About
399
Publications
113,112
Reads
How we measure 'reads'
A 'read' is counted each time someone views a publication summary (such as the title, abstract, and list of authors), clicks on a figure, or views or downloads the full-text. Learn more
12,157
Citations
Introduction
Additional affiliations
December 2003 - present
Publications
Publications (399)
The marine aquaculture industry and regulators are in the process of implementing environmental DNA (eDNA) metabarcoding of microbial communities for compliance monitoring. This requires standardization of sampling, laboratory, and data analysis protocols. Towards this goal, we in this study completed two further milestones using samples collected...
Considering the critical issue of overexploited stocks due to overfishing, the EU's Data Collection Framework (DCF) was established. Within the DCF, member states collect and analyze data relevant to sustainable fisheries management. To evaluate the status of fisheries, it is necessary to categorize fishing fleets into fleet segments. However, the...
Oxford Nanopore Technologies has recently launched a duplex sequencing strategy and announced an improved error rate which is in a similar order of magnitude as Illumina sequencing. We therefore conducted a pilot study to assess whether Nanopore duplex sequencing has potential to be used as a technology in eDNA-based marine biomonitoring. Specifica...
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 reg...
Organic enrichment associated with marine finfish aquaculture is a local stressor of marine coastal ecosystems. To maintain ecosystem services, the implementation of biomonitoring programs focusing on benthic diversity is required. Traditionally, impact-indices are determined by extracting and identifying benthic macroinvertebrates from samples. Ho...
The freshwater species, Euplotes mazeii n. sp., and the marine species, E. balteatus (Dujardin, 1841) Diesing, 1850 were collected from China and investigated based on their living morphology, ciliary pattern, and small subunit ribosomal RNA (SSU rRNA) gene sequence data. Euplotes mazeii n. sp. was characterized by its small cell size ((40–55)µm ×(...
Mesoscale eddies which origin in Eastern Boundary Upwelling Systems (EBUS) such as the Canary Current System entrap nutrient rich coastal water and travel offshore while ageing. We have analyzed the protistan plankton community structures in the deep chlorophyll maximum (DCM), sub-DCM and oxygen minimum zone (OMZ) of three differently aged cyclonic...
Coral reef ecosystems in the Persian Gulf are frequently exposed to crude oil spills. We investigated benthic bacterial and eukaryote community structures at such coral reef sites subjected to different degrees of polycyclic aromatic hydrocarbon (PAH) pollution using environmental DNA (eDNA) metabarcoding. Both bacterial and eukaryote communities r...
Ciliates of the genus Urotricha are widely distributed and occur in almost any freshwater body. Thus far, almost all species have been described from morphology only. Here, we applied an integrative approach on the morphology, molecular phylogeny and biogeography of two species isolated from high mountain lakes in the Central Alps, Austria. As thes...
The present work investigated Hastatella radians Erlanger, 1890 (type species), and H. aesculacantha Jarocki & Jakubowska, 1927, isolated from Chongming Island, Shanghai, China, based on light microscopy observations of live individuals, silver staining and molecular phylogeny methods. Hastatella radians is characterized by its size (about 30-75 μm...
Species of the ciliate genus Urotricha are key players in freshwater plankton communities. In the pelagial of lakes, about 20 urotrich species occur throughout an annual cycle, some of which play a pivotal role in aquatic food webs. For example, during the phytoplankton spring bloom, they consume a remarkable proportion of the algal production. In...
We established a new species, Euplotes tuffraui, and described the morphology and phylogeny of this species (Lian et al. 2021). Helmut Berger (Salzburg, Austria) informed us that Euplotes tuffraui Lian et al., 2021 is a junior primary homonym of E. tuffraui Berger, 1965 (Berger, 2001, Berger, 1965). Both species are valid. According to article 57.2...
To avoid loss of genetic information in environmental DNA (eDNA) field samples, the preservation of nucleic acids during field sampling is a critical step. In the development of standard operating procedures (SOPs) for eDNA-based compliance monitoring, the effect of different routinely used sediment preservations on biological community structures...
Environmental DNA (eDNA) metabarcoding (parallel sequencing of DNA/RNA for identification of whole communities within a targeted group) is revolutionizing the field of aquatic biomonitoring. To date, most metabarcoding studies aiming to assess the ecological status of aquatic ecosystems have focused on water eDNA and macroinvertebrate bulk samples....
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 mi...
The morphology and SSU rDNA-based phylogeny of two small marine euplotid species isolated from China, Euplotes tuffraui sp. nov. and E. shii sp. nov., were investigated. Euplotes tuffraui sp. nov. has a combination of features including body size (35–50 μm × 15–35 μm), body shape (generally triangle-shaped) adoral membranelles gradually bending at...
Environmental DNA metabarcoding is a powerful approach for use in biomonitoring and impact assessments. Amplicon-based eDNA sequence data are characteristically highly divergent in sequencing depth (total reads per sample) as influenced inter alia by the number of samples simultaneously analyzed per sequencing run. The random forest (RF) machine le...
The analysis of benthic bacterial community structure has emerged as a powerful alternative to traditional microscopy-based taxonomic approaches to monitor aquaculture disturbance in coastal environments. However, local bacterial diversity and community composition vary with season, biogeographic region, hydrology, sediment texture, and aquafarm-sp...
The analysis of benthic bacterial community structure has emerged as a powerful alternative to traditional microscopy-based taxonomic approaches to monitor aquaculture disturbance in coastal environments. However, local bacterial diversity and community composition vary with season, biogeographic region, hydrology, sediment texture, and aquafarm-sp...
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 wa...
Species of the genus Coleps are one of the most common planktonic ciliates in lake ecosystems. The study aimed to identify the phenotypic plasticity and genetic variability of different Coleps isolates from various water bodies and from culture collections. We used an integrative approach to study the strains by (i) cultivation in a suitable cultur...
Network analyses of biological communities allow for identifying potential consequences of climate change on the resilience of ecosystems and their robustness to resist stressors. Using DNA metabarcoding datasets from a three-year-sampling (73 samples), we constructed the protistan plankton co-occurrence network of Lake Zurich, a model lake ecosyst...
Salmon aquaculture is one of the fastest growing food sectors in the world. Because aquaculture can have a significant impact on the benthic environment, frequent monitoring is required by law. Recently, eDNA (environmental DNA) metabarcoding of benthic bacterial communities emerged as a very powerful tool to infer ecological quality based on ampli...
Marine coastal ecosystems offer numerous ecosystem services and are therefore subject to a variety of stressors from anthropogenic activities. Environmental biomonitoring programs for effective management and conservation of coastal marine ecosystems are therefore crucial. Traditional monitoring has been based on macrofauna indices which are labori...
With an increasing demand for finfish from aquaculture, the importance of monitoring the impact of aquaculture installations on coastal ecosystems becomes more and more important. The traditional approach employs macroinvertebrates as bioindicators to assess the ecological quality (EQ) of near-field benthic ecosystem, which is costly and time consu...
Bioindication has become an indispensable part of water quality monitoring in most countries of the world, with the presence and abundance of bioindicator taxa, mostly multicellular eukaryotes, used for biotic indices. In contrast, microbes (bacteria, archaea and protists) are seldom used as bioindicators in routine assessments, although they have...
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 th...
The effect of oceanic mesoscale cyclonic eddies in an eastern boundary upwelling system on protistan community structures was examined using V9 18S rRNA gene amplicons. Therefore, we collected samples along a distance gradient from the centre of a cyclonic eddy towards the eddy periphery. At each transect station we sampled three depths (deep chlor...
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...
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 evaluate...
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 binu...
Environmental DNA metabarcoding of benthic bacterial communities emerged as a very powerful technology to assess environmental disturbance effects of coastal salmon aquaculture. A prerequisite for the implementation of this approach into compliance monitoring regulations is its robustness and reproducibility of obtained results. In the framework of...
With highly specialized morphology and unexplored functional capacities, ciliates from extreme habitats are drawing increasing attention. During a microbial investigation of a solar saltern pond (salinity 240‰) on Mallorca, Spain, a previously unknown scuticociliate, Platynematum rosellomorai sp. n. was isolated, cultured and studied using a tripar...
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, tec...
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...
A decade after environmental scientists integrated high-throughput sequencing technologies in their toolbox, the genomics-based monitoring of anthropogenic impacts on biodiversity and ecosystems is yet to be implemented by regulatory frameworks. Despite the broadly acknowledged potential of environmental DNA and RNA to cost-efficiently and accurate...
As the ecologically important recipient channels for riverine ecosystems, tributaries provide unique microhabitats for microorganisms, among which zooplankton constitutes the most important heterotrophic organisms. In particular, the reduced water velocity caused by dams is more favorable for zooplankton development; therefore, dammed rivers are ex...
Effective and precise grouping of highly similar sequences remains a major bottleneck in the evaluation of high‐throughput sequencing (HTS) 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 o...
Induction of an axenic filamentous‐like callus growth from the brown algae Fucus vesiculosus is described. Different treatments were investigated in various combinations to develop axenic cultures based on identification of surface symbionts via 18S ribosomal RNA. Moreover, viability was confirmed after such processes by 2,3,5‐triphenyl tetrazolium...
Ciliates represent central nodes in freshwater planktonic food webs, and many species show pronounced seasonality, with short-lived maxima of a few dominant taxa while many being rare or ephemeral. These observations are primarily based on morphospecies counting methods, which, however, have limitations concerning the amount and volume of samples t...
WE (Fotedar et al.) established a new species, viz., Euplotes qatarensis, and described its morphology, ontogenesis, and phylogenetic relationships in this electronic-only journal. As this work does not contain ZooBank registration, it is not published in the sense of nomenclature (ICZN, Articles 8.5, 9.11), that is, it is not a work in which a nam...
A new hypotrichous ciliate, Schmidtiella ultrahalophila gen. nov. spec. nov., was isolated from a solar saltern on the island of Sal, Cape Verde. The possession of only one short dorsal kinety clearly distinguishes Schmidtiella ultrahalophila from other known hypotrichous genera and species. Further diagnostic characters include: a flexible and sle...
Diatoms constitute a diverse lineage of unicellular organisms abundant and ecologically important in aquatic ecosystems. Compared to other protists, their biology and taxonomy are well-studied, offering the opportunity to combine traditional approaches and new technologies. We examined a dataset of diatom 18S rRNA- and rDNA- (V4 region) reads from...
We isolated an encysted ciliate from a geothermal field in Iceland. The morphological features of this isolate fit the descriptions of Dexiotricha colpidiopsis (Kahl, 1926) Jankowski, 1964 very well. These comprise body shape and size in vivo, the number of somatic
kineties, and the positions of macronucleus and contractile vacuole. Using state-of-...
Genomics is fast becoming a routine tool in medical diagnostics and cutting-edge biotechnologies. Yet, its use for environmental biomonitoring is still considered a futuristic ideal. Until now, environmental genomics was mainly used as a replacement of the burdensome morphological identification, to screen known morphologically distinguishable bioi...
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 disc...
Ciliates are powerful indicators for monitoring the impact of aquaculture and other industrial activities in the marine environment. Here we tested the efficiency of four different genetic markers (V4 and V9 regions of the SSU rRNA gene, D1 and D2 regions of the LSU rRNA gene, obtained from environmental (e)DNA and environmental (e)RNA) of benthic...
Biodiversity monitoring is the standard for environmental impact assessment of anthropogenic activities. Several recent studies showed that high‐throughput amplicon sequencing of environmental DNA (eDNA metabarcoding) could overcome many limitations of the traditional morphotaxonomy‐based bioassessment. Recently, we demonstrated that supervised mac...
Knowledge-driven management for wastewater treatment plant (WWTP) performance becomes increasingly important considering the globally growing production of wastewater and the rising demand of clean water supply. Even though the potential of microbial organisms (bacteria and protists) as bioindicators for WWTP performance is well known, it is far fr...
Members of the class Armophorea occur in microaerophilic and anaerobic habitats, including the digestive tract of invertebrates and vertebrates. Phylogenetic kinships of metopid and clevelandellid armophoreans conflict with traditional morphology‐based classifications. To reconcile their relationships and understand their morphological evolution an...
The ciliate genus Chlamydodon is characterized by a unique cross-striated band (CSB) along the cell perimeter. To date, more than 15 nominal species have been assigned to this genus, all of which are exclusively from marine or brackish water. In the present work, we have revised the genus according to the available data and suggest an illustrated k...
Tropical animals and plants are known to have high alpha diversity within forests, but low beta diversity between forests. By contrast, it is unknown if microbes inhabiting the same ecosystems exhibit similar biogeographic patterns. To evaluate the biogeographies of tropical protists, we used metabarcoding data of species sampled in the soils of th...
We evaluated benthic bacterial communities as bioindicators in environmental impact assessments of salmon aquaculture, a rapidly growing sector of seafood industry. Sediment samples (n=72) were collected from below salmon cages towards distant reference sites. Bacterial community profiles inferred from DNA metabarcodes were compared to reference da...
The backbone of benthic marine monitoring programs is the biological component, traditionally the macrofauna inventory. Such macrofauna-based environmental impact assessments (EIA), however, are very time consuming and expensive. To overcome these shortcomings, we used environmental metabarcoding to test the potential of protists as bioindicators i...
Background
Benthic ciliates and the environmental factors shaping their distribution are far from being completely understood. Likewise, deep-sea systems are amongst the least understood ecosystems on Earth. In this study, using high-throughput DNA sequencing, we investigated the diversity and community composition of benthic ciliates in different...
Three new cyrtophorian ciliates isolated from coastal areas of China were described based on morphological and genetic data. The Chlamydodon mnemosyne-like species Chlamydodon similis sp. n. differs from its congeners mainly by its number of somatic kineties. Chlamydodon oligochaetus sp. n. is distinguished from its congeners mainly by having fewer...
We collected a heterotrich ciliate from hypersaline waters on the Cape Verde island Sal. After living observation and protargol-staining, it closely matched Blepharisma halophilum Ruinen, 1938. However, because (i) Ruinen most likely described several different species as B. halophilum, and (ii) he provided only very scarce diagnostic features, we...
Recent advances in molecular technology have revolutionized research on allaspects of the biology of organisms, including ciliates, and created unprecedented opportunities for pursuing a more integrative approach to investigationsof biodiversity. However, this goal is complicated by large gaps and inconsistencies that still exist in the foundation...
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 pr...
The ongoing decrease in sea ice thickness and extent is expected to have significant implications for protists in the Arctic Ocean. We analyzed protist community composition and diversity in water and sea ice samples to elucidate the impact of sea ice retreat and sea ice origin. Samples were collected during 2 summer periods with contrasting sea ic...