Ciliate Diversity From Aquatic Environments in the Brazilian Atlantic Forest as Revealed by High-Throughput DNA Sequenci
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ENVIRONMENTAL MICROBIOLOGY
Ciliate Diversity From Aquatic Environments in the Brazilian Atlantic Forest as Revealed by High-Throughput DNA Sequencing Noemi M. Fernandes 1
&
Pedro H. Campello-Nunes 1 & Thiago S. Paiva 1 & Carlos A. G. Soraes 2 & Inácio D. Silva-Neto 1
Received: 22 June 2020 / Accepted: 22 September 2020 # Springer Science+Business Media, LLC, part of Springer Nature 2020
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 onethird 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. Keywords Alveolates . Metabarcoding . Eukaryote diversity . Protists . V4-18S rDNA
Introduction The phylum Ciliophora Doflein, 1901 is one of the most abundant and investigated groups of unicellular eukaryotes. They are morphologically diverse protists and essential elements in trophic networks of aquatic environments [1], acting as bacterial grazers, predators of other protists or micrometazoans, while serving as the prey for metazoans [2]. As ubiquitous organisms, they are also found in other habitats, such as soil [3, 4], bromeliad tanks, and mosses [5, 6]. The ciliates constitute a monophyletic lineage and their phylogeny, mostly
Electronic supplementary material The online version of this article (https://doi.org/10.1007/s00248-020-01612-8) contains supplementary material, which is available to authorized users. * Noemi M. Fernandes [email protected] 1
Departamento de Zoologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-617, Brazil
2
Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-617, Brazil
based on ribosomal markers, is well established and has recently been re-examined with phylogenomic data [7–11]. Relatively little is known about the microbial eukaryotic communities from tropical and subtropical ecosystems. The Brazilian Atlantic Forest is composed no
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