang Agricultural University, Shenyang 110866, China
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18
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Kavehei A, Hose GC, Chariton AA, Gore DB. Application of environmental DNA for assessment of contamination downstream of a legacy base metal mine. JOURNAL OF HAZARDOUS MATERIALS 2021; 416:125794. [PMID: 33862483 DOI: 10.1016/j.jhazmat.2021.125794] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Revised: 03/11/2021] [Accepted: 03/26/2021] [Indexed: 06/12/2023]
Abstract
Acid Rock Drainage (ARD) from legacy mines can negatively impact the biota in sediments and waters for tens of kilometers downstream. Here we used environmental (e)DNA metabarcoding to assess the impacts of metal contaminants on biota in sediment and water downstream of a legacy base metal sulfide mine in southeastern Australia, as exemplar of similar mines elsewhere. Concentrations of metals in water were below Australian water quality guideline values at 20 km downstream for copper (Cu), 40 km downstream for zinc (Zn) and 10 km downstream for lead (Pb). Sediment metal concentrations were below national guideline concentrations at 10 km downstream for Cu, 60 km downstream for Zn and 20 km downstream for Pb. In contrast, metabarcoding showed that biological communities from sediment samples at 10 km and 20 km downstream were similar to sites close to the mine and thus indicative of being impacted, despite metal concentrations being relatively low. As we illustrate, when combined with sediment and water chemistry, metabarcoding can provide more ecological robust perspective on the downstream effects of legacy mines, capturing the sensitivities of a diverse range of organisms.
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Affiliation(s)
- Armin Kavehei
- Department of Earth and Environmental Sciences, Macquarie University, Sydney 2109, Australia.
| | - Grant C Hose
- Department of Biological Sciences, Macquarie University, Sydney 2109, Australia
| | - Anthony A Chariton
- Department of Biological Sciences, Macquarie University, Sydney 2109, Australia
| | - Damian B Gore
- Department of Earth and Environmental Sciences, Macquarie University, Sydney 2109, Australia
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19
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Zhu C, Liu W, Li X, Xu Y, El-Serehy HA, Al-Farraj SA, Ma H, Stoeck T, Yi Z. High salinity gradients and intermediate spatial scales shaped similar biogeographical and co-occurrence patterns of microeukaryotes in a tropical freshwater-saltwater ecosystem. Environ Microbiol 2021; 23:4778-4796. [PMID: 34258839 DOI: 10.1111/1462-2920.15668] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Revised: 06/12/2021] [Accepted: 07/09/2021] [Indexed: 11/26/2022]
Abstract
Microeukaryotes play key ecological roles in the microbial web of aquatic ecosystems. However, large knowledge gaps urgently need to be filled regarding the biogeography with associated shaping mechanisms and co-occurrence patterns of microeukaryotes under freshwater-saltwater gradients, especially true in tropical regions. Here, we investigated microeukaryotes of six mixed freshwater-saltwater regions in the Pearl River Estuary and surrounding coasts in southern China, with salinity ranging 0.1-32.0% and distances spanned up to 500 km, using molecular ecological methods. Results indicate that the biogeography of abundant and rare microeukaryotic communities was similar, both their co-occurrence patterns and biogeographical patterns were driven by deterministic and stochastic processes. The environmental factors with higher selective pressure than dispersal limitation meant that the role of deterministic process in structuring communities was more significant than that of stochastic process, and salinity played important role in structuring both microeukaryotic communities and networks. The abundant communities had stronger influence on entire microeukaryotic communities and seemed to be more sensitive to environmental changes than their rare counterparts, while rare ones had stronger interspecific relationships. Finally, the geographic scale and environmental gradients of study regions should firstly be clarified in future research on the ecological processes of microeukaryotes before conclusions are drawn.
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Affiliation(s)
- Changyu Zhu
- Institute of Evolution & Marine Biodiversity, and College of Fisheries, Ocean University of China, Qingdao, 266003, China.,Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Weiwei Liu
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China.,Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Science, Guangzhou, 510301, China
| | - Xinghao Li
- Key Laboratory of Regional Development and Environmental Response, and Hubei Engineering Research Center for Rural Drinking Water Security, Hubei University, Wuhan, 430062, China
| | - Yusen Xu
- Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Hamed A El-Serehy
- Zoology Department, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia.,Department of Oceanography, College of Science, Port Said University, Port Said, 42511, Egypt
| | - Saleh A Al-Farraj
- Zoology Department, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Honggang Ma
- Institute of Evolution & Marine Biodiversity, and College of Fisheries, Ocean University of China, Qingdao, 266003, China
| | - Thorsten Stoeck
- Department of Ecology, University of Technology Kaiserslautern, Kaiserslautern, 67663, Germany
| | - Zhenzhen Yi
- Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
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20
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Høyer AK, Hodkinson TR. Hidden Fungi: Combining Culture-Dependent and -Independent DNA Barcoding Reveals Inter-Plant Variation in Species Richness of Endophytic Root Fungi in Elymus repens. J Fungi (Basel) 2021; 7:jof7060466. [PMID: 34207673 PMCID: PMC8226481 DOI: 10.3390/jof7060466] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 05/27/2021] [Accepted: 06/01/2021] [Indexed: 01/04/2023] Open
Abstract
The root endophyte community of the grass species Elymus repens was investigated using both a culture-dependent approach and a direct amplicon sequencing method across five sites and from individual plants. There was much heterogeneity across the five sites and among individual plants. Focusing on one site, 349 OTUs were identified by direct amplicon sequencing but only 66 OTUs were cultured. The two approaches shared ten OTUs and the majority of cultured endophytes do not overlap with the amplicon dataset. Media influenced the cultured species richness and without the inclusion of 2% MEA and full-strength MEA, approximately half of the unique OTUs would not have been isolated using only PDA. Combining both culture-dependent and -independent methods for the most accurate determination of root fungal species richness is therefore recommended. High inter-plant variation in fungal species richness was demonstrated, which highlights the need to rethink the scale at which we describe endophyte communities.
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21
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Arthur AL, Crawford A, Houdusse A, Titus MA. VASP-mediated actin dynamics activate and recruit a filopodia myosin. eLife 2021; 10:68082. [PMID: 34042588 PMCID: PMC8352590 DOI: 10.7554/elife.68082] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 05/20/2021] [Indexed: 11/17/2022] Open
Abstract
Filopodia are thin, actin-based structures that cells use to interact with their environments. Filopodia initiation requires a suite of conserved proteins but the mechanism remains poorly understood. The actin polymerase VASP and a MyTH-FERM (MF) myosin, DdMyo7 in amoeba, are essential for filopodia initiation. DdMyo7 is localized to dynamic regions of the actin-rich cortex. Analysis of VASP mutants and treatment of cells with anti-actin drugs shows that myosin recruitment and activation in Dictyostelium requires localized VASP-dependent actin polymerization. Targeting of DdMyo7 to the cortex alone is not sufficient for filopodia initiation; VASP activity is also required. The actin regulator locally produces a cortical actin network that activates myosin and together they shape the actin network to promote extension of parallel bundles of actin during filopodia formation. This work reveals how filopodia initiation requires close collaboration between an actin-binding protein, the state of the actin cytoskeleton and MF myosin activity.
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Affiliation(s)
- Ashley L Arthur
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, United States
| | - Amy Crawford
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, United States
| | - Anne Houdusse
- Structural Motility, Institut Curie, Paris Université Sciences et Lettres, Sorbonne Université, Paris, France
| | - Margaret A Titus
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, United States
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Abstract
Filopodia, microvilli and stereocilia represent an important group of plasma membrane protrusions. These specialized projections are supported by parallel bundles of actin filaments and have critical roles in sensing the external environment, increasing cell surface area, and acting as mechanosensors. While actin-associated proteins are essential for actin-filament elongation and bundling in these protrusions, myosin motors have a surprising role in the formation and extension of filopodia and stereocilia and in the organization of microvilli. Actin regulators and specific myosins collaborate in controlling the length of these structures. Myosins can transport cargoes along the length of these protrusions, and, in the case of stereocilia and microvilli, interactions with adaptors and cargoes can also serve to anchor adhesion receptors to the actin-rich core via functionally conserved motor-adaptor complexes. This review highlights recent progress in understanding the diverse roles myosins play in filopodia, microvilli and stereocilia.
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Affiliation(s)
- Anne Houdusse
- Structural Motility, Institut Curie, Paris Université Sciences et Lettres, Sorbonne Université, CNRS UMR144, 75005 Paris, France.
| | - Margaret A Titus
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455, USA.
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Munir S, Sun J, Morton SL. The First Record and Classification of Planktonic Radiolarian ( Phylum Retaria) and Phaeodarian ( Phylum Cercozoa) in the Eastern Indian Ocean. BIOLOGY 2021; 10:biology10030202. [PMID: 33800496 PMCID: PMC8002099 DOI: 10.3390/biology10030202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 03/04/2021] [Accepted: 03/05/2021] [Indexed: 11/16/2022]
Abstract
Simple Summary Phylum Retaria and Phylum Cercozoa consists of the siliceous planktonic organisms, commonly referred to as Radiolarians, were investigated from 200 m depth to the surface in the eastern Indian Ocean (80.00°–96.10° E, 10.08° N–6.00° S) during a 2 months cruise (10 April–13 May 2014). Samples collected from 44 locations were analyzed by using both light and electron microscopy. Out of 168 taxa, 60 newly recorded species from the groups i.e., Acantharia, Collodaria, Pheodaria, Taxopodida and Polycystinea were recorded for the first time. Abstract Siliceous planktonic species of the phyla Retaria and Cercozoa were investigated from the surface to a 200 m depth around the eastern Indian Ocean (80.00°–96.10° E, 10.08° N–6.00° S) during a 2-month cruise (10 April–13 May 2014). These species are commonly referred to as Radiolarians and are found in all of the world’s oceans; however, this is a detailed investigation of the species’ diversity in the eastern Indian Ocean. Samples were collected from the eastern Indian Ocean using a plankton towing net during a vertical haul from 44 sampling stations, which resulted in 168 taxa, including 60 species that were newly recorded in the study area. The main purpose of this work was to identify members of the phyla Retaria and Cercozoa and their distribution in the eastern Indian Ocean. The species’ morphology, identification, notes, and new geographical records are briefly described.
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Affiliation(s)
- Sonia Munir
- Research Centre for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin 300457, China;
| | - Jun Sun
- Research Centre for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin 300457, China;
- College of Marine Science and Technology, China University of Geosciences, Wuhan 430074, China
- Correspondence: ; Tel.: +86-60-601-116
| | - Steve L. Morton
- National Ocean Service, NOAA, 331 Fort Johnson Road, Charleston, SC 29412, USA;
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Ros-Rocher N, Pérez-Posada A, Leger MM, Ruiz-Trillo I. The origin of animals: an ancestral reconstruction of the unicellular-to-multicellular transition. Open Biol 2021; 11:200359. [PMID: 33622103 PMCID: PMC8061703 DOI: 10.1098/rsob.200359] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
How animals evolved from a single-celled ancestor, transitioning from a unicellular lifestyle to a coordinated multicellular entity, remains a fascinating question. Key events in this transition involved the emergence of processes related to cell adhesion, cell–cell communication and gene regulation. To understand how these capacities evolved, we need to reconstruct the features of both the last common multicellular ancestor of animals and the last unicellular ancestor of animals. In this review, we summarize recent advances in the characterization of these ancestors, inferred by comparative genomic analyses between the earliest branching animals and those radiating later, and between animals and their closest unicellular relatives. We also provide an updated hypothesis regarding the transition to animal multicellularity, which was likely gradual and involved the use of gene regulatory mechanisms in the emergence of early developmental and morphogenetic plans. Finally, we discuss some new avenues of research that will complement these studies in the coming years.
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Affiliation(s)
- Núria Ros-Rocher
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Catalonia, Spain
| | - Alberto Pérez-Posada
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Catalonia, Spain.,Centro Andaluz de Biología del Desarrollo (CSIC-Universidad Pablo de Olavide), Carretera de Utrera Km 1, 41013 Sevilla, Andalusia, Spain
| | - Michelle M Leger
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Catalonia, Spain
| | - Iñaki Ruiz-Trillo
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Catalonia, Spain.,Departament de Genètica, Microbiologia i Estadística, Institut de Recerca de la Biodiversitat, Universitat de Barcelona, Avinguda Diagonal 643, 08028 Barcelona, Catalonia, Spain.,ICREA, Passeig Lluís Companys 23, 08010 Barcelona, Catalonia, Spain
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Dumack K, Duckert C, Meinhardt R, Lara E, Bonkowski M. Description of Phaeobola aeris gen. nov., sp. nov (Rhizaria, Cercozoa, Euglyphida) Sheds Light on Euglyphida's Dark Matter. J Eukaryot Microbiol 2020; 68:e12835. [PMID: 33222324 DOI: 10.1111/jeu.12835] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 10/06/2020] [Accepted: 10/26/2020] [Indexed: 11/30/2022]
Abstract
The majority of Euglyphida species are characterised by shells with imbricated silica scales. Environmental surveys indicate a large unexplored diversity and recent efforts hinted at a certain diversity of yet undescribed, inconspicuous, scale-lacking Euglyphida. Here we describe Phaeobola aeris gen. nov., sp. nov. that shows a variety of morphological characters typical for the Euglyphida but lacks silica scales-instead, this species bears an agglutinated test. Neither its morphology nor phylogenetic placement allows its assignment to any currently described family. We erected the yet monospecific genus Phaeobola gen. nov., which with yet available data remain Euglyphida incertae sedis.
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Affiliation(s)
- Kenneth Dumack
- Terrestrial Ecology, Institute of Zoology, University of Cologne, Zülpicher Str. 47b, Köln, 50674, Germany
| | - Clément Duckert
- Laboratory of Soil Biodiversity, Institute of Biology, University of Neuchâtel, Rue Emile-Argand 11, Neuchâtel, CH-2000, Switzerland
| | - Raphaela Meinhardt
- Terrestrial Ecology, Institute of Zoology, University of Cologne, Zülpicher Str. 47b, Köln, 50674, Germany
| | - Enrique Lara
- Real Jardín Botánico, CSIC, Plaza de Murillo 2, Madrid, 28014, Spain
| | - Michael Bonkowski
- Terrestrial Ecology, Institute of Zoology, University of Cologne, Zülpicher Str. 47b, Köln, 50674, Germany
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Hittorf M, Letsch-Praxmarer S, Windegger A, Bass D, Kirchmair M, Neuhauser S. Revised Taxonomy and Expanded Biodiversity of the Phytomyxea (Rhizaria, Endomyxa). J Eukaryot Microbiol 2020; 67:648-659. [PMID: 32654223 PMCID: PMC7756720 DOI: 10.1111/jeu.12817] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 05/21/2020] [Accepted: 06/25/2020] [Indexed: 12/27/2022]
Abstract
Phytomyxea (phytomyxids) is a group of obligate biotrophic pathogens belonging to the Rhizaria. Some phytomyxids are well studied and include known plant pathogens such as Plasmodiophora brassicae, the causal agent of clubroot disease. Despite this economic importance, the taxonomy and biodiversity of this group are largely cryptic, with many species described in the premolecular area. Some of these species were key for establishing the morphotaxonomic concepts that define most genera to this day, but systematic efforts to include and integrate those species into molecular studies are still lacking. The aim of this study was to expand our understanding of phytomyxid biodiversity in terrestrial environments. Thirty-eight environmental samples from habitats in which novel and known diversity of Phytomyxea was expected were analysed. We were able to generate 18S rRNA sequences from Ligniera verrucosa, a species which is well defined based on ultrastructure. Phylogenetic analyses of the collected sequences rendered the genera Lignera, Plasmodiophora and Spongospora polyphyletic, and identified two novel and apparently diverse lineages (clade 17, clade 18). Based on these findings and on data from previous studies, we formally establish the new genera Pseudoligniera n. gen. for L. verrucosa,Hillenburgia n. gen. for Spongospora nasturtii and revert Plasmodiophora diplantherae to its original name Ostenfeldiella diplantherae.
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Affiliation(s)
- Michaela Hittorf
- Institute of Microbiology, University of Innsbruck, Technikerstr. 25, 6020, Innsbruck, Austria
| | | | - Alexandra Windegger
- Institute of Microbiology, University of Innsbruck, Technikerstr. 25, 6020, Innsbruck, Austria
| | - David Bass
- Department of Life Sciences, The Natural History Museum, Cromwell Road, London, SW7 5BD, United Kingdom.,Centre for Environment, Fisheries and Aquaculture Science (Cefas), Barrack Road, The Nothe, Weymouth, DT4 8UB, United Kingdom
| | - Martin Kirchmair
- Institute of Microbiology, University of Innsbruck, Technikerstr. 25, 6020, Innsbruck, Austria
| | - Sigrid Neuhauser
- Institute of Microbiology, University of Innsbruck, Technikerstr. 25, 6020, Innsbruck, Austria
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Shiratori T, Yabuki A, Ishida KI. Morphology, Ultrastructure, and Phylogeny of Two Novel Species of Ventrifissura (V. oblonga n. sp. and V. velata n. sp., Thecofilosea, Cercozoa). Protist 2020; 171:125731. [PMID: 32464531 DOI: 10.1016/j.protis.2020.125731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 02/05/2020] [Accepted: 04/03/2020] [Indexed: 10/24/2022]
Abstract
Ventrifissura is a group of poorly studied heterotrophic biflagellates in the phylum Cercozoa. Despite a phylogenetic placement with only weak support and a lack of ultrastructural data, Ventrifissura was assigned to Thecofilosea. In the presented study, we established cultures of two novel species of Ventrifissura (V. oblonga n. sp. and V. velata n. sp.) isolated from coastal marine environments in Japan, and performed light and electron microscopy observations and molecular phylogenetic analysis. Transmission electron microscopy revealed that V. oblonga shares several ultrastructural characteristics with thecofilosean flagellates, including permanently condensed chromosomes, a extracellular theca, and slender extrusomes. Molecular phylogenetic analysis could not resolve the phylogenetic position, but the possibility that Ventrifissura clusters into Ventrifilosa was supported by approximately unbiased tests. Based on both morphological and phylogenetic findings, we concluded that Ventrifissura is a basal lineage of Thecofilosea.
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Affiliation(s)
- Takashi Shiratori
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan; Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima, Yokosuka, Kanagawa, 237-0061, Japan.
| | - Akinori Yabuki
- Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima, Yokosuka, Kanagawa, 237-0061, Japan
| | - Ken-Ichiro Ishida
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
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Xu H, Zhang S, Ma G, Zhang Y, Li Y, Pei H. 18S rRNA gene sequencing reveals significant influence of anthropogenic effects on microeukaryote diversity and composition along a river-to-estuary gradient ecosystem. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 705:135910. [PMID: 31837544 DOI: 10.1016/j.scitotenv.2019.135910] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 11/28/2019] [Accepted: 12/01/2019] [Indexed: 06/10/2023]
Abstract
Microeukaryotes play key roles in the structure and functioning of lotic ecosystems; however, little is known about the relative importance of the processes that drive planktonic microeukaryotic biogeography in rivers, especially the effects of anthropogenic inputs (e.g., wastewater discharge and pesticide and fertilizer use) on the taxonomic and functional diversity of microeukaryotes. Herein 18S ribosomal RNA sequencing was used to examine the assembly of microeukaryotes in samples from Xiaoqing River, a mid-sized river in north China that runs through urban and agricultural areas and then discharges into the Bohai Sea. We found that diversity of microeukaryote declined obviously due to the excessive disturbance of the urban and agricultural activities in the midstream of the river. Our results support the concept that species sorting caused by local pollution can largely determine microeukaryotic community structure when significant environmental gradients exist in polluted running-water ecosystems and that compositional dissimilarity increased with increases in the Euclidean distance of environmental variables. Variation of microeukaryotic diversity was mainly determined by changes in levels of nutrients, dissolved oxygen, turbidity, and salinity and they can affect the rare subcommunities significantly. Furthermore, zooplankton were dominated in rare taxa, meanwhile phytoplankton was composed by the abundant taxa mainly. These findings confirmed the dynamic character of riverine ecosystems and the significance of human activities in shaping microeukaryote diversity in rivers.
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Affiliation(s)
- Hangzhou Xu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China; School of Environmental Science and Engineering, Shandong University, Qingdao 266237, China
| | - Shasha Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China; School of Environmental Science and Engineering, Shandong University, Qingdao 266237, China
| | - Guangxiang Ma
- Shandong Academy of Environmental Sciences Co., Ltd., Jinan 250013, China
| | - Yanfang Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China; School of Environmental Science and Engineering, Shandong University, Qingdao 266237, China
| | - Yizhen Li
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China; School of Environmental Science and Engineering, Shandong University, Qingdao 266237, China
| | - Haiyan Pei
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China; School of Environmental Science and Engineering, Shandong University, Qingdao 266237, China; Shandong Provincial Engineering Center on Environmental Science and Technology, Jinan 250061, China.
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29
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Hervé V, Lopez PJ. Analysis of interdomain taxonomic patterns in urban street mats. Environ Microbiol 2020; 22:1280-1293. [PMID: 31997567 DOI: 10.1111/1462-2920.14933] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 01/15/2020] [Accepted: 01/27/2020] [Indexed: 11/28/2022]
Abstract
Streets are constantly crossed by billions of vehicles and pedestrians. Their gutters, which convey stormwater and contribute to waste management, and are important for human health and well-being, probably play a number of ecological roles. Street surfaces may also represent an important part of city surface areas. To better characterize the ecology of this yet poorly explored compartment, we used filtration and DNA metabarcoding to address microbial community composition and assembly across the city of Paris, France. Diverse bacterial and eukaryotic taxonomic groups were identified, including members involved in key biogeochemical processes, along with a number of parasites and putative pathogens of human, animals and plants. We showed that the beta diversity patterns between bacterial and eukaryotic communities were correlated, suggesting interdomain associations. Beta diversity analyses revealed the significance of biotic factors (cohesion metrics) in shaping gutter microbial community assembly and, to a lesser extent, the contribution of abiotic factors (pH and conductivity). Co-occurrences analysis confirmed contrasting non-random patterns both within and between domains of life, specifically when comparing diatoms and fungi. Our results highlight microbial coexistence patterns in streets and reinforce the need to further explore biodiversity in urban ground transportation infrastructures.
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Affiliation(s)
- Vincent Hervé
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse 10, 35043, Marburg, Germany
| | - Pascal Jean Lopez
- Laboratoire Biologie des ORganismes et Ecosystèmes Aquatiques (BOREA), Muséum national d'Histoire naturelle, Centre National de la Recherche Scientifique, Sorbonne Université, Institut de Recherche pour le Développement, Université de Caen Normandie, Université des Antilles, 43 rue Cuvier, 75005, Paris, France
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30
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Degrune F, Dumack K, Fiore-Donno AM, Bonkowski M, Sosa-Hernández MA, Schloter M, Kautz T, Fischer D, Rillig MC. Distinct communities of Cercozoa at different soil depths in a temperate agricultural field. FEMS Microbiol Ecol 2019; 95:5420472. [DOI: 10.1093/femsec/fiz041] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 03/21/2019] [Indexed: 11/13/2022] Open
Affiliation(s)
- Florine Degrune
- Freie Universität Berlin, Institut für Biologie, Altensteinstr. 6, 14195 Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Altensteinstr. 34, 14195 Berlin, Germany
| | - Kenneth Dumack
- Terrestrial Ecology, Institute of Zoology, University of Cologne, Zülpicher Str. 47b, 50674 Köln, Germany
| | - Anna Maria Fiore-Donno
- Terrestrial Ecology, Institute of Zoology, University of Cologne, Zülpicher Str. 47b, 50674 Köln, Germany
| | - Michael Bonkowski
- Terrestrial Ecology, Institute of Zoology, University of Cologne, Zülpicher Str. 47b, 50674 Köln, Germany
| | - Moisés A Sosa-Hernández
- Freie Universität Berlin, Institut für Biologie, Altensteinstr. 6, 14195 Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Altensteinstr. 34, 14195 Berlin, Germany
| | - Michael Schloter
- Research Unit for Environmental Genomics, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Timo Kautz
- Humboldt-Universität zu Berlin. Albrecht Daniel Thaer-Institut für Agrar- und Gartenbauwissenschaften, Albrecht-Thaer-Weg 5, 14195 Berlin, Germany
| | - Doreen Fischer
- Research Unit for Environmental Genomics, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Matthias C Rillig
- Freie Universität Berlin, Institut für Biologie, Altensteinstr. 6, 14195 Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Altensteinstr. 34, 14195 Berlin, Germany
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A time travel story: metagenomic analyses decipher the unknown geographical shift and the storage history of possibly smuggled antique marble statues. ANN MICROBIOL 2019. [DOI: 10.1007/s13213-019-1446-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
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Ward GM, Feist SW, Noguera P, Marcos-López M, Ross S, Green M, Urrutia A, Bass D. Detection and characterisation of haplosporidian parasites of the blue mussel Mytilus edulis, including description of the novel parasite Minchinia mytili n. sp. DISEASES OF AQUATIC ORGANISMS 2019; 133:57-68. [PMID: 31089003 DOI: 10.3354/dao03326] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The edible mussel Mytilus edulis is a major aquaculture commodity in Europe, with 168000 t produced in 2015. A number of abundant, well characterised parasites of the species are known, though none are considered to cause significant mortality. Haplosporida (Rhizaria, Endomyxa) is an order of protistan parasites of aquatic invertebrates, the best studied of which are the oyster pathogens Haplosporidium nelsoni and Bonamia ostreae. While these species are well characterised within their hosts, the diversity, life-cycle and modes of transmission of haplosporidians are very poorly understood. Haplosporidian parasites have previously been reported from Mytilus spp., however the majority of these remain uncharacterised, and no molecular data exist for any species. In this study, we identified 2 novel haplosporidian parasites of M. edulis present in the UK. The first of these, observed by light microscopy and in situ hybridisation infecting the gills, mantle, gonadal tubules and digestive connective tissues of mussels in the Tamar estuary, England, we describe as Minchinia mytili on the basis of 18S sequence data. The second, observed infecting a single archive specimen collected in Loch Spelve, Mull, Scotland, infects the foot muscle, gills and connective tissue of the digestive gland. Sequence data places this parasite in an uncharacterised clade of sequences amplified from tropical bivalve guts and water samples, sister to H. nelsoni. Screening of water and sediment samples collected at the sample site in the Tamar estuary revealed the presence of both sequence types in the water column, suggesting host-free or planktonic life stages.
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Affiliation(s)
- Georgia M Ward
- Department of Life Sciences, Natural History Museum, London SW7 5BD, UK
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Irwin NA, Tikhonenkov DV, Hehenberger E, Mylnikov AP, Burki F, Keeling PJ. Phylogenomics supports the monophyly of the Cercozoa. Mol Phylogenet Evol 2019; 130:416-423. [DOI: 10.1016/j.ympev.2018.09.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 09/06/2018] [Indexed: 01/09/2023]
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Phylogeny and Classification of Novel Diversity in Sainouroidea (Cercozoa, Rhizaria) Sheds Light on a Highly Diverse and Divergent Clade. Protist 2018; 169:853-874. [DOI: 10.1016/j.protis.2018.08.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 08/09/2018] [Accepted: 08/10/2018] [Indexed: 01/08/2023]
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Cavalier-Smith T, Chao EE, Lewis R. Multigene phylogeny and cell evolution of chromist infrakingdom Rhizaria: contrasting cell organisation of sister phyla Cercozoa and Retaria. PROTOPLASMA 2018; 255:1517-1574. [PMID: 29666938 PMCID: PMC6133090 DOI: 10.1007/s00709-018-1241-1] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 03/12/2018] [Indexed: 05/18/2023]
Abstract
Infrakingdom Rhizaria is one of four major subgroups with distinct cell body plans that comprise eukaryotic kingdom Chromista. Unlike other chromists, Rhizaria are mostly heterotrophic flagellates, amoebae or amoeboflagellates, commonly with reticulose (net-like) or filose (thread-like) feeding pseudopodia; uniquely for eukaryotes, cilia have proximal ciliary transition-zone hub-lattices. They comprise predominantly flagellate phylum Cercozoa and reticulopodial phylum Retaria, whose exact phylogenetic relationship has been uncertain. Given even less clear relationships amongst cercozoan classes, we sequenced partial transcriptomes of seven Cercozoa representing five classes and endomyxan retarian Filoreta marina to establish 187-gene multiprotein phylogenies. Ectoreta (retarian infraphyla Foraminifera, Radiozoa) branch within classical Cercozoa as sister to reticulose Endomyxa. This supports recent transfer of subphylum Endomyxa from Cercozoa to Retaria alongside subphylum Ectoreta which embraces classical retarians where capsules or tests subdivide cells into organelle-containing endoplasm and anastomosing pseudopodial net-like ectoplasm. Cercozoa are more homogeneously filose, often with filose pseudopodia and/or posterior ciliary gliding motility: zooflagellate Helkesimastix and amoeboid Guttulinopsis form a strongly supported clade, order Helkesida. Cercomonads are polyphyletic (Cercomonadida sister to glissomonads; Paracercomonadida deeper). Thecofilosea are a clade, whereas Imbricatea may not be; Sarcomonadea may be paraphyletic. Helkesea and Metromonadea are successively deeper outgroups within cercozoan subphylum Monadofilosa; subphylum Reticulofilosa (paraphyletic on site-heterogeneous trees) branches earliest, Granofilosea before Chlorarachnea. Our multiprotein trees confirm that Rhizaria are sisters of infrakingdom Halvaria (Alveolata, Heterokonta) within chromist subkingdom Harosa (= SAR); they further support holophyly of chromist subkingdom Hacrobia, and are consistent with holophyly of Chromista as sister of kingdom Plantae. Site-heterogeneous rDNA trees group Kraken with environmental DNA clade 'eSarcomonad', not Paracercomonadida. Ectoretan fossil dates evidence ultrarapid episodic stem sequence evolution. We discuss early rhizarian cell evolution and multigene tree coevolutionary patterns, gene-paralogue evidence for chromist monophyly, and integrate this with fossil evidence for the age of Rhizaria and eukaryote cells, and revise rhizarian classification.
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Affiliation(s)
| | - Ema E Chao
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK
| | - Rhodri Lewis
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK
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Page KA, Flannery MK. Microbial Epiphytes of Deep-Water Moss in Crater Lake, Oregon. NORTHWEST SCIENCE 2018. [DOI: 10.3955/046.092.0402] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Kathleen A. Page
- Southern Oregon University Department of Biology, 1250 Siskiyou Boulevard, Ashland, Oregon 97520
| | - Meghan K. Flannery
- Southern Oregon University Department of Biology, 1250 Siskiyou Boulevard, Ashland, Oregon 97520
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Distinct patterns and processes of abundant and rare eukaryotic plankton communities following a reservoir cyanobacterial bloom. ISME JOURNAL 2018; 12:2263-2277. [PMID: 29899512 PMCID: PMC6092360 DOI: 10.1038/s41396-018-0159-0] [Citation(s) in RCA: 295] [Impact Index Per Article: 49.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2018] [Revised: 04/29/2018] [Accepted: 05/01/2018] [Indexed: 11/08/2022]
Abstract
Plankton communities normally consist of few abundant and many rare species, yet little is known about the ecological role of rare planktonic eukaryotes. Here we used a 18S ribosomal DNA sequencing approach to investigate the dynamics of rare planktonic eukaryotes, and to explore the co-occurrence patterns of abundant and rare eukaryotic plankton in a subtropical reservoir following a cyanobacterial bloom event. Our results showed that the bloom event significantly altered the eukaryotic plankton community composition and rare plankton diversity without affecting the diversity of abundant plankton. The similarities of both abundant and rare eukaryotic plankton subcommunities significantly declined with the increase in time-lag, but stronger temporal turnover was observed in rare taxa. Further, species turnover of both subcommunities explained a higher percentage of the community variation than species richness. Both deterministic and stochastic processes significantly influenced eukaryotic plankton community assembly, and the stochastic pattern (e.g., ecological drift) was particularly pronounced for rare taxa. Co-occurrence network analysis revealed that keystone taxa mainly belonged to rare species, which may play fundamental roles in network persistence. Importantly, covariations between rare and non-rare taxa were predominantly positive, implying multispecies cooperation might contribute to the stability and resilience of the microbial community. Overall, these findings expand current understanding of the ecological mechanisms and microbial interactions underlying plankton dynamics in changing aquatic ecosystems.
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Marteilia refringens and Marteilia pararefringens sp. nov. are distinct parasites of bivalves and have different European distributions. Parasitology 2018; 145:1483-1492. [PMID: 29886855 PMCID: PMC6137380 DOI: 10.1017/s003118201800063x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Marteilia refringens causes marteiliosis in oysters, mussels and other bivalve molluscs. This parasite previously comprised two species, M. refringens and Marteilia maurini, which were synonymized in 2007 and subsequently referred to as M. refringens ‘O-type’ and ‘M-type’. O-type has caused mass mortalities of the flat oyster Ostrea edulis. We used high throughput sequencing and histology to intensively screen flat oysters and mussels (Mytilus edulis) from the UK, Sweden and Norway for infection by both types and to generate multi-gene datasets to clarify their genetic distinctiveness. Mussels from the UK, Norway and Sweden were more frequently polymerase chain reaction (PCR)-positive for M-type (75/849) than oysters (11/542). We did not detect O-type in any northern European samples, and no histology-confirmed Marteilia-infected oysters were found in the UK, Norway and Sweden, even where co-habiting mussels were infected by the M-type. The two genetic lineages within ‘M. refringens’ are robustly distinguishable at species level. We therefore formally define them as separate species: M. refringens (previously O-type) and Marteilia pararefringens sp. nov. (M-type). We designed and tested new Marteilia-specific PCR primers amplifying from the 3’ end of the 18S rRNA gene through to the 5.8S gene, which specifically amplified the target region from both tissue and environmental samples.
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Schuelke T, Pereira TJ, Hardy SM, Bik HM. Nematode-associated microbial taxa do not correlate with host phylogeny, geographic region or feeding morphology in marine sediment habitats. Mol Ecol 2018; 27:1930-1951. [DOI: 10.1111/mec.14539] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2017] [Revised: 12/18/2017] [Accepted: 01/02/2018] [Indexed: 01/18/2023]
Affiliation(s)
- Taruna Schuelke
- Department of Nematology; University of California, Riverside; Riverside CA USA
| | - Tiago José Pereira
- Department of Nematology; University of California, Riverside; Riverside CA USA
| | - Sarah M. Hardy
- School of Fisheries and Ocean Sciences; University of Alaska; Fairbanks AK USA
| | - Holly M. Bik
- Department of Nematology; University of California, Riverside; Riverside CA USA
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Flues S, Blokker M, Dumack K, Bonkowski M. Diversity of Cercomonad Species in the Phyllosphere and Rhizosphere of Different Plant Species with a Description of Neocercomonas epiphylla (Cercozoa, Rhizaria) a Leaf-Associated Protist. J Eukaryot Microbiol 2018; 65:587-599. [PMID: 29377417 DOI: 10.1111/jeu.12503] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 01/16/2018] [Accepted: 01/16/2018] [Indexed: 12/15/2022]
Abstract
Cercomonads are among the most abundant and diverse groups of heterotrophic flagellates in terrestrial systems and show an affinity to plants. However, we still lack basic knowledge of plant-associated protists. We isolated 75 Cercomonadida strains from the phyllosphere and rhizosphere of plants from three functional groups: grasses (Poa sp.), legumes (Trifolium sp.) and forbs (Plantago sp.), representing 28 OTUs from the genera Cercomonas, Neocercomonas and Paracercomonas. The community composition differed clearly between phyllosphere and rhizosphere, but was not influenced by plant species identity. From these isolates we describe three novel cercomonad species including Neocercomonas epiphylla that was consistently and exclusively isolated from the phyllosphere. For each new species we provide a detailed morphological description as well as an 18S rDNA gene sequence as a distinct marker of species identity. Our data contribute to a better resolution of the systematics of cercomonads and their association with plants, by describing three novel species and adding gene sequences of 10 new cercomonad genotypes and of nine previously described species. In view of the functional importance of cercozoan communities in the phyllosphere and rhizosphere of plants, a more detailed understanding of their composition, function and predator-prey interactions are clearly required.
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Affiliation(s)
- Sebastian Flues
- Department of Terrestrial Ecology, Institute for Zoology, University of Cologne, Cologne, 50674, Germany
| | - Malte Blokker
- Department of Terrestrial Ecology, Institute for Zoology, University of Cologne, Cologne, 50674, Germany
| | - Kenneth Dumack
- Department of Terrestrial Ecology, Institute for Zoology, University of Cologne, Cologne, 50674, Germany
| | - Michael Bonkowski
- Department of Terrestrial Ecology, Institute for Zoology, University of Cologne, Cologne, 50674, Germany.,Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne, 50674, Germany
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Cavalier-Smith T. Kingdom Chromista and its eight phyla: a new synthesis emphasising periplastid protein targeting, cytoskeletal and periplastid evolution, and ancient divergences. PROTOPLASMA 2018; 255:297-357. [PMID: 28875267 PMCID: PMC5756292 DOI: 10.1007/s00709-017-1147-3] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 07/18/2017] [Indexed: 05/18/2023]
Abstract
In 1981 I established kingdom Chromista, distinguished from Plantae because of its more complex chloroplast-associated membrane topology and rigid tubular multipartite ciliary hairs. Plantae originated by converting a cyanobacterium to chloroplasts with Toc/Tic translocons; most evolved cell walls early, thereby losing phagotrophy. Chromists originated by enslaving a phagocytosed red alga, surrounding plastids by two extra membranes, placing them within the endomembrane system, necessitating novel protein import machineries. Early chromists retained phagotrophy, remaining naked and repeatedly reverted to heterotrophy by losing chloroplasts. Therefore, Chromista include secondary phagoheterotrophs (notably ciliates, many dinoflagellates, Opalozoa, Rhizaria, heliozoans) or walled osmotrophs (Pseudofungi, Labyrinthulea), formerly considered protozoa or fungi respectively, plus endoparasites (e.g. Sporozoa) and all chromophyte algae (other dinoflagellates, chromeroids, ochrophytes, haptophytes, cryptophytes). I discuss their origin, evolutionary diversification, and reasons for making chromists one kingdom despite highly divergent cytoskeletons and trophic modes, including improved explanations for periplastid/chloroplast protein targeting, derlin evolution, and ciliary/cytoskeletal diversification. I conjecture that transit-peptide-receptor-mediated 'endocytosis' from periplastid membranes generates periplastid vesicles that fuse with the arguably derlin-translocon-containing periplastid reticulum (putative red algal trans-Golgi network homologue; present in all chromophytes except dinoflagellates). I explain chromist origin from ancestral corticates and neokaryotes, reappraising tertiary symbiogenesis; a chromist cytoskeletal synapomorphy, a bypassing microtubule band dextral to both centrioles, favoured multiple axopodial origins. I revise chromist higher classification by transferring rhizarian subphylum Endomyxa from Cercozoa to Retaria; establishing retarian subphylum Ectoreta for Foraminifera plus Radiozoa, apicomonad subclasses, new dinozoan classes Myzodinea (grouping Colpovora gen. n., Psammosa), Endodinea, Sulcodinea, and subclass Karlodinia; and ranking heterokont Gyrista as phylum not superphylum.
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Sapp M, Ploch S, Fiore-Donno AM, Bonkowski M, Rose LE. Protists are an integral part of the Arabidopsis thaliana
microbiome. Environ Microbiol 2017; 20:30-43. [DOI: 10.1111/1462-2920.13941] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Revised: 09/19/2017] [Accepted: 09/21/2017] [Indexed: 11/29/2022]
Affiliation(s)
- Melanie Sapp
- Institute of Population Genetics, Universitätstrasse 1; Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University; Universitätstrasse 40225 Düsseldorf Germany
- Institute of Zoology, Department of Terrestrial Ecology, Zülpicher Str 47b; Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne; Zülpicher Strasse 50674 Köln Germany
| | - Sebastian Ploch
- Institute of Population Genetics, Universitätstrasse 1; Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University; Universitätstrasse 40225 Düsseldorf Germany
- Biodiversity and Climate Research Centre, Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25; 60325 Frankfurt am Main Germany
| | - Anna M. Fiore-Donno
- Institute of Zoology, Department of Terrestrial Ecology, Zülpicher Str 47b; Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne; Zülpicher Strasse 50674 Köln Germany
| | - Michael Bonkowski
- Institute of Zoology, Department of Terrestrial Ecology, Zülpicher Str 47b; Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne; Zülpicher Strasse 50674 Köln Germany
| | - Laura E. Rose
- Institute of Population Genetics, Universitätstrasse 1; Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University; Universitätstrasse 40225 Düsseldorf Germany
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Fiore-Donno AM, Rixen C, Rippin M, Glaser K, Samolov E, Karsten U, Becker B, Bonkowski M. New barcoded primers for efficient retrieval of cercozoan sequences in high-throughput environmental diversity surveys, with emphasis on worldwide biological soil crusts. Mol Ecol Resour 2017; 18:229-239. [PMID: 29058814 DOI: 10.1111/1755-0998.12729] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Revised: 08/31/2017] [Accepted: 10/16/2017] [Indexed: 02/07/2023]
Abstract
We describe the performance of a new metabarcoding approach to investigate the environmental diversity of a prominent group of widespread unicellular organisms, the Cercozoa. Cercozoa is an immensely large group of protists, and although it may dominate in soil and aquatic ecosystems, its environmental diversity remains undersampled. We designed PCR primers targeting the hypervariable region V4 of the small subunit ribosomal RNA (SSU or 18S) gene, which is the recommended barcode marker for Cercozoa. The length of the amplified fragment (c. 350 bp) is suitable for Illumina MiSeq, the most cost-effective platform for molecular environmental surveys. We provide barcoded primers, an economical alternative to multiple libraries for multiplex sequencing of over a hundred samples. In silico, our primers matched 68% of the cercozoan sequences of the reference database and performed better than previously proposed new-generation sequencing primers. In mountain grassland soils and in biological soil crusts from a variety of climatic regions, we were able to detect cercozoan sequences encompassing nearly the whole range of the phylum. We obtained 901 operational taxonomic units (OTUs) at 97% similarity threshold from 26 samples, with c. 50,000 sequences per site, and only 8% of noncercozoan sequences. We could report a further increase in the diversity of Cercozoa, as only 43% of the OTUs were 97%-100% similar to any known sequence. Our study thus provides an advanced tool for cercozoan metabarcoding and to investigate their diversity and distribution in the environment.
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Affiliation(s)
- Anna Maria Fiore-Donno
- Institute of Zoology, Terrestrial Ecology, Cluster of Excellence in Plant Sciences, University of Cologne, Cologne, Germany
| | - Christian Rixen
- Institute for Snow and Avalanche Research SLF, Davos Dorf, Switzerland
| | - Martin Rippin
- Institute of Botany, University of Cologne, Cologne, Germany
| | - Karin Glaser
- Institute of Biological Sciences, Applied Ecology and Phycology, University of Rostock, Rostock, Germany
| | - Elena Samolov
- Institute of Biological Sciences, Applied Ecology and Phycology, University of Rostock, Rostock, Germany
| | - Ulf Karsten
- Institute of Biological Sciences, Applied Ecology and Phycology, University of Rostock, Rostock, Germany
| | - Burkhard Becker
- Institute of Botany, University of Cologne, Cologne, Germany
| | - Michael Bonkowski
- Institute of Zoology, Terrestrial Ecology, Cluster of Excellence in Plant Sciences, University of Cologne, Cologne, Germany
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Morga B, Renault T, Faury N, Lerond S, Garcia C, Chollet B, Joly JP, Lapègue S, Harrang E, Arzul I. Contribution of in Vivo Experimental Challenges to Understanding Flat Oyster Ostrea edulis Resistance to Bonamia ostreae. Front Cell Infect Microbiol 2017; 7:433. [PMID: 29057216 PMCID: PMC5635048 DOI: 10.3389/fcimb.2017.00433] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 09/21/2017] [Indexed: 12/28/2022] Open
Abstract
Bonamiosis due to the parasite Bonamia ostreae has been associated with massive mortality outbreaks in European flat oyster stocks in Europe. As eradication and treatment are not possible, the control of the disease mainly relies on transfer restriction. Moreover, selection has been applied to produce resistant flat oyster families, which present better survival and lower prevalence than non-selected oysters. In order to better understand the mechanisms involved in resistance to bonamiosis, cellular and molecular responses of 2 oyster groups (selected oysters and wild-type oysters) were analyzed in the context of experimental injection and cohabitation infections. Cellular responses including non-specific esterases detection, ROS production and phagocytosis activity were analyzed by flow cytometry. Four genes homologous to those shown to be involved in immunity were selected (Inhibitor of apotosis OeIAP, Fas ligand OeFas-ligand, Oe-SOD, and OeEc-SOD) and monitored by quantitative reverse-transcription PCR (qRT-PCR). Infected oysters showed higher phagocytosis activity than controls. Infected selected oyster show a lower phagocytosis activity which might be a protection against the parasite infection. The expression of OeIAP and OeFas-ligand gene was significantly increased in selected oysters at 5 days post-injection. OeIAP gene expression appeared to be significantly increased in wild-type oysters at 8 days post-injection. Our results suggest that resistance to bonamiosis partly relies on the ability of the oysters to modulate apoptosis.
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Affiliation(s)
- Benjamin Morga
- Laboratoire de Génétique et Pathologie des Mollusques Marins, IFREMER Institut Français de Recherche pour l'Exploitation de la Mer, La Tremblade, France
| | - Tristan Renault
- Département Ressources Biologiques et Environnement, IFREMER Institut Français de Recherche pour l'Exploitation de la Mer, Nantes, France
| | - Nicole Faury
- Laboratoire de Génétique et Pathologie des Mollusques Marins, IFREMER Institut Français de Recherche pour l'Exploitation de la Mer, La Tremblade, France
| | - Sophie Lerond
- Laboratoire de Génétique et Pathologie des Mollusques Marins, IFREMER Institut Français de Recherche pour l'Exploitation de la Mer, La Tremblade, France
| | - Céline Garcia
- Laboratoire de Génétique et Pathologie des Mollusques Marins, IFREMER Institut Français de Recherche pour l'Exploitation de la Mer, La Tremblade, France
| | - Bruno Chollet
- Laboratoire de Génétique et Pathologie des Mollusques Marins, IFREMER Institut Français de Recherche pour l'Exploitation de la Mer, La Tremblade, France
| | - Jean-Pierre Joly
- Laboratoire de Génétique et Pathologie des Mollusques Marins, IFREMER Institut Français de Recherche pour l'Exploitation de la Mer, La Tremblade, France
| | - Sylvie Lapègue
- Laboratoire de Génétique et Pathologie des Mollusques Marins, IFREMER Institut Français de Recherche pour l'Exploitation de la Mer, La Tremblade, France
| | - Estelle Harrang
- Laboratoire de Génétique et Pathologie des Mollusques Marins, IFREMER Institut Français de Recherche pour l'Exploitation de la Mer, La Tremblade, France
| | - Isabelle Arzul
- Laboratoire de Génétique et Pathologie des Mollusques Marins, IFREMER Institut Français de Recherche pour l'Exploitation de la Mer, La Tremblade, France
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Carrasco N, Voorbergen-Laarman M, Lacuesta B, Furones D, Engelsma MY. Application of a competitive real time PCR for detection of Marteilia refringens genotype “O” and “M” in two geographical locations: The Ebro Delta, Spain and the Rhine-Meuse Delta, the Netherlands. J Invertebr Pathol 2017; 149:51-55. [DOI: 10.1016/j.jip.2017.07.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Revised: 07/06/2017] [Accepted: 07/17/2017] [Indexed: 10/19/2022]
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Rhogostomidae (Cercozoa) from soils, roots and plant leaves (Arabidopsis thaliana): Description of Rhogostoma epiphylla sp. nov. and R. cylindrica sp. nov. Eur J Protistol 2017; 60:76-86. [DOI: 10.1016/j.ejop.2017.06.001] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Revised: 05/18/2017] [Accepted: 06/06/2017] [Indexed: 11/17/2022]
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47
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Dumack K, Mylnikov AP, Bonkowski M. Evolutionary Relationship of the Scale-Bearing Kraken (incertae sedis, Monadofilosa, Cercozoa, Rhizaria): Combining Ultrastructure Data and a Two-Gene Phylogeny. Protist 2017; 168:362-373. [DOI: 10.1016/j.protis.2017.04.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Revised: 04/24/2017] [Accepted: 04/30/2017] [Indexed: 11/29/2022]
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Polyphyly in the Thecate Amoeba Genus Lecythium (Chlamydophryidae, Tectofilosida, Cercozoa), Redescription of its Type Species L. hyalinum, Description of L. jennyae sp. nov. and the Establishment of Fisculla gen. nov. and Fiscullidae fam. nov. Protist 2017; 168:294-310. [PMID: 28499131 DOI: 10.1016/j.protis.2017.03.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2016] [Revised: 02/21/2017] [Accepted: 03/04/2017] [Indexed: 11/21/2022]
Abstract
Although testate amoebae have attracted great interest of protistologists for more than a century, some groups, especially those with a hyaline, organic test (=theca) are still poorly known. One of those is the genus Lecythium Hertwig et Lesser, 1874. Only recently Lecythium spp. were characterized by morphological and molecular means, but data on the type species Lecythium hyalinum Hertwig et Lesser, 1874, was still lacking. In this study, we screened for L. hyalinum in freshwater samples of Germany and the Netherlands. Four different isolates of L. hyalinum and one novel species were cultured and characterized by light microscopy. Phylogenetic analyses based on the small ribosomal subunit (SSU) RNA gene show that the genus Lecythium forms two robust clades, one forming a sister group to the Rhizaspididae/Pseudodifflugiidae clade (Tectofilosida), the other branching within 'Novel Clade 4' (Tectofilosida). We untangle this polyphyly by establishing Fisculla gen. nov. and the Fiscullidae fam. nov. for the former of these two clades.
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Shedding Light on the Polyphyletic Thecate Amoeba Genus Plagiophrys: Transition of Some of its Species to Rhizaspis (Tectofilosida, Thecofilosea, Cercozoa) and the Establishment of Sacciforma gen. nov. and Rhogostomidae fam. nov. (Cryomonadida, Thecofilosea, Cercozoa). Protist 2017; 168:92-108. [DOI: 10.1016/j.protis.2016.11.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Revised: 10/24/2016] [Accepted: 11/26/2016] [Indexed: 11/20/2022]
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50
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Laila R, Robin AHK, Yang K, Choi GJ, Park JI, Nou IS. Detection of Ribosomal DNA Sequence Polymorphisms in the Protist Plasmodiophora brassicae for the Identification of Geographical Isolates. Int J Mol Sci 2017; 18:E84. [PMID: 28054984 PMCID: PMC5297718 DOI: 10.3390/ijms18010084] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Revised: 12/21/2016] [Accepted: 12/23/2016] [Indexed: 11/16/2022] Open
Abstract
Clubroot is a soil-borne disease caused by the protist Plasmodiophora brassicae (P. brassicae). It is one of the most economically important diseases of Brassica rapa and other cruciferous crops as it can cause remarkable yield reductions. Understanding P. brassicae genetics, and developing efficient molecular markers, is essential for effective detection of harmful races of this pathogen. Samples from 11 Korean field populations of P. brassicae (geographic isolates), collected from nine different locations in South Korea, were used in this study. Genomic DNA was extracted from the clubroot-infected samples to sequence the ribosomal DNA. Primers and probes for P. brassicae were designed using a ribosomal DNA gene sequence from a Japanese strain available in GenBank (accession number AB526843; isolate NGY). The nuclear ribosomal DNA (rDNA) sequence of P. brassicae, comprising 6932 base pairs (bp), was cloned and sequenced and found to include the small subunits (SSUs) and a large subunit (LSU), internal transcribed spacers (ITS1 and ITS2), and a 5.8s. Sequence variation was observed in both the SSU and LSU. Four markers showed useful differences in high-resolution melting analysis to identify nucleotide polymorphisms including single- nucleotide polymorphisms (SNPs), oligonucleotide polymorphisms, and insertions/deletions (InDels). A combination of three markers was able to distinguish the geographical isolates into two groups.
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Affiliation(s)
- Rawnak Laila
- Department of Horticulture, Sunchon National University, Suncheon 540-950, Korea.
| | | | - Kiwoung Yang
- Department of Horticulture, Sunchon National University, Suncheon 540-950, Korea.
| | - Gyung Ja Choi
- Center for Eco-friendly New Materials, Korea Research Institute of Chemical Technology, Daejeon 34114, Korea.
| | - Jong-In Park
- Department of Horticulture, Sunchon National University, Suncheon 540-950, Korea.
| | - Ill-Sup Nou
- Department of Horticulture, Sunchon National University, Suncheon 540-950, Korea.
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