Ciliates play a key role in most ecosystems. Their abundance in natural samples is crucial for answering many ecological questions. Traditional methods of quantifying individual species, which rely on microscopy, are often labour‐intensive, time‐consuming and can be highly biassed. As a result, we investigated the potential of digital polymerase chain reaction (dPCR) for quantifying ciliates. A significant challenge in this pr...

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...

Summary Microeukaryotes play key ecological roles in the microbial web of aquatic ecosystems. However, large knowledge gaps urgently need to be filled regarding the biogeography with associated shaping mechanisms and co‐occurrence patterns of microeukaryotes under freshwater‐saltwater gradients, especially true in tropical regions. Here, we investigated microeukaryotes of six mixed freshwater‐saltwater regions in the Pearl Riv...

Increasing anthropogenic impact and global change effects on natural ecosystems has prompted the development of less expensive and more efficient bioassessments methodologies. One promising approach is the integration of DNA metabarcoding in environmental monitoring. A critical step in this process is the inference of ecological quality (EQ) status from identified molecular bioindicator signatures that mirror environmental cla...

A decade after environmental scientists integrated high‐throughput sequencing technologies in their toolbox, the genomics‐based monitoring of anthropogenic impacts on the biodiversity and functioning of ecosystems is yet to be implemented by regulatory frameworks. Despite the broadly acknowledged potential of environmental genomics to this end, technical limitations and conceptual issues still stand in the way of its broad app...

Unraveling geographic distribution patterns of planktonic protists is a central goal in marine microbial ecology. Using a novel combination of recently developed phylogenetic and network analyses on a V4 18S rDNA metabarcoding dataset, we here analyzed the genetic diversity of marine planktonic ciliate communities in Chinese and European coastal waters. Thereby, our approach provided an unprecedented perspective on geographic...

Studies on cyrtophorian ciliates (Cyrtophoria) have accumulated much knowledge on morphological taxonomy and molecular phylogeny, and the general classification and phylogenetic relationships of most families have thereby been revealed. However, the phylogenetic position of the family Gastronautidae Deroux, 1994 remains uncertain. This is due to the presence of specialized characteristics (in particular a circumoral kinety in...

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...

Microbial planktonic communities are the basis of food webs in aquatic ecosystems since they contribute substantially to primary production and nutrient recycling. Network analyses of DNA metabarcoding data sets emerged as a powerful tool to untangle the complex ecological relationships among the key players in food webs. In this study, we evaluated co‐occurrence networks constructed from time‐series metabarcoding data sets (1...

The ciliate genus Uronychia is a marine group with extremely differentiated cortical and ciliary structures. These structures define its unique evolutionary position in the whole subclass Euplotia. However, to date, few data about the ultrastructure of this genus and related taxa is available. In the present work, a dominant species, Uronychia binucleata , was investigated using scanning electron microscopy and transmission el...

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...