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Campello-Nunes PH, da Silva-Neto ID, da S Paiva T, Soares CAG, Fernandes NM. Ciliate diversity in rodrigo de freitas lagoon (Rio de Janeiro, Brazil) from an integrative standpoint. Braz J Microbiol 2024; 55:1489-1505. [PMID: 38401009 PMCID: PMC11153468 DOI: 10.1007/s42770-024-01291-4] [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: 09/25/2023] [Accepted: 02/18/2024] [Indexed: 02/26/2024] Open
Abstract
The Rodrigo de Freitas Lagoon is a highly eutrophic lacustrine system and has one of the longest histories of exploration and anthropic alteration in Brazil. Despite its relevance, limited studies explored the diversity of micro-eukaryotes in the lagoon. Ciliates (Alveolata, Ciliophora) are overlooked in environmental microbiology, especially in tropical and subtropical ecosystems, resulting in limited knowledge about their diversity and functional relevance in South American habitats, particularly in coastal lagoons. To fill this gap, here we investigated the diversity of ciliates in a brackish coastal lagoon in an urban area of Rio de Janeiro, Brazil, applying and comparing the performance of morphological and metabarcoding approaches. The metabarcoding analysis, based on high-throughput sequencing of the hipervariable region V4 of the 18S rRNA genes detected 37 molecular operational taxonomic units (MOTUs) assigned to Ciliophora, representing only about a half (56.9%) of the diversity detected by microscopy, which counted 65 ciliate morphotypes. The most representative classes in both approaches were Spirotrichea and Oligohymenophorea. The metabarcoding analysis revealed that 35.3% of the ciliate MOTUs had less than 97% similarity to available sequences in the NCBI database, indicating that more than one-third of these MOTUs potentially represents still not represented or undescribed ciliate species in current databases. Our findings indicate that metabarcoding techniques can significantly enhance the comprehension of ciliate diversity in tropical environments, but the scarcity of reference sequences of brackish ciliates in molecular databases represents a challenge to the taxonomic assignment of the MOTUs. This study provides new insights into the diversity of ciliates in a threatened coastal lagoon, revealing a vast array of still unknown and rare ciliate taxonomic units in tropical environments.
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Affiliation(s)
- Pedro H Campello-Nunes
- Laboratório de Protistologia, Departamento de Zoologia, Universidade Federal Do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Inácio D da Silva-Neto
- Laboratório de Protistologia, Departamento de Zoologia, Universidade Federal Do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Thiago da S Paiva
- Laboratório de Protistologia, Departamento de Zoologia, Universidade Federal Do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Carlos A G Soares
- Laboratório de Genética Molecular de Eucariontes E Simbiontes, Departamento de Genética, Universidade Federal Do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Noemi M Fernandes
- Laboratório de Protistologia, Departamento de Zoologia, Universidade Federal Do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.
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2
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Carvalho da Silva V, Fernandes N. Protist taxonomic and functional diversity in aquatic ecosystems of the Brazilian Atlantic Forest. PeerJ 2023; 11:e15762. [PMID: 37547721 PMCID: PMC10402703 DOI: 10.7717/peerj.15762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 06/27/2023] [Indexed: 08/08/2023] Open
Abstract
The Brazilian Atlantic Forest and its associated ecosystems are highly biodiverse but still understudied, especially with respect to eukaryotic microbes. Protists represent the largest proportion of eukaryotic diversity and play important roles in nutrient cycling and maintenance of the ecosystems in which they occur. However, much of protist diversity remains unknown, particularly in the Neotropics. Understanding the taxonomic and functional diversity of these organisms is urgently needed, not only to fill this gap in our knowledge, but also to enable the development of public policies for biological conservation. This is the first study to investigate the taxonomic and trophic diversity of the major protist groups in freshwater systems and brackish coastal lagoons located in fragments of the Brazilian Atlantic Forest by DNA metabarcoding, using high-throughput sequencing of the gene coding for the V4 region of the 18S rRNA gene. We compared α and β diversity for all protist communities and assessed the relative abundance of phototrophic, consumer, and parasitic taxa. We found that the protist communities of coastal lagoons are as diverse as the freshwater systems studied in terms of α diversity, although differed significantly in terms of taxonomic composition. Our results still showed a notable functional homogeneity between the trophic groups in freshwater environments. Beta diversity was higher among freshwater samples, suggesting a greater level of heterogeneity within this group of samples concerning the composition and abundance of OTUs.Ciliophora was the most represented group in freshwater, while Diatomea dominated diversity in coastal lagoons.
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3
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Méndez-Sánchez D, Pomahač O, Rotterová J, Bourland WA, Čepička I. Morphology and phylogenetic position of three anaerobic ciliates from the classes Odontostomatea and Muranotrichea (Ciliophora). J Eukaryot Microbiol 2023; 70:e12965. [PMID: 36727275 DOI: 10.1111/jeu.12965] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 12/17/2022] [Accepted: 01/27/2023] [Indexed: 02/03/2023]
Abstract
The diversity of the classes Odontostomatea and Muranotrichea, which contain solely obligate anaerobes, is poorly understood. We studied two populations of Mylestoma sp., one of Saprodinium dentatum (Odontostomatea), two of Muranothrix felix sp. nov., and one of Muranothrix sp. (Muranotrichea) employing live observation, protargol impregnation, scanning electron microscopy, and 18S rRNA gene sequencing. Conspecificity of Mylestoma sp., described here, with a previously described species of this genus cannot be excluded since no species have been studied with modern methods. Phylogenetically, the genus Mylestoma is closely related to the odontostomatid Discomorphella pedroeneasi, although the phylogenetic position of class Odontostomatea itself remains unresolved. The newly described muranotrichean species, Muranothrix felix sp. nov., is morphologically similar to M. gubernata but can be distinguished by its fewer macronuclear nodules and fewer adoral membranelles; moreover, it is clearly distinguished from M. gubernata by its 18S rRNA gene sequence. Another population, designated here as Muranothrix sp., most likely represents a separate species.
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Affiliation(s)
- Daniel Méndez-Sánchez
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Ondřej Pomahač
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Johana Rotterová
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic.,Graduate School of Oceanography, University of Rhode Island, Narragansett, Rhode Island, USA
| | - William A Bourland
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Ivan Čepička
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
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4
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Ye T, Jiang Y, Chen S, Xu Y, Li L, Shin MK, Chen X. The widely reported but poorly studied ciliate family Folliculinidae (Protozoa, Ciliophora, Heterotrichea): a revision with notes on its taxonomy, morphology and phylogenetic relationships. MARINE LIFE SCIENCE & TECHNOLOGY 2022; 4:471-492. [PMID: 37078084 PMCID: PMC10077228 DOI: 10.1007/s42995-022-00152-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 10/17/2022] [Indexed: 05/03/2023]
Abstract
Ciliates of the heterotrich family Folliculinidae are widespread in various habitats and are distinguished by their transparent loricae of various shapes, conspicuous peristomial lobes, and dimorphic life cycles. They usually attach firmly to the surface of substrates, feed on bacteria and microalgae, and play a significant role in energy flow and material cycling in the microbial food web. However, little is known regarding their biodiversity and systematics. In this work, we establish the terminology of the family Folliculinidae and select six crucial features for genus recognition. Based on previous studies, we revise the classification of Folliculinidae, supply improved diagnoses for each of the 33 folliculinid genera, and provide a key to their identification. Moreover, phylogenetic analyses based on small subunit ribosomal DNA (SSU rDNA) sequences revealed that the family is monophyletic and comprises two subclades (subclades I II) which can be identified by the flexibility of their peristomial lobes and the sculpturing of their necks. Furthermore, we investigate the evolutionary relationships of folliculinids using the six chosen generic features. Supplementary Information The online version contains supplementary material available at 10.1007/s42995-022-00152-z.
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Affiliation(s)
- Tingting Ye
- School of Marine Sciences, Ningbo University, Ningbo, 315800 China
- Laboratory of Marine Protozoan Biodiversity and Evolution, Marine College, Shandong University, Weihai, 264209 China
| | - Yaohan Jiang
- Institute of Evolution and Marine Biodiversity, and College of Fisheries, Ocean University of China, Qingdao, 266003 China
| | - Shuchang Chen
- School of Marine Sciences, Ningbo University, Ningbo, 315800 China
| | - Yixiang Xu
- School of Marine Sciences, Ningbo University, Ningbo, 315800 China
| | - Lifang Li
- Laboratory of Marine Protozoan Biodiversity and Evolution, Marine College, Shandong University, Weihai, 264209 China
| | - Mann Kyoon Shin
- Department of Biological Sciences, University of Ulsan, Ulsan, 44610 South Korea
| | - Xiangrui Chen
- School of Marine Sciences, Ningbo University, Ningbo, 315800 China
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5
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Rotterová J, Edgcomb VP, Čepička I, Beinart R. Anaerobic Ciliates as a Model Group for Studying Symbioses in Oxygen-depleted Environments. J Eukaryot Microbiol 2022; 69:e12912. [PMID: 35325496 DOI: 10.1111/jeu.12912] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Anaerobiosis has independently evolved in multiple lineages of ciliates, allowing them to colonize a variety of anoxic and oxygen-depleted habitats. Anaerobic ciliates commonly form symbiotic relationships with various prokaryotes, including methanogenic archaea and members of several bacterial groups. The hypothesized functions of these ecto- and endosymbionts include the symbiont utilizing the ciliate's fermentative end-products to increase host's anaerobic metabolic efficiency, or the symbiont directly providing the host with energy by denitrification or photosynthesis. The host, in turn, may protect the symbiont from competition, the environment, and predation. Despite rapid advances in sampling, molecular, and microscopy methods, as well as the associated broadening of the known diversity of anaerobic ciliates, many aspects of these ciliate symbioses, including host-specificity and co-evolution, remain largely unexplored. Nevertheless, with the number of comparative genomic and transcriptomic analyses targeting anaerobic ciliates and their symbionts on the rise, insights into the nature of these symbioses and the evolution of the ciliate transition to obligate anaerobiosis continue to deepen. This review summarizes the current body of knowledge regarding the complex nature of symbioses in anaerobic ciliates, the diversity of these symbionts, their role in the evolution of ciliate anaerobiosis and their significance in ecosystem-level processes.
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Affiliation(s)
- Johana Rotterová
- Graduate School of Oceanography, University of Rhode Island, Narragansett, Rhode Island, USA.,Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Virginia P Edgcomb
- Department of Geology and Geophysics, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
| | - Ivan Čepička
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Roxanne Beinart
- Graduate School of Oceanography, University of Rhode Island, Narragansett, Rhode Island, USA
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6
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Campello-Nunes PH, Silva-Neto ID, Sales MH, Soares CA, Paiva TS, Fernandes NM. Morphological and phylogenetic investigations shed light on evolutionary relationships of the enigmatic genus Copemetopus (Ciliophora, Alveolata), with the proposal of Copemetopus verae sp. nov. Eur J Protistol 2022; 83:125878. [DOI: 10.1016/j.ejop.2022.125878] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Revised: 02/06/2022] [Accepted: 02/14/2022] [Indexed: 11/30/2022]
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7
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Fokin SI, Serra V. Bacterial Symbiosis in Ciliates (Alveolata, Ciliophora): Roads Traveled and Those Still to be Taken. J Eukaryot Microbiol 2022; 69:e12886. [PMID: 35006645 PMCID: PMC9539572 DOI: 10.1111/jeu.12886] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 01/05/2022] [Accepted: 01/06/2022] [Indexed: 11/30/2022]
Abstract
The diversity of prokaryotic symbionts in Ciliophora and other protists is fascinatingly rich; they may even include some potentially pathogenic bacteria. In this review, we summarize currently available data on biodiversity and some morphological and biological peculiarities of prokaryotic symbionts mainly within the genera Paramecium and Euplotes. Another direction of ciliate symbiology, neglected for a long time and now re‐discovered, is the study of epibionts of ciliates. This promises a variety of interesting outcomes. Last, but not least, we stress the new technologies, such as next generation sequencing and the use of genomics data, which all can clarify many new aspects of relevance. For this reason, a brief overview of achievements in genomic studies on ciliate's symbionts is provided. Summing up the results of numerous scientific contributions, we systematically update current knowledge and outline the prospects as to how symbiology of Ciliophora may develop in the near future.
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Affiliation(s)
- Sergei I Fokin
- University of Pisa, Pisa, Italy.,St. Petersburg State University, St. Petersburg, Russia
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8
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Morphology, Life Cycle, and SSU rDNA-based Phylogeny of Two Folliculinid Ciliates (Ciliophora, Heterotrichea, Folliculinidae) Collected from Subtropical Coastal Wetlands of China. Protist 2021; 172:125844. [PMID: 34916151 DOI: 10.1016/j.protis.2021.125844] [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: 07/10/2021] [Revised: 11/05/2021] [Accepted: 11/05/2021] [Indexed: 11/22/2022]
Abstract
Most ciliates of the heterotrich family Folliculinidae are flagship periphytic species. They are characterized by their transparent lorica, conspicuous peristomial lobes, and dimorphic life cycle. However, the understanding of their biodiversity and systematics is relatively poor. In the present study, we investigate the morphology and phylogenetic affinities of Ampullofolliculina lageniformis Hadži, 1951 and Metafolliculina producta (Wright, 1859) Dons, 1934, collected from subtropical coastal wetlands in China. An integrative approach combining investigations of their morphology, life cycle and ecology was used. Phylogenetic analyses based on small subunit ribosomal DNA (SSU rDNA) sequences showed that: all folliculinid genera form a monophyletic clade; the two genera with flexible peristomial lobes, Metafolliculina and Eufolliculina, are closely related; the other three genera with inflexible peristomial lobes, Ampullofolliculina, Diafolliculina and Folliculina, group together.
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9
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Serra V, Fokin SI, Gammuto L, Nitla V, Castelli M, Basuri CK, Satyaveni A, Sandeep BV, Modeo L, Petroni G. Phylogeny of
Neobursaridium
reshapes the systematics of
Paramecium
(Oligohymenophorea, Ciliophora). ZOOL SCR 2020. [DOI: 10.1111/zsc.12464] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
| | - Sergei I. Fokin
- Department of Biology University of Pisa Pisa Italy
- Department of Invertebrate Zoology St. Petersburg State University St. Petersburg Russia
- St. Petersburg Branch of the S.I. Vavilov Institute of History of Science and Technology Russian Academy of Sciences St. Petersburg Russia
| | | | | | - Michele Castelli
- Department of Biology and Biotechnology ‘Lazzaro Spallanzani’ Pavia University Pavia Italy
| | - Charan Kumar Basuri
- National Centre for Coastal Research Ministry of Earth Sciences Government of IndiaNIOT Campus Pallikaranai, Chennai India
- Department of Zoology Andhra University Visakhapatnam India
| | | | | | - Letizia Modeo
- Department of Biology University of Pisa Pisa Italy
- CIME Centro Interdipartimentale di Microscopia Elettronica Università di Pisa Pisa Italy
- CISUP, Centro per l'Integrazione della Strumentazione dell'Università di Pisa Pisa Italy
| | - Giulio Petroni
- Department of Biology University of Pisa Pisa Italy
- CIME Centro Interdipartimentale di Microscopia Elettronica Università di Pisa Pisa Italy
- CISUP, Centro per l'Integrazione della Strumentazione dell'Università di Pisa Pisa Italy
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10
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Rotterová J, Salomaki E, Pánek T, Bourland W, Žihala D, Táborský P, Edgcomb VP, Beinart RA, Kolísko M, Čepička I. Genomics of New Ciliate Lineages Provides Insight into the Evolution of Obligate Anaerobiosis. Curr Biol 2020; 30:2037-2050.e6. [PMID: 32330419 DOI: 10.1016/j.cub.2020.03.064] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Revised: 03/10/2020] [Accepted: 03/24/2020] [Indexed: 02/07/2023]
Abstract
Oxygen plays a crucial role in energetic metabolism of most eukaryotes. Yet adaptations to low-oxygen concentrations leading to anaerobiosis have independently arisen in many eukaryotic lineages, resulting in a broad spectrum of reduced and modified mitochondrion-related organelles (MROs). In this study, we present the discovery of two new class-level lineages of free-living marine anaerobic ciliates, Muranotrichea, cl. nov. and Parablepharismea, cl. nov., that, together with the class Armophorea, form a major clade of obligate anaerobes (APM ciliates) within the Spirotrichea, Armophorea, and Litostomatea (SAL) group. To deepen our understanding of the evolution of anaerobiosis in ciliates, we predicted the mitochondrial metabolism of cultured representatives from all three classes in the APM clade by using transcriptomic and metagenomic data and performed phylogenomic analyses to assess their evolutionary relationships. The predicted mitochondrial metabolism of representatives from the APM ciliates reveals functional adaptations of metabolic pathways that were present in their last common ancestor and likely led to the successful colonization and diversification of the group in various anoxic environments. Furthermore, we discuss the possible relationship of Parablepharismea to the uncultured deep-sea class Cariacotrichea on the basis of single-gene analyses. Like most anaerobic ciliates, all studied species of the APM clade host symbionts, which we propose to be a significant accelerating factor in the transitions to an obligately anaerobic lifestyle. Our results provide an insight into the evolutionary mechanisms of early transitions to anaerobiosis and shed light on fine-scale adaptations in MROs over a relatively short evolutionary time frame.
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Affiliation(s)
- Johana Rotterová
- Department of Zoology, Faculty of Science, Charles University, Prague 128 43, Czech Republic.
| | - Eric Salomaki
- Institute of Parasitology, Biology Centre Czech Academy of Sciences, České Budějovice 370 05, Czech Republic
| | - Tomáš Pánek
- Department of Zoology, Faculty of Science, Charles University, Prague 128 43, Czech Republic
| | - William Bourland
- Department of Biological Sciences, Boise State University, Boise, ID 83725-1515, USA
| | - David Žihala
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava 710 00, Czech Republic
| | - Petr Táborský
- Institute of Parasitology, Biology Centre Czech Academy of Sciences, České Budějovice 370 05, Czech Republic
| | - Virginia P Edgcomb
- Department of Geology and Geophysics, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA
| | - Roxanne A Beinart
- Graduate School of Oceanography, University of Rhode Island, Narragansett, RI 02882, USA
| | - Martin Kolísko
- Institute of Parasitology, Biology Centre Czech Academy of Sciences, České Budějovice 370 05, Czech Republic; Department of Molecular Biology and Genetics, Faculty of Science, University of South Bohemia, 370 05 České Budějovice, Czech Republic
| | - Ivan Čepička
- Department of Zoology, Faculty of Science, Charles University, Prague 128 43, Czech Republic
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