Metabarcoding advances for ecology and biogeography of Neotropical protists: what do we know, where do we go?

Abstract

The Neotropics is one of the most diverse regions of the globe in terms of plants and animal species. Regarding the microbial world, however, little is known about the diversity and biogeography patterns of microorganisms in the Neotropics. The biogeography of several microbial taxonomic groups is still missing and/or incomplete, such as the protists. Despite the hard taxonomic identification of protists, the advance of molecular techniques (e.g., metabarcoding) have allowed to better explore the distribution of several protistan groups. Our goal here was to summarize the available information of Neotropical protists, focusing on metabarcoding studies, to explore what these data evidence on their ecology and biogeography. For this, we reviewed the findings from all articles that focused on or included the terrestrial protists using a metabarcoding approach and identified the gaps and future perspectives in this research field. We found that Neotropical protistan diversity patterns seem to be, at least in part, congruent with that of macro-organisms and, different than plants and bacteria, just weakly explained by environmental variables. We argue that studies with standardized protocols including different ecoregions are necessary, such as temperate forests, grasslands, and savannas from Southern of South America and Northern Atlantic Forest, to fully characterize the ecology and biogeography on Neotropical protists. Furthermore, dismembering evolutionary lineages and functional guilds of protists are important to better understand the relationship between diversity, dispersal abilities, and functionality of particular taxa of protists in their habitats.

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

“…To assess the diversity of microscopic eukaryotes, most studies used primers to 18S rRNA genes (Ritter et al, 2021) even with specific primers, non-target taxa sequences are commonly amplified (Pastorelli et al, 2022). The ITS primers we used in this study were designed for fungi (Liu K. et al, 2012), but often these primers did not fail to amplify a plethora of other domains, such as Alveolata, Amoebozoa, Heterolobosea, Metazoa, Rhizaria and Eukaryota kingdoms of uncertain taxonomic attribution.…”

“…Over the last decades the possibility to reduce damage to soil by minimizing tillage has gained much attention from both researchers and practitioners. Although there are many reports about bacterial and fungal biodiversity estimated metagenomically under minimal and/or no tillage, alveolates have remained relatively understudied (Ritter et al, 2021). While assessing the ITS2 region DNA sequence reads diver sity, using the ITS3_KYO2/ITS4 primer set (Liu K. et al, 2012), under different tillage practices in the chernozem in the south of West Siberia (Naumova et al, 2022), we found that those fungal primers also amplified DNA belonging to other domains, specifically Alveolata, Amoebozoa, Heterolobosea, Metazoa, Rhizaria and Eukaryota kingdoms of uncertain taxonomic attribution.…”

Above‐ and below‐ground biodiversity responses to the prolonged flood pulse in central‐western Amazonia, Brazil

“…It is conceivable that protists may respond in different ways to the environmental gradient due to divergent lifestyles (parasitic to free living) and guilds (autotrophs to heterotrophs) (Adl et al, 2012; Geisen et al, 2018; Ritter, Machado, et al, 2020). Consequently, an effect of the flooding gradient on the protist community composition may be masked.…”