Ciliates are single celled eukaryotes recognized as key players in the microbial loop of aquatic ecosystems. The present study was carried out on the Krka River (Croatia), a karst freshwater ecosystem characterized by tufa barriers, biomineralization and highly diverse aquatic communities. The main aims of the study were to investigate ciliate community structure in the biofilm (i.e. periphyton) samples collected from light- and dark-exposed lithified tufa/stones. Furthermore, by establishing links between ciliate community patterns and environmental parameters, we aimed to assess the bioindicator potential of specific ciliate taxa for environmental monitoring of freshwater habitats. The periphyton sampling was performed at four representative sites of the river source, upstream, middle and downstream river sections. Ciliate community was investigated via traditional microscopy analyses and environmental DNA (eDNA) metabarcoding (Illumina sequencing of the hypervariable V9-region of the SSU rRNA gene). The molecular approach recorded a substantially higher number of ciliate taxa, most of which taxonomically belonging to genera typically occurring in tufa barriers. The results from microscopy analyses did not show any links between ciliate community structure and sampling location. However, eDNA approach indicated significant differences among the sampling locations regarding the ciliate community structure. Thereby, hydrological parameters and saprobiological classification of the sampling sites were the main structuring factors for ciliate community. The coupling of eDNA metabarcoding with the morphological approach provides a robust, in-depth analytical system in elucidating the bioindicator potential of ciliated protists.
The second leg of the Polarstern expedition PS93 to the Arctic started on 21st July 2015 in Tromso (Norway) and ended on 15th August 2015, again in Tromso (Fig. 1.1). The cruise led to the deep-sea observatory HAUSGARTEN in the Fram Strait (approx. 78°30’N - 80°00’N, 05°00’W - 11°00’E). The total duration of the expedition was 24 days; about 285 hours (almost 12 days) were spent for station work. The remaining time was used to reach the study area, for steaming between individual stations, and for the transit from 79°N back to Tromso. More than 30 stations were sampled, thereby usually deploying several scientific instruments per site. The total length of the expedition was approx. 1,800 nautical miles.
The scientific work during expedition PS93.2 supported the time-series studies at the LTER (Long-Term Ecological Research) observatory HAUSGARTEN, where we document Global Change induced environmental variations on a polar deep-water ecosystem. This work was carried out in close co-operation between the HGF-MPG Joint Research Group on Deep-Sea Ecology and Technology, the PEBCAO Group (Phytoplankton Ecology and Biogeochemistry in the Changing Arctic Ocean) at AWI, and the Helmholtz Young Investigators Group SEAPUMP (Seasonal and regional food web interactions with the biological pump), representing a joint effort between AWI and the MARUM - Center for Marine Environmental Sciences at the University of Bremen.
The expedition was also used to accomplish installations for the HGF infrastructure project FRAM (FRontiers in Arctic marine Monitoring). The FRAM Ocean Observing System aims at permanent presence at sea, from surface to depth, for the provision of near real-time data on Earth system dynamics, climate variability and ecosystem change. It serves national and international tasks towards a better understanding of the effects of change in ocean circulation, water mass properties and sea-ice retreat on Arctic marine ecosystems and their main functions and services. Within the framework of a ‘Trans-National Access’ (TNA) initiative of the European project FixO3 (Fixed-point Open Ocean Observatories), the expedition provided access to the FRAM Ocean Observing System thereby supporting external and joint scientific projects logistically.
Beside the more “traditional” instruments used for marine research (e.g. water sampler, plankton nets, sediment sampler, moorings, bottom-lander) we operated a deep-diving Work-Class Remotely Operated Vehicle (ROV) as well as an Autonomous Underwater Vehicle (AUV) and different autonomous Unmanned Aerial Vehicles (UAVs) during the overall technically and logistically very challenging expedition.
The effective cooperation between the scientific party and the ship’s crew, in combination with perfect weather conditions during most times of the cruise, made this expedition a great success.
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 salt ponds (salinities 4%-44%) from South America and Europe. Statistical analyses of protistan community profiles identified four salinity classes, which strongly selected for different protistan communities: 4-9%, 14-24%, 27-36% and 38-44%. The proportion of organisms unknown to science is highest in the 14-24% salinity class, showing that environments within this salinity range are an unappreciated reservoir of as yet undiscovered organisms. Distinct higher-rank taxon groups dominated in the four salinity classes in terms of diversity. As increasing salinities require different cellular responses to cope with salt, our results suggest that different evolutionary lineages of protists have evolved distinct haloadaptation strategies. Salinity appears to be a stronger selection factor for the structuring of protistan communities than geography. Yet, we find a higher degree of endemism in shallow salt ponds compared with less isolated ecosystems such as the open ocean. Thus, rules for biogeographic structuring of protistan communities are not universal, but depend on the ecosystem under consideration.
Background: High-throughput sequencing technologies are lifting major limitations to molecular-based ecological studies of eukaryotic microbial diversity, but in silico analyses of the resulting millions of short amplicons remain a major bottleneck for these approaches. Here, we introduced the analytical and statistical framework of sequence similarity networks, increasingly used in evolutionary studies and graph theory, into the field of ecology to analyze novel pyrosequenced V4 SSU-rDNA sequence data sets in the context of previous studies, including SSU-rDNA Sanger sequence data from cultured ciliates and from previous environmental diversity inventories. Results: Our broadly applicable protocol quantified progress in the description of genetic diversity of ciliates by environmental rRNA amplicons studies, detected a fundamental historical bias, the tendency to recover already known groups, in these surveys, and revealed substantial amounts of hidden microbial diversity. Moreover, network measures demonstrated that ciliates are not globally dispersed, but present strong local patterns at intermediate geographical scale, as observed for bacteria, plants, and animals. Conclusions: Although currently available ‘universal’ primers used for local in-depth sequencing surveys provide little hope to exhaust the significantly higher ciliate (and most likely microbial) diversity than previously thought, sequence similarity networks, since they identify groups of divergence sequences sharing distinctive similarities, offer a promising way to guide the design of novel primers and to further explore such a vast and structured microbial diversity.
Background: High-throughput sequencing technologies are lifting major limitations to molecular-based ecological studies of eukaryotic microbial diversity, but in silico analyses of the resulting millions of short amplicons remain a major bottleneck for these approaches. Here, we introduced the analytical and statistical framework of sequence similarity networks, increasingly used in evolutionary studies and graph theory, into the field of ecology to analyze novel pyrosequenced V4 SSU-rDNA sequence data sets in the context of previous studies, including SSU-rDNA Sanger sequence data from cultured ciliates and from previous environmental diversity inventories. Results: Our broadly applicable protocol quantified progress in the description of genetic diversity of ciliates by environmental rRNA amplicons studies, detected a fundamental historical bias, the tendency to recover already known groups, in these surveys, and revealed substantial amounts of hidden microbial diversity. Moreover, network measures demonstrated that ciliates are not globally dispersed, but present strong local patterns at intermediate geographical scale, as observed for bacteria, plants, and animals. Conclusions: Although currently available ‘universal’ primers used for local in-depth sequencing surveys provide little hope to exhaust the significantly higher ciliate (and most likely microbial) diversity than previously thought, sequence similarity networks, since they identify groups of divergence sequences sharing distinctive similarities, offer a promising way to guide the design of novel primers and to further explore such a vast and structured microbial diversity.
file : Novel_diversity_V4_BIOM_cDNA.fasta see details in Testing ecological theories with sequence similarity networks: marine ciliates exhibit similar geographic dispersal patterns as multicellular organisms (file : readme_Forster_et_al_BMC) http://dx.doi.org/10.6084/m9.figshare.1264013 Background: High-throughput sequencing technologies are lifting major limitations to molecular-based ecological studies of eukaryotic microbial diversity, but in silico analyses of the resulting millions of short amplicons remain a major bottleneck for these approaches. Here, we introduced the analytical and statistical framework of sequence similarity networks, increasingly used in evolutionary studies and graph theory, into the field of ecology to analyze novel pyrosequenced V4 SSU-rDNA sequence data sets in the context of previous studies, including SSU-rDNA Sanger sequence data from cultured ciliates and from previous environmental diversity inventories. Results: Our broadly applicable protocol quantified progress in the description of genetic diversity of ciliates by environmental rRNA amplicons studies, detected a fundamental historical bias, the tendency to recover already known groups, in these surveys, and revealed substantial amounts of hidden microbial diversity. Moreover, network measures demonstrated that ciliates are not globally dispersed, but present strong local patterns at intermediate geographical scale, as observed for bacteria, plants, and animals. Conclusions: Although currently available ‘universal’ primers used for local in-depth sequencing surveys provide little hope to exhaust the significantly higher ciliate (and most likely microbial) diversity than previously thought, sequence similarity networks, since they identify groups of divergence sequences sharing distinctive similarities, offer a promising way to guide the design of novel primers and to further explore such a vast and structured microbial diversity.
Nearly 6000 SSU rRNA sequences of ciliated protists, compiled from 50 marine and terrestrial sampling sites worldwide were analysed to identify environmental barriers spatially relating ciliate communities. The hypotheses were: (i) oxygen is a dispersal barrier for strict anaerobes, allowing allopatric speciation in isolated habitats and resulting in high diversity; (ii) as salinity affects metabolism it may lead to distinct clusters with evolutionarily separated lineages; (iii) different oceanic realms support significantly different ciliate communities. Based on the α-diversity of the ciliate sequences in each habitat and the shared diversity among different habitats, ecological and geographic boundaries were revealed. Community similarities between pairs of habitats and all habitats were depicted with a metric distance matrix. Anoxia and salinity emerged as decisive determinants structuring the communities, with anoxia largely overlaying the effect of other environmental parameters. Measurements of α-diversity suggest a tremendous diversity of ciliates in anoxic environments, exceeding the one in normoxic environments. Salinity also exerts a high selection pressure on ciliates, contributing to community structure, composition and distribution patterns. However, marine–freshwater transitions seem to be more recent in ciliates compared with most other protistan taxa. The theory of island biogeography seems to apply to anoxic habitats, making these sites promising targets for the discovery of novel diversity.
ABSTRACT. At its discovery in 1982, the ciliate genus Colpodidium was assigned to the Class Colpodea. Redescriptions of the type species Colpodidium caudatum caused the establishment of a new family (Colpodidiidae). Based on ontogenetic data, eventually a new order—Colpodidiida—was established and hypothesized to belong to the Class Nassophorea. Despite a remarkable increase in the number of colpodidiid species, no sequence data were available to confirm or reject either class assignment or to assess the phylogenetic validity of the Colpodidiidae and the Colpodidiida. We here retrieved and phylogenetically analyzed the SSrDNA sequences of C. caudatum from a Namibian soil and an as‐yet undescribed colpodidiid ciliate from the Chobe River floodplain, Botswana. Bayesian inference methods and evolutionary distance analyses confirmed the assignment of these taxa to the class Nassophorea.
Neokeronopsis (Afrokeronopsis) aurea nov. subgen., nov. spec. was discovered in soil from the floodplain of a small river in the Krueger National Park, Republic of South Africa. Its morphology, ontogenesis, and 18S rDNA were studied with standard methods. Furthermore, we supplemented the data on N. (N.) spectabilis by reinvestigating the preparations deposited in the British Museum of Natural History. Neokeronopsis (Afrokeronopsis) aurea is a very conspicuous ciliate because it has an average size of 330 × 120 μm and is golden yellow due to the orange-coloured cytoplasm and citrine cortical granules. Further main characteristics include the semirigid body; the urostylid cirral pattern with a distinct corona of frontal and pseudobuccal cirri both originating from the midventral rows; multiple anterior fragmentation of dorsal kineties 1-3; multiple posterior fragmentation of kinety 3, commencing with an unique whirl of kinetofragments; three caudal cirri; an oxytrichid/cyrtohymenid oral apparatus with polystichad paroral membrane and buccal depression; a single oral primordium developing along the transverse cirral row; and an oxytrichid 18S rDNA. These peculiarities are used to establish the new oxytrichid family Neokeronopsidae, the new subgenus Afrokeronopsis, and the new species N. (A.) aurea. Further, these features confirm the CEUU hypothesis, i.e., convergent evolution of a midventral cirral pattern in urostylid and oxytrichid hypotrichs; additionally, N. (A.) aurea is the first (semi)rigid hypotrich with cortical granules and the second one with midventral rows, breaking the granule and flexibility dogmas. These and other observations show that the phylogeny of the hypotrichs is full of convergences. Thus, only a combined effort of classical and molecular phylogeneticists will provide the data needed for a natural classification. Based on the CEUU hypothesis, the molecular data, and literature evidence, we suggest that midventral oxytrichids should be ranked as distinct families; accordingly, we establish a further new family, the Uroleptidae, which forms a distinct clade within the oxytrichid molecular trees. Neokeronopsis is possibly related to Pattersoniella because it has the same special mode of forming the buccal cirri and possesses a buccal depression found also in Steinia, a close relative of Pattersoniella. The large size and conspicuous colour make N. (A.) aurea a biogeographic flagship possibly confined to Africa or Gondwana, while Neokeronopsis (N.) spectabilis (Kahl, 1932) is an Eurasian flagship.
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