Environmental DNA sequencing is the gold standard to reveal microbial community structures. In most applications, a one‐fragment PCR approach is applied to amplify a taxonomic marker gene, usually a hypervariable region of the 16S rRNA gene. We used a new reverse complement (RC)‐PCR‐based assay that amplifies seven out of the nine hypervariable regions of the 16S rRNA gene, to interrogate bacterial communities in sediment samp...

We isolated a population of Oxytricha granulifera granulifera Foissner and Adam (1983) from a hot spring in Iceland. The pure culture of this isolate was established at room temperature in the laboratory. This allowed for a detailed investigation, informed by integrated approaches, of the isolate’s morphology and morphogenesis, as well as molecular phylogeny. Results showed that the morphological and morphogenetic characterist...

Summary Effective and precise grouping of highly similar sequences remains a major bottleneck in the evaluation of high‐throughput sequencing datasets. Amplicon sequence variants (ASVs) offer a promising alternative that may supersede the widely used operational taxonomic units (OTUs) in environmental sequencing studies. We compared the performance of a recently developed pipeline based on the algorithm DADA2 for obtaining ASV...

Summary Remane's Artenminimum at the horohalinicum is a fundamental concept in ecology to describe and explain the distribution of organisms along salinity gradients. However, a recent metadata analysis challenged this concept for protists, proposing a species maximum in brackish waters. Due to data bias, this literature‐based investigation was highly discussed. Reliable data verifying or rejecting the species minimum for prot...

Summary The identification of environmental barriers which govern species distribution is a fundamental concern in ecology. Even though salt was previously identified as a major transition boundary for micro‐ and macroorganisms alike, the salinities causing species turnover in protistan communities are unknown. We investigated 4.5 million high‐quality protistan metabarcodes (V4 region of the SSU rDNA) obtained from 24 shallow...

Microbial eukaryotes hold a key role in aquatic ecosystem functioning. Yet, their diversity in freshwater lakes, particularly in high‐mountain lakes, is relatively unknown compared with the marine environment. Low nutrient availability, low water temperature and high ultraviolet radiation make most high‐mountain lakes extremely challenging habitats for life and require specific molecular and physiological adaptations. We there...

Summary Protists play a crucial role for ecosystem function(ing) and oxygen is one of the strongest barriers against their local dispersal. However, protistan diversity in freshwater habitats with oxygen gradients received very little attention. We applied high‐throughput sequencing of the V9 region ( 18S rRNA gene) to provide a hitherto unique spatiotemporal analysis of protistan diversity along the oxygen gradient of a fresh...

Summary Analyses of high‐throughput environmental sequencing data have become the ‘gold‐standard’ to address fundamental questions of microbial diversity, ecology and biogeography. Findings that emerged from sequencing are, e.g. the discovery of the extensive ‘rare microbial biosphere’ and its potential function as a seed‐bank. Even though applied since several years, results from high‐throughput environmental sequencing have...