Protistan community analysis: key findings of a large-scale molecular sampling

Abstract

Protists are perhaps the most lineage-rich of microbial lifeforms, but remain largely unknown. High-throughput sequencing technologies provide opportunities to screen whole habitats in depth and enable detailed comparisons of different habitats to measure, compare and map protistan diversity. Such comparisons are often limited by low sample numbers within single studies and a lack of standardisation between studies. Here, we analysed 232 samples from 10 sampling campaigns using a standardised PCR protocol and bioinformatics pipeline. We show that protistan community patterns are highly consistent within habitat types and geographic regions, provided that sample processing is standardised. Community profiles are only weakly affected by fluctuations of the abundances of the most abundant taxa and, therefore, provide a sound basis for habitat comparison beyond random short-term fluctuations in the community composition. Further, we provide evidence that distribution patterns are not solely resulting from random processes. Distinct habitat types and distinct taxonomic groups are dominated by taxa with distinct distribution patterns that reflect their ecology with respect to dispersal and habitat colonisation. However, there is no systematic shift of the distribution pattern with taxon abundance.

Geographic distance and mountain ranges structure freshwater protist communities on a European scalе

“…In fact, we found a low taxon overlap between lakes and a correspondingly high contribution to beta-diversity of individual habitats. In accordance with our findings, a large genetic divergence between distinct lake microbial communities has been reported in recent deep-sequencing campaigns, in particular for the rare biosphere (Filker et al 2016, Grossmann et al 2016b, Triadó-Margarit and Casamayor 2012. In particular, distribution patterns of rare taxa seem to vary widely and to deviate from the rather uniform patterns in abundant protists (Grossmann et al 2016a, Schiaffino et al 2016).…”

“…Seasonal taxon fluctuations influence protist community composition and may interfere with spatial analyses when samples originate from different seasons (Bock et al 2014, Massana et al 2015, Nolte et al 2010. Considering that all samples in our campaign were taken in August 2012 and that seasonal effects and plankton succession dynamics is presumably lower in mid-summer lake plankton communities than in spring succession communities (Naselli-Flores et al 2003), the observed divergence presumably reflects largely spatial differentiation of lake plankton communities rather than seasonal variation (Grossmann et al 2016b). However, due to the large area included in the analysis a certain bias due to differential stages of the seasonal succession cannot be excluded.…”

Parasites dominate hyperdiverse soil protist communities in Neotropical rainforests

“…3). This pattern of dominating parasites contrasts with the prevailing view that soil protist communities are dominated by predators of bacteria 34 , although a considerable presence of protist predators of fungi and animals, as well as protist parasites, has been observed elsewhere [35][36][37][38][39][40][41] . These dominating protist parasites also potentially contribute to the high animal diversity in the rainforests by the same mechanisms that other parasites contribute to high tree diversity as hypothesized in the Janzen-Connell model 4,5 .…”

Microplastic-Associated Biofilms: A Comparison of Freshwater and Marine Environments

“…Little is known about plastic-associated microbial eukaryotes in freshwaters, and there is a need for analyses targeting these organisms, not the least as they are known to occur on marine plastics [48,49]. Several advances have improved the suitability of metabarcoding for analyzing fungi, diatoms, and protists [85][86][87]. This approach is based on taxonomically informative markers and provides no direct information on metabolic activities.…”