Discrepancies Between Molecular and Morphological Databases of Soil Ciliates Studied for Temperate Grasslands of Central Europe

Ciliate diversity in rodrigo de freitas lagoon (Rio de Janeiro, Brazil) from an integrative standpoint

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.

Soil Alveolata diversity in the undisturbed steppe and wheat agrocenoses under different tillage

Microeukaryotes are vital for maintaining soil quality and ecosystem functioning, however, their communities are less studied than bacterial and fungal ones, especially by high throughput sequencing techniques. Alveolates are important members of soil microbial communities, being consumers and/or prey for other microorganisms. We studied alveolate diversity in soil under the undisturbed steppe (US) and cropped for wheat using two tillage practices (conventional, CT, and no-till, NT) by amplifying the ITS2 marker with ITS3_KYO2/ITS4 primers and sequencing amplicons using Illumina MiSeq. A total of 198 Alveolata OTUs were identified, with 158 OTUs attributed to the Ciliophora phylum, containing five classes: Litostomatea, Spirotrichea and Oligohymenophorea, Nassophorea and Phyllopharyngea. Litostomatea and Phyllopharyngea were more abundant in US as compared with CT and NT. The observed OTU richness was higher in US than in CT and NT. The β-biodiversity of soil ciliates also very distinctly differentiated the US field from CT and NT. In the US, Nassophorea and Spirotrichea correlated positively with sand and negatively with clay, silt and SOM contents. This is the first report about soil ciliates diversity in Siberia as assessed by metabarcoding technique. The revealed clear effect of land use on the relative abundance of some taxa and a lack of tillage effect suggest the importance of the quantity and quality of plant material input for shaping the prey for ciliates. The ITS-metabarcoding technique was used for the first time in the research of ciliates diversity; further studies, embracing diverse aspects of soil ciliates by combining -omics methodology with the traditional one, are needed to get a better insight on the ecological roles of the main ciliate taxa in the complex soil system.

Interpreting phylogenetic placements for taxonomic assignment of environmental DNA

Taxonomic assignment of operational taxonomic units (OTUs) is an important bioinformatics step in analyzing environmental sequencing data. Pairwise alignment and phylogenetic-placement methods represent two alternative approaches to taxonomic assignments, but their results can differ. Here we used available colpodean ciliate OTUs from forest soils to compare the taxonomic assignments of VSEARCH (which performs pairwise alignments) and EPA-ng (which performs phylogenetic placements). We showed that when there are differences in taxonomic assignments between pairwise alignments and phylogenetic placements at the subtaxon level, there is a low pairwise similarity of the OTUs to the reference database. We then showcase how the output of EPA-ng can be further evaluated using GAPPA to assess the taxonomic assignments when there exist multiple equally likely placements of an OTU, by taking into account the sum over the likelihood weights of the OTU placements within a subtaxon, and the branch distances between equally likely placement locations. We also inferred the evolutionary and ecological characteristics of the colpodean OTUs using their placements within subtaxa. This study demonstrates how to fully analyze the output of EPA-ng, by using GAPPA in conjunction with knowledge of the taxonomic diversity of the clade of interest.

Ciliate SSU-rDNA reference alignments and trees for phylogenetic placements of metabarcoding data

Although ciliates are one of the most dominant microbial eukaryotic groups in many environments, there is a lack of updated global ciliate alignments and reference trees that can be used for phylogenetic placement methods to analyze environmental metabarcoding data. Here we fill this gap by providing reference alignments and trees for those ciliates taxa with available SSU-rDNA sequences derived from identified species. Each alignment contains 478 ciliate and six outgroup taxa, and they were made using different masking strategies for alignment positions (unmasked, masked and masked except the hypervariable V4 region). We constrained the monophyly of the major ciliate groups based on the recently updated classification of protists and based on phylogenomic data. Taxa of uncertain phylogenetic position were kept unconstrained, except for Mesodinium species that we constrained to form a clade with the Litostomatea. These ciliate reference alignments and trees can be used to perform taxonomic assignments of metabarcoding data, discover novel ciliate clades, estimate species richness, and overlay measured ecological parameters onto the phylogenetic placements.

A new species of Cynomops (Chiroptera: Molossidae) from the northwestern slope of the Andes

The systematics and taxonomy of the broadly distributed bats of the genus Cynomops has changed considerably in the last few years. Among the major changes, Cynomops abrasus was split into two species of large-bodied forms (Cynomops mastivus and C. abrasus) distributed east of the Andes. However, large Colombian specimens identified as C. abrasus from the western side of the Andes had yet to be included in any revisionary work. Phylogenetic analysis performed in this study, using mtDNA sequences (Cytochrome-b), revealed that these Colombian individuals are more closely related to Cynomops greenhalli. Morphological and molecular data allowed us to recognize populations from western Colombia, western Ecuador and northwestern Peru, as members of a new species of Cynomops. Characters that allow for its differentiation from C. greenhalli include a larger forearm, paler but more uniform ventral pelage, more globular braincase, and well-developed zygomatic processes of the maxilla (almost reaching the postorbital constriction). This study serves as another example of the importance of including multiple lines of evidence in the recognition of a new species. Given its rarity and the advanced transformation of its habitat, this new species is particularly important from a conservation perspective.

Colpodean ciliate phylogeny and reference alignments for phylogenetic placements

The Colpodea form a major clade of ciliates that are often found in environmental DNA sequencing studies. They are united by similar somatic ciliature, but differentiated by complex oral structures. Although there are four well supported colpodean subclades, there is disagreement in molecular phylogenetic inferences about their branching order. Using available nuclear SSU-rRNA sequences, we evaluated if the bursariomorphids or the platyophryids are sister to the remaining colpodeans. We inferred the "platyophryids-early" topologies using different alignment and masking methods, but constrained analyses could not reject the "bursariomorphids-early" topology. Both bursariomorphids and platyophryids clades have a similar number of nucleotide positions shared with the outgroup, and both are interconnected with the outgroup in phylogenetic networks. Based on these discordant results, it is hard to determine which clade branched off first, although the "platyophryids-early topology" is also supported by mitochondrial SSU-rRNA data. We also offer different reference alignments that can be used to phylogenetically place short- and long-read data from environmental DNA sequencing studies, and we propose some tentative evolutionary and ecological interpretations of those placements.

First Records of 'Flagship' Soil Ciliates in North America

'Flagship' ciliates were investigated from soil samples collected in Florida, USA. This was undertaken to determine if species thought to be restricted to a given world region could be uncovered from similar habitats in a novel location, e.g. another continent. Two species of Condylostomides were discovered, and recorded from the North American continent for the first time. Condylostomides etoschensis was known only from Africa, but was found to be thriving in a Florida study site. An 18S rDNA sequence for this species was determined for the first time. Also discovered from the same study site was the ciliate Condylostomides coeruleus, previously known only from Central and South America. These two 'flagship' ciliates were found in the same habitat, from a continent well outside of their previously recorded biogeographies. Molecular sequencing and microscopy investigations were conducted to form the baseline for future work within this genus. Soil ciliates can obtain large population numbers and form cysts and are therefore likely able to disperse globally. These new records provide additional evidence that large distances, even between continents, do not hinder microbes from thriving globally. The absence of these conspicuously-colored gold and blue ciliates from previous studies is likely due to undersampling, rather than to any physical barriers.

The global-scale distributions of soil protists and their contributions to belowground systems

Protists are ubiquitous in soil, where they are key contributors to nutrient cycling and energy transfer. However, protists have received far less attention than other components of the soil microbiome. We used amplicon sequencing of soils from 180 locations across six continents to investigate the ecological preferences of protists and their functional contributions to belowground systems. We complemented these analyses with shotgun metagenomic sequencing of 46 soils to validate the identities of the more abundant protist lineages. We found that most soils are dominated by consumers, although parasites and phototrophs are particularly abundant in tropical and arid ecosystems, respectively. The best predictors of protist composition (primarily annual precipitation) are fundamentally distinct from those shaping bacterial and archaeal communities (namely, soil pH). Some protists and bacteria co-occur globally, highlighting the potential importance of these largely undescribed belowground interactions. Together, this study allowed us to identify the most abundant and ubiquitous protists living in soil, with our work providing a cross-ecosystem perspective on the factors structuring soil protist communities and their likely contributions to soil functioning.