Protist diversity of the Atlantic Forest in Southeastern Brazil via DNA metabarcoding

Abstract

Protists are highly diverse unicellular microeukaryotes found in a wide range of habitats. They play important roles in nutrient cycling and ecosystem maintenance. However, much of protist diversity remains unknown, particularly in the Neotropical region. Due to their high sensitivity to environmental changes, these organisms are widely used as biological indicators of organic pollution. Therefore, understanding the taxonomic and functional diversity of these organisms is urgently needed, not only to fill gaps in our knowledge but also to enable the development of public policies for biological conservation. In this study, using high-throughput sequencing of the gene encoding the V4 region of the 18S rRNA gene through DNA metabarcoding technique, we investigated the taxonomic and trophic diversity of the main groups of protists in freshwater systems and brackish coastal lagoons located in fragments of the Brazilian Atlantic Forest. The protist communities of coastal lagoons were as diverse as the freshwater systems studied in terms of alpha diversity, differing significantly in terms of taxonomic composition. Remarkable functional homogeneity was observed among trophic groups in freshwater environments. Beta diversity was higher among freshwater samples, suggesting a higher level of heterogeneity regarding the composition and abundance of OTUs. Ciliophora was the most represented group in freshwater, while Diatoms dominated diversity in coastal lagoons. Subsequently, using the same technique, the molecular diversity of ciliated protists was investigated at seven strategic points along the Sapucaí River (Itajubá, Minas Gerais, Brazil) to assess the impact of urban pollution on the richness, abundance, and diversity indices of these communities. For each sampling point, values of physico-chemical parameters were also recorded. The composition of ciliates varied significantly along the course of the Sapucaí River. Samples collected in urban areas showed lower richness and diversity, corroborating the influence of pollution gradient on these communities. Physico-chemical parameters showed little variation between samples and were not linked to observed changes in ciliate communities, revealing that these organisms are strongly affected by environmental changes and respond more sensitively to these disturbances than physico-chemical parameters, emphasizing their potential as bioindicators.