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Ciliate Diversity From Aquatic Environments in the Brazilian Atlantic Forest as Revealed by High-Throughput DNA Sequencing

  • Environmental Microbiology
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A Correction to this article was published on 20 January 2021

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Abstract

Rainforest aquatic ecosystems include complex habitats with scarce information on their unicellular eukaryote diversity and community structure. We have investigated the diversity of ciliates in freshwater and brackish environments along the Brazilian Atlantic Forest, based on the hypervariable V4 region of the 18S-rDNA obtained by high-throughput DNA sequencing. Our analyses detected 409 ciliate taxonomic units (OTUs), mostly attributed to the classes Oligohymenophorea and Spirotrichea. A total of 11 classes, 12 subclasses, 112 genera, and 144 species were reported. We found the following: (a) the ciliate communities are more diverse in freshwater- than in Atlantic Forest-associated brackish environments; (b) the ciliate communities are composed by a small amount of highly abundant OTUs, but a high number of low-abundant or rare OTUs; (c) nearly one-third of the ciliate OTUs share less than 97% sequence identity to reference sequences and (d) phylogenetic inference supports the hypothesis that the V4 region of the Ciliophora 18S-rDNA is a suitable marker for accurate evolutionary inferences at class level. Our results showed that a considerable fraction of the HTS-detected diversity of ciliates from Brazilian Atlantic Forest is not represented in the currently available molecular databases.

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Acknowledgments

We are grateful to Dr. Daniel Carvalho (GenOne Biotechnologies) for his technical support with Illumina sequencing. The help of Marcelo Sales and Caroline Souza de Almeida with the photographic records was also much appreciated. This work was supported by grants from Fundação de Amparo à Pesquisa do Estado do Rio de Janeiro (FAPERJ) to N.M.F (grants number E-26/202.325/2018 and E-26/202.326/2018) and from Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq, grant number 426648/2016-1). CNPq also provided research fellowships to P.H.C.N. (process number 140627/2019-7) and I.D.S.N. (304093/2016-5; 311577/2019-9).

Funding

This study was supported by funding agencies for science research Fundação de Amparo à Pesquisa do Estado do Rio de Janeiro (FAPERJ) and Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq).

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Authors and Affiliations

  1. Departamento de Zoologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941-617, Brazil

    Noemi M. Fernandes, Pedro H. Campello-Nunes, Thiago S. Paiva & Inácio D. Silva-Neto

  2. Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941-617, Brazil

    Carlos A. G. Soares

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  1. Noemi M. Fernandes
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  2. Pedro H. Campello-Nunes
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  3. Thiago S. Paiva
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  4. Carlos A. G. Soares
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  5. Inácio D. Silva-Neto
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Correspondence to Noemi M. Fernandes.

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The original online version of this article was revised: It contained an error in the assignment of the author Carlos A. G. Soares name.

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Table S1

OTUs assigned to Ciliophora, their taxonomic annotations, and sklearn confidence values (TXT 31 kb)

Table S2

Richness and alpha-diversity measures (DOCX 13 kb)

Table S3

Ciliate OTU Feature-IDs and their respective % identities to top-hit sequences from GenBank database (TXT 19 kb)

Table S4

Absolute abundances of ciliate genera per sample (TXT 7 kb)

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Fernandes, N.M., Campello-Nunes, P.H., Paiva, T.S. et al. Ciliate Diversity From Aquatic Environments in the Brazilian Atlantic Forest as Revealed by High-Throughput DNA Sequencing. Microb Ecol 81, 630–643 (2021). https://doi.org/10.1007/s00248-020-01612-8

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