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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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Guimarães Durán CL, Lansac-Tôha FM, Meira BR, Santana LO, Oliveira FR, Matos MHDO, Velho LFM. Upstream cascade reservoirs drive temporal beta diversity increases through species loss in a dammed river. FEMS Microbiol Ecol 2024; 100:fiad165. [PMID: 38192043 PMCID: PMC10799717 DOI: 10.1093/femsec/fiad165] [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: 06/01/2023] [Revised: 11/21/2023] [Accepted: 01/03/2024] [Indexed: 01/10/2024] Open
Abstract
Changes in the biodiversity of aquatic environments over time and space due to human activities are a topic of theoretical and conservational interest in ecology. Thus, variation in taxonomic beta diversity of the planktonic ciliates community was investigated along a temporal and spatial gradient in two subsystems of a Neotropical floodplain, one impacted by dams (Paraná) and the other free of them along its course (Ivinhema). For the spatial analysis, the Paraná subsystem did not show a significant decrease in beta diversity, presenting a pattern like that observed for the Ivinhema subsystem. Therefore, biotic homogenization was not observed for the ciliate's community downstream of the dams. It was noted that there was a fluctuation in the relevance of the components of beta diversity, regardless of the subsystem analyzed. For the temporal analysis there was a significant change in species composition from the first to the last year investigated, essentially for the subsystem impacted by dams, and that this was determined mainly by species loss. Although spatial beta diversity remained high without a clear process of biotic homogenization, dams promoted remarkable changes in ciliate species composition over the years mainly by continuous loss of species.
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Affiliation(s)
- Carolina Leite Guimarães Durán
- Programa de Pós-Graduação em Ecologia de Ambientes Aquáticos Continentais (PEA), Department of Biology, Núcleo de Pesquisas em Limnologia, Ictiologia e Aquicultura (Nupélia), Universidade Estadual de Maringá (UEM). Av. Colombo, 5790, CEP 87020-900. Maringá, Parana State, Brazil
| | - Fernando Miranda Lansac-Tôha
- Programa de Pós-Graduação em Ecologia de Ambientes Aquáticos Continentais (PEA), Department of Biology, Núcleo de Pesquisas em Limnologia, Ictiologia e Aquicultura (Nupélia), Universidade Estadual de Maringá (UEM). Av. Colombo, 5790, CEP 87020-900. Maringá, Parana State, Brazil
| | - Bianca Ramos Meira
- Programa de Pós-Graduação em Ecologia de Ambientes Aquáticos Continentais (PEA), Department of Biology, Núcleo de Pesquisas em Limnologia, Ictiologia e Aquicultura (Nupélia), Universidade Estadual de Maringá (UEM). Av. Colombo, 5790, CEP 87020-900. Maringá, Parana State, Brazil
| | - Loiani Oliveira Santana
- Programa de Pós-Graduação em Ecologia de Ambientes Aquáticos Continentais (PEA), Department of Biology, Núcleo de Pesquisas em Limnologia, Ictiologia e Aquicultura (Nupélia), Universidade Estadual de Maringá (UEM). Av. Colombo, 5790, CEP 87020-900. Maringá, Parana State, Brazil
| | - Felipe Rafael Oliveira
- Programa de Pós-Graduação em Ecologia de Ambientes Aquáticos Continentais (PEA), Department of Biology, Núcleo de Pesquisas em Limnologia, Ictiologia e Aquicultura (Nupélia), Universidade Estadual de Maringá (UEM). Av. Colombo, 5790, CEP 87020-900. Maringá, Parana State, Brazil
| | - Matheus Henrique de Oliveira Matos
- Programa de Pós-Graduação em Ecologia de Ambientes Aquáticos Continentais (PEA), Department of Biology, Núcleo de Pesquisas em Limnologia, Ictiologia e Aquicultura (Nupélia), Universidade Estadual de Maringá (UEM). Av. Colombo, 5790, CEP 87020-900. Maringá, Parana State, Brazil
| | - Luiz Felipe Machado Velho
- Programa de Pós-Graduação em Ecologia de Ambientes Aquáticos Continentais (PEA), Department of Biology, Núcleo de Pesquisas em Limnologia, Ictiologia e Aquicultura (Nupélia), Universidade Estadual de Maringá (UEM). Av. Colombo, 5790, CEP 87020-900. Maringá, Parana State, Brazil
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