Functional diversity of aquatic ciliates

Comparing the Environmental Influences and Community Assembly of Protist Communities in Two Anthropogenic Coastal Areas

Anthropogenic stresses are intensively affecting the structure and function of microbial communities in coastal ecosystems. Despite being essential components of coastal ecosystems, the environmental influences and assembly processes of protist communities remain largely unknown in areas with severe disturbance. Here, we used 18S rRNA gene high-throughput sequencing to compare the composition, assembly process, and functional structure of the protist communities from the coastal areas of the Northern Yellow Sea (NYS) and the Eastern Bohai Sea (EBS). These two areas are separated by the Liaodong Peninsula and experience different anthropogenic stresses due to varying degrees of urbanization. We detected significant differences between the protist communities of the two areas. Environmental and geographic factors both influenced the composition of protist communities, with environmental factors playing a greater role. The neutral community model indicated that the assembly of protist communities was governed by deterministic processes, with stochastic processes having a stronger influence in the EBS area compared to the NYS area. The phototrophic and consumer communities, influenced by different environmental factors, differed significantly between the two areas. Our results provide insights into the biogeography and assembly of protist communities in estuaries under anthropogenic stresses, which may inform future coastal management.

Removal and assessment of cadmium contamination based on the toxic responds of a soil ciliate Colpoda sp

Bioremediation of cadmium (Cd) pollution, a recognized low-carbon green environmental protection technology, is significantly enhanced by the discovery of Cd-tolerant microorganisms and their underlying tolerance mechanisms. This study presents Colpoda sp., a soil ciliate with widespread distribution, as a novel bioindicator and bioremediator for Cd contamination. With a 24 h-LC50 of 5.39 mg l-1 and an IC50 of 24.85 μg l-1 in Cd-contaminated water, Colpoda sp. achieves a maximum bioaccumulation factor (BAF) of 3.58 and a Cd removal rate of 32.98 ± 0.74 % within 96 h. The toxic responses of Colpoda sp. to Cd stress were assessed through cytological observation with transmission electron microscopy (TEM), oxidative stress kinase activity, and analysis of Cd-metallothionein (Cd-MTs) and the cd-mt gene via qRT-PCR. The integrated biomarker response index version 2 (IBRv2) and structural equation models (SEM) were utilized to analyze key factors and mechanisms, revealing that the up-regulation of Cd-MTs and cd-mt expression, rather than the oxidative stress system, is the primary determinant of Cd accumulation and tolerance in Colpoda sp. The ciliate's ability to maintain growth under 24.85 μg l-1 Cd stress and its capacity to absorb and accumulate Cd particles from water into cells are pivotal for bioremediation. A new mathematical formula and regression equations based on Colpoda sp.'s response parameters have been established to evaluate environmental Cd removal levels and design remediation schemes for contaminated sites. These findings provide a novel bioremediation and monitoring pathway for Cd remobilization and accumulation in soil and water, potentially revolutionizing the governance of Cd pollution.

Comparison of mixotrophic and heterotrophic chrysomonads of similar size regarding bacterivory and growth rate

Small chrysomonads are important bacterivores in aquatic ecosystems with a high molecular diversity compared to low morphological differences observed by light microscopy. The high diversity of these morphologically almost indistinguishable species leads to the question to which extent their functional role in ecosystems differs and how their ecological traits can be defined. The present study investigates the prey size and population growth rate of different chrysomonad species. Eleven phylogenetically well-defined strains representing seven strains of heterotrophic and four strains of mixotrophic chrysomonads were compared. All investigated strains belonged to the same functional group of bacterivorous flagellates, feeding on the same bacteria size range, while population growth rates of chrysomonads depended on nutritional strategy and species-specific differences. We observed a high individual variability of growth rates within a population. Our results point to the necessity to consider not only differences in ecological traits among species but also among specimens within a population.

Numerical and Thermal Response of the Bacterivorous Ciliate Colpidium kleini, a Species Potentially at Risk of Extinction by Rising Water Temperatures

We investigated the food-dependent growth and thermal response of the freshwater ciliate Colpidium kleini using numerical response (NR) experiments. This bacterivorous ciliate occurs in lotic water and the pelagial of lakes and ponds. The C. kleini strain used in this work was isolated from a small alpine lake and identified by combining detailed morphological inspections with molecular phylogeny. Specific growth rates (rmax) were measured from 5 to 21 °C. The ciliate did not survive at 22 °C. The threshold bacterial food levels (0.3 - 2.2 × 106 bacterial cells mL-1) matched the bacterial abundance in the alpine lake from which C. kleini was isolated. The food threshold was notably lower than previously reported for C. kleini and two other Colpidium species. The threshold was similar to levels reported for oligotrich and choreotrich ciliates if expressed in terms of bacterial biomass (0.05 - 0.43 mg C L-1). From the NR results, we calculated physiological mortality rates at zero food concentration. The mean mortality (0.55 ± 0.17 d-1) of C. kleini was close to the mean estimate obtained for other planktonic ciliates that do not encyst. We used the data obtained by the NR experiments to fit a thermal performance curve (TPC). The TPC yielded a temperature optimum at 17.3 °C for C. kleini, a maximum upper thermal tolerance limit of 21.9 °C, and a thermal safety margin of 4.6 °C. We demonstrated that combining NR with TPC analysis is a powerful tool to predict better a species' fitness in response to temperature and food.

Correlated responses to selection across diverse environments during experimental evolution of Tetrahymena thermophila

Correlated responses to selection have long been observed and studied; however, it remains unclear when they will arise, and in what direction. To contribute to a growing understanding of correlated responses to selection, we used experimental evolution of the ciliate Tetrahymena thermophila to study direct and correlated responses in a variety of different environmental conditions. One experiment focused on adaptation to two different temperatures and the correlated responses across temperatures. Another experiment used inhibitory concentrations of a variety of compounds to test direct and correlated responses to selection. We found that all populations adapted to the environments in which they evolved. We also found many cases of correlated evolution across environments; few conditions resulted in trade-offs and many resulted in a positive correlated response. Surprisingly, in many instances, the correlated response was of a larger magnitude than the direct response. We find that ancestral fitness predicts the extent of adaptation, consistent with diminishing returns epistasis. Unexpectedly, we also find that this pattern of diminishing returns holds across environments regardless of the environment in which evolution occurs. We also found that the correlated response is asymmetric across environments, that is, the fitness of a population evolved in one environment and assayed in a second was inversely related to the fitness of a population evolved in the second environment and assayed in the first. These results support the notion that positive correlated responses to selection across environments are frequent, and worth further study.

Using digital PCR to predict ciliate abundance from ribosomal RNA gene copy numbers

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 process is the high variation in the copy number of the taxonomic marker gene (ribosomal RNA [rRNA]). We first quantified the rRNA gene copy numbers (GCN) of the model ciliate, Paramecium tetraurelia, during different stages of the cell cycle and growth phases. The per-cell rRNA GCN varied between approximately 11,000 and 130,000, averaging around 50,000 copies per cell. Despite these variations in per-cell rRNA GCN, we found a highly significant correlation between GCN and cell numbers. This is likely due to the coexistence of different cellular stages in an uncontrolled (environmental) ciliate population. Thanks to the high sensitivity of dPCR, we were able to detect the target gene in a sample that contained only a single cell. The dPCR approach presented here is a valuable addition to the molecular toolbox in protistan ecology. It may guide future studies in quantifying and monitoring the abundance of targeted (even rare) ciliates in natural samples.

Quality matters: Response of bacteria and ciliates to different allochthonous dissolved organic matter sources as a pulsed disturbance in shallow lakes

Shallow lake ecosystems are particularly prone to disturbances such as pulsed dissolved organic matter (allochthonous-DOM; hereafter allo-DOM) loadings from catchments. However, the effects of allo-DOM with contrasting quality (in addition to quantity) on the planktonic communities of microbial loop are poorly understood. To determine the impact of different qualities of pulsed allo-DOM disturbance on the coupling between bacteria and ciliates, we conducted a mesocosm experiment with two different allo-DOM sources added to mesocosms in a single-pulse disturbance event: Alder tree leaf extract, a more labile (L) source and HuminFeed® (HF), a more recalcitrant source. Allo-DOM sources were used as separate treatments and in combination (HFL) relative to the control without allo-DOM additions (C). Our results indicate that the quality of allo-DOM was a major regulator of planktonic microbial community biomass and/or composition through which both bottom-up and top-down forces were involved. Bacteria biomass showed significant nonlinear responses in L and HFL with initial increases followed by decreases to pre-pulse conditions. Ciliate biomass was significantly higher in L compared to all other treatments. In terms of composition, bacterivore ciliate abundance was significantly higher in both L and HFL treatments, mainly driven by the bacterial biomass increase in the same treatments. GAMM models showed negative interaction between metazoan zooplankton biomass and ciliates, but only in the L treatment, indicating top-down control on ciliates. Ecosystem stability analyses revealed overperformance, high resilience and full recovery of bacteria in the HFL and L treatments, while ciliates showed significant shift in compositional stability in HFL and L with incomplete taxonomic recovery. Our study highlights the importance of allo-DOM quality shaping the response within the microbial loop not only through triggering different scenarios in biomass, but also the community composition, stability, and species interactions (top-down and bottom-up) in bacteria and plankton.

Upstream cascade reservoirs drive temporal beta diversity increases through species loss in a dammed river

Changes in the biodiversity of aquatic environments over time and space due to human activities are a topic of theoretical and conservational interest in ecology. Thus, variation in taxonomic beta diversity of the planktonic ciliates community was investigated along a temporal and spatial gradient in two subsystems of a Neotropical floodplain, one impacted by dams (Paraná) and the other free of them along its course (Ivinhema). For the spatial analysis, the Paraná subsystem did not show a significant decrease in beta diversity, presenting a pattern like that observed for the Ivinhema subsystem. Therefore, biotic homogenization was not observed for the ciliate's community downstream of the dams. It was noted that there was a fluctuation in the relevance of the components of beta diversity, regardless of the subsystem analyzed. For the temporal analysis there was a significant change in species composition from the first to the last year investigated, essentially for the subsystem impacted by dams, and that this was determined mainly by species loss. Although spatial beta diversity remained high without a clear process of biotic homogenization, dams promoted remarkable changes in ciliate species composition over the years mainly by continuous loss of species.

Influence of Ecological Multiparameters on Facets of β-Diversity of Freshwater Plankton Ciliates

Understanding the relative importance of the factors that drive global patterns of biodiversity is among the major topics of ecological and biogeographic research. In freshwater bodies, spatial, temporal, abiotic, and biotic factors are important structurers of these ecosystems and can trigger distinct responses according to the facet of biodiversity considered. The objective was to evaluate how different facets of β-diversity (taxonomic, functional, and phylogenetic) based on data from the planktonic ciliate community of a Neotropical floodplain, are influenced by temporal, spatial, abiotic, and biotic factors. The research was conducted in the upper Paraná River floodplain between the years 2010 and 2020 in different water bodies. All predictors showed significant importance on the facets of β-diversity, except the abiotic predictors on species composition data, for the taxonomic facet. The functional and phylogenetic facets were mostly influenced by abiotic, biotic, and spatial factors. For temporal predictors, results showed influence on taxonomic (structure and composition data) and functional (structure data) facets. Also, a fraction of shared explanation between the temporal and abiotic components was observed for the distinct facets. Significant declines in β-diversity in continental ecosystems have been evidenced, especially those with drastic implications for ecosystemic services. Therefore, the preservation of a high level of diversity in water bodies, also involving phylogenetic and functional facets, should be a priority in conservation plans and goals, to ensure the maintenance of important ecological processes involving ciliates.

Toxicological sensitivity of protozoa to pesticides and nanomaterials: A prospect review

Protozoa are sensitive indicators of pollutant toxicity. This review presents and discusses the toxicological studies of protozoa and the toxicological conventional test species (Daphnia magna) by pesticides and nanomaterials, particularly comparing the sensitivity of through relative tolerance analysis, Z-score, and species sensitivity index. The sensitivity of different species of protozoa varies greatly. The protozoa Paramecium sp. and Tetrahymena sp. are not sensitive species; conversely, Urostyla sp. is sensitive to dimethoate and nanomaterials Ag-NPs, respectively ZnO-NPs, and CuO-NPs, fits the use as an indicator species on these substances. The prospects to explore scientific toxicity exposure protocols, expand the protozoan species examined, and screen the sensitive species under the protocols are discussed. This prospect review advances the knowledge for including the sensitive protozoa as an indicator species in comprehensive toxicological analysis for pesticides and nanomaterials.

The photic-aphotic divide is a strong ecological and evolutionary force determining the distribution of ciliates (Alveolata, Ciliophora) in the ocean

The bulk of knowledge on marine ciliates is from shallow and/or sunlit waters. We studied ciliate diversity and distribution across epi- and mesopelagic oceanic waters, using DNA metabarcoding and phylogeny-based metrics. We analyzed sequences of the 18S rRNA gene (V4 region) from 369 samples collected at 12 depths (0-1000 m) at the Bermuda Atlantic Time-series Study site of the Sargasso Sea (North Atlantic) monthly for 3 years. The comprehensive depth and temporal resolutions analyzed led to three main findings. First, there was a gradual but significant decrease in alpha-diversity (based on Faith's phylogenetic diversity index) from surface to 1000-m waters. Second, multivariate analyses of beta-diversity (based on UniFrac distances) indicate that ciliate assemblages change significantly from photic to aphotic waters, with a switch from Oligotrichea to Oligohymenophorea prevalence. Third, phylogenetic placement of sequence variants and clade-level correlations (EPA-ng and GAPPA algorithms) show Oligotrichea, Litostomatea, Prostomatea, and Phyllopharyngea as anti-correlated with depth, while Oligohymenophorea (especially Apostomatia) have a direct relationship with depth. Two enigmatic environmental clades include either prevalent variants widely distributed in aphotic layers (the Oligohymenophorea OLIGO5) or subclades differentially distributed in photic versus aphotic waters (the Discotrichidae NASSO1). These results settle contradictory relationships between ciliate alpha-diversity and depth reported before, suggest functional changes in ciliate assemblages from photic to aphotic waters (with the prevalence of algivory and mixotrophy vs. omnivory and parasitism, respectively), and indicate that contemporary taxon distributions in the vertical profile have been strongly influenced by evolutionary processes. Integration of DNA sequences with organismal data (microscopy, functional experiments) and development of databases that link these sources of information remain as major tasks to better understand ciliate diversity, ecological roles, and evolution in the ocean.

Further insights into the phylogeny of facultative parasitic ciliates associated with tetrahymenosis (Ciliophora, Oligohymenophorea) based on multigene data

Tetrahymenosis, caused by about 10 Tetrahymena species, is an emerging problem inflicting a significant economic loss on the aquaculture industry worldwide. However, in the order Tetrahymenida, there are many unresolved evolutionary relationships among taxa. Here we report 21 new sequences, including SSU-rRNA, ITS1-5.8S-ITS2 rRNA and LSU-rRNA, genes of 10 facultative parasitic Tetrahymena associated with tetrahymenosis, and conduct phylogenetic analyses based on each individual gene and a three-gene concatenated dataset. The main findings are: (1) All the parasitic and facultative parasitic species cluster in borealis group. (2) With the addition of new sequences, Tetrahymena is still divided into three groups, namely the "borealis group", the "australis group," and the "paravorax group." (3) the cluster pattern of all the newly sequenced facultative parasitic Tetrahymena species shows that members of the "borealis" group may be more susceptible to parasitism. (4) phylogeny based on concatenated genes show that T. pyriformis, T. setosa, and T. leucophrys have close relationship.

Predation of Cyclopoid Copepods on the Theronts of Ichthyophthirius multifiliis: Shedding Light on Biocontrol of White Spot Disease

White spot disease, caused by the parasitic ciliate Ichthyophthirius multifiliis, is a significant threat to the freshwater fish farming industry worldwide, resulting in massive mortality and economic losses. Eliminating the free-swimming theronts from the culture environment is considered crucial for the control of I. multifiliis infection. It is well-documented that planktonic ciliates are valuable food resources for macro-zooplankton in aquatic ecosystems. In this study, we developed a fluorescence labeling method for alive theronts and found that cyclopoid copepods Thermocyclops taihokuensis, Mesocyclops spp., Macrocyclops sp., and Paracyclopina sp. present predation on the theronts in co-culture experiments. Laboratory challenge tests further confirmed that the presence of zooplankton in the culture water body significantly reduced the infection of I. multifiliis in goldfish (p < 0.01). Results from this study revealed that cyclopoid copepods have the potential to be used as biological control agents against white spot disease in aquaculture.

Toxicological impacts and likely protein targets of bisphenol a in Paramecium caudatum

Bisphenol A (BPA) is a widely used plasticizer agent and a well-known ubiquitous endocrine disruptor, which is frequently associated with a series of reproductive, developmental, and transgenerational effects over wildlife, livestocks, and humans. Although extensive toxicological data is available for metazoans, the impact of BPA over unicellular eukaryotes, which represents a considerable proportion of eukaryotic diversity, remains largely overlooked. Here, we used acute end-point toxicological assay and an inverted virtual-screening (IVS) approach to evaluate cellular impairments infringed by BPA over the cosmopolitan ciliated protist, Paramecium caudatum. Our data indicate a clear time-dependent effect over P. caudatum survival, which seems to be a consequence of disruptions to multiple core cellular functions, such as DNA and cell replication, transcription, translation and signaling pathways. Finally, the use of this ciliate as a biosensor to monitor BPA within environments and the relevance of bioinformatic methods to leverage our current knowledge on the impacts of emerging contaminants to biological systems are discussed.

Planktonic ciliate community driven by environmental variables and cyanobacterial blooms: A 9-year study in two subtropical reservoirs

It is well-established that environmental variability and cyanobacterial blooms have major effects on the assembly and functioning of bacterial communities in both marine and freshwater habitats. It remains unclear, however, how the ciliate community responds to such changes over the long-term, particularly in subtropical lake and reservoir ecosystems. We analysed 9-year planktonic ciliate data series from the surface water of two subtropical reservoirs to elucidate the role of cyanobacterial bloom and environmental variabilities on the ciliate temporal dynamics. We identified five distinct periods of cyanobacterial succession in both reservoirs. Using multiple time-scale analyses, we found that the interannual variability of ciliate communities was more strongly related to cyanobacterial blooms than to other environmental variables or to seasonality. Moreover, the percentage of species turnover across cyanobacterial bloom and non-bloom periods increased significantly with time over the 9-year period. Phylogenetic analyses further indicated that 84 %-86 % of ciliate community turnover was governed by stochastic dispersal limitation or undominated processes, suggesting that the ciliate communities in subtropical reservoirs were mainly controlled by neutral processes. However, short-term blooms increased the selection pressure and drove 30 %-53 % of the ciliate community turnover. We found that the ciliate community composition was influenced by environmental conditions with nutrients, cyanobacterial biomass and microzooplankton having direct and/or indirect significant effects on the ciliate taxonomic or functional community dynamics. Our results provide new insights into the long-term temporal dynamics of planktonic ciliate communities under cyanobacterial bloom disturbance.

The relative roles of multiple drivers on benthic ciliate communities in an intertidal zone

Intertidal biodiversity is being severely disrupted as a result of increased anthropogenic activity. However, our knowledge about how natural gradients, human induced disturbance and biotic interactions affect biodiversity is limited. So, we investigated how three facets of alpha diversity and community composition of benthic ciliates responded to environmental and biological gradients in the intertidal zone of Zhejiang, China. The key determinants and their relative effects on ciliate communities were identified using structural equation modeling, distance-based redundancy analysis and variation partitioning analysis. Our results revealed that sediment grain size was the most important factor affecting alpha diversity and community composition. Human induced eutrophication had significant effects on phylogenetic alpha diversity and community composition. However, the effects of biotic interactions on ciliate communities were relatively small. Moreover, we found community composition was more sensitive to human disturbance than alpha diversity, thus, more suitable for indicating human-induced eutrophication.

Bacterial, Archaeal, and Eukaryote Diversity in Planktonic and Sessile Communities Inside an Abandoned and Flooded Iron Mine (Quebec, Canada)

Abandoned and flooded ore mines are examples of hostile environments (cold, dark, oligotrophic, trace metal) with a potential vast diversity of microbial communities rarely characterized. This study aimed to understand the effects of depth, the source of water (surface or groundwater), and abiotic factors on the communities present in the old Forsyth iron mine in Quebec (Canada). Water and biofilm samples from the mine were sampled by a team of technical divers who followed a depth gradient (0 to 183 m deep) to study the planktonic and sessile communities’ diversity and structure. We used 16S/18S rRNA amplicon to characterize the taxonomic diversity of Bacteria, Archaea, and Eukaryotes. Our results show that depth was not a significant factor explaining the difference in community composition observed, but lifestyle (planktonic/sessile) was. We discovered a vast diversity of microbial taxa, with taxa involved in carbon- and sulfur-cycling. Sessile communities seem to be centered on C1-cycling with fungi and heterotrophs likely adapted to heavy-metal stress. Planktonic communities were dominated by ultra-small archaeal and bacterial taxa, highlighting harsh conditions in the mine waters. Microbial source tracking indicated sources of communities from surface to deeper layers and vice versa, suggesting the dispersion of organisms in the mine, although water connectivity remains unknown.

Changes in Phylogenetic and Functional Diversity of Ciliates along the Course of a Mediterranean Karstic River

Ciliates are a group of phagotrophic protists found in a wide variety of ecosystems. This study builds on recent studies of ciliates in the Krka river and investigates changes in the phylogenetic and functional diversity of ciliates in biofilm to predict the phylogenetic and functional structure of ciliates in other karstic rivers. Biofilm samples were collected from four representative locations: upstream (Krka spring), midstream (Marasovine), and downstream (Roški slap, Skradinski buk) of the Krka river to test for differences in phylogenetic and functional diversity of ciliates in relation to location and positioning on tufa stones (light/dark-exposed side of tufa stone). Our results showed that Krka spring had higher phylogenetic species variability, lower phylogenetic diversity, and lower functional richness than Skradinski buk, suggesting phylogenetic overdispersal at Krka spring. This could be due to environmental filtering, competitive exclusion, or a combination of these factors. As the first study of its kind in the Mediterranean, our results shed light on the phylogenetic and functional diversity of ciliates in karst ecosystems and provide a basis for future ecological and conservation efforts.

FISHing for ciliates: Catalyzed reporter deposition fluorescence in situ hybridization for the detection of planktonic freshwater ciliates

Planktonic ciliate species form multiple trophic guilds and are central components of freshwater food webs. Progress in molecular analytical tools has opened new insight into ciliate assemblages. However, high and variable 18S rDNA copy numbers, typical for ciliates, make reliable quantification by amplicon sequencing extremely difficult. For an exact determination of abundances, the classical morphology-based quantitative protargol staining is still the method of choice. Morphotype analyses, however, are time consuming and need specific taxonomic expertise. Catalyzed reporter deposition fluorescence in situ hybridization (CARD-FISH) may represent a promising tool for the analysis of planktonic ciliates by combining molecular identification with microscopic quantification. We tested the applicability of CARD-FISH using nine cultured ciliate species. Eight species- and three genus-specific oligonucleotide probes were designed based on their 18S rRNA genes. The CARD-FISH protocol was adapted and the specificity of probes was established. We subsequently examined the precision of quantitation by CARD-FISH on single cultures and mock assemblages. Successful tests on lake water samples proved that planktonic ciliates could be identified and quantified in field samples by CARD-FISH. Double hybridizations allowed studying interspecific predator prey interactions between two ciliate species. In summary, we demonstrate that CARD-FISH with species-specific probes can facilitate studies on the population dynamics of closely related, small sized or cryptic species at high sampling frequencies.

The Effects of Paroxetine on Benthic Microbial Food Web and Nitrogen Transformation in River Sediments

Paroxetine is a common pharmaceutical to treat depression and has been found to pose threats to aquatic organisms. However, little is known about the effects of paroxetine on the nutrient cycle in aquatic environments. Therefore, DNA metabarcoding is used in this study to analyze the effects of paroxetine on multi-trophic microorganisms and nitrogen transformation in river sediments. Although paroxetine has no significant effect on the diversity of microbenthos, changes in benthic nitrogen-converting bacteria are consistent with the change in the various forms of nitrogen in the sediment, indicating that paroxetine affects the nitrogen conversion process by affecting nitrogen-converting bacteria. In addition, it is found that paroxetine has the ability to influence nitrogen transformation in an indirect way by affecting the trophic transfer efficiency of higher trophic levels (meiofauna and protozoa, protozoa and protozoa), subsequently affecting the growth of nitrogen-converting bacteria through a top-down mechanism (i.e., predation).The results show that paroxetine affects nitrogen transformation directly by affecting nitrogen-converting bacteria and indirectly through top-down effects, emphasizing that the assessment of paroxetine's ecological risks should consider species within different trophic levels.

Taxonomically and Functionally Distinct Ciliophora Assemblages Inhabiting Baltic Sea Ice

Ciliophora is a phylum of unicellular eukaryotes that are common and have pivotal roles in aquatic environments. Sea ice is a marine habitat, which is composed of a matrix of solid ice and pockets of saline water in which Ciliophora thrive. Here, we used phylogenetic placement to identify Ciliophora 18S ribosomal RNA reads obtained from wintertime water and sea ice, and assigned functions to the reads based on this taxonomic information. Based on our results, sea-ice Ciliophora assemblages are poorer in taxonomic and functional richness than under-ice water and water-column assemblages. Ciliophora diversity stayed stable throughout the ice-covered season both in sea ice and in water, although the assemblages changed during the course of our sampling. Under-ice water and the water column were distinctly predominated by planktonic orders Choreotrichida and Oligotrichida, which led to significantly lower taxonomic and functional evenness in water than in sea ice. In addition to planktonic Ciliophora, assemblages in sea ice included a set of moderately abundant surface-oriented species. Omnivory (feeding on bacteria and unicellular eukaryotes) was the most common feeding type but was not as predominant in sea ice as in water. Sea ice included cytotrophic (feeding on unicellular eukaryotes), bacterivorous and parasitic Ciliophora in addition to the predominant omnivorous Ciliophora. Potentially mixotrophic Ciliophora predominated the water column and heterotrophic Ciliophora sea ice. Our results highlight sea ice as an environment that creates a set of variable habitats, which may be threatened by the diminishing extent of sea ice due to changing climate.

Ecology of planktonic ciliates in a changing world: Concepts, methods, and challenges

Plankton ecologists ultimately focus on forecasting, both applied and environmental outcomes. We review how appreciating planktonic ciliates has become central to these predictions. We explore the 350-year-old canon on planktonic ciliates and examine its steady progression, which has been punctuated by conceptual insights and technological breakthroughs. By reflecting on this process, we offer suggestions as to where future leaps are needed, with an emphasis on predicting outcomes of global warming. We conclude that in terms of climate change research: (i) climatic hotspots (e.g. polar oceans) require attention; (ii) simply adding ciliate measurements to zooplankton/phytoplankton-based sampling programs is inappropriate; (iii) elucidating the rare biosphere's functional ecology requires culture-independent genetic methods; (iv) evaluating genetic adaptation (microevolution) and population composition shifts is required; (v) contrasting marine and freshwaters needs attention; (vi) mixotrophy needs attention; (vii) laboratory and field studies must couple automated measurements and molecular assessment of functional gene expression; (viii) ciliate trophic diversity requires appreciation; and (ix) marrying gene expression and function, coupled with climate change scenarios is needed. In short, continued academic efforts and financial support are essential to achieve the above; these will lead to understanding how ciliates will respond to climate change, providing tools for forecasting.

Structure and Dynamics of Periphyton in a Neotropical Freshwater Lake, with Emphasis on Ciliates and Their Relationships with Bacterial Taxa

Periphyton communities in freshwater systems play an essential role in biogeochemical processes, but knowledge of their structure and dynamics lags far behind other environments. We used eDNA metabarcoding of 16S and 18S rRNA markers to investigate the formation and establishment of a periphytic community, in addition to a morphology-based approach for peritrich ciliate determinations, its most abundant group. We sampled two nearby sites within a large Neotropical lake at four time points, aiming to assess whether periphyton establishment can be replicated on this local scale. Producers and denitrifiers were abundant in the community, illustrating the relevant role of biofilms in freshwater nutrient recycling. Among microeukaryotes, peritrich ciliates dominated the community, with genera Epistylis and Vorticella being the most abundant and showing a clear succession at both sites. Other ciliates were morphologically identified and, in some cases, their occurrence was strongly related to bacterial abundance. The structure of both prokaryotic and eukaryotic components of periphyton was not different, while the turnover dynamics differed between the two sites, in spite of their adjacent locations and similar abiotic properties. This indicates that the establishment of these communities can vary even on a local scale within a lake ecosystem.

Light dependence in the phototrophy-phagotrophy balance of constitutive and non-constitutive mixotrophic protists

Mixotrophic protists display contrasting nutritional strategies and are key groups connecting planktonic food webs. They comprise constitutive mixotrophs (CMs) that have an innate photosynthetic ability and non-constitutive mixotrophs (NCMs) that acquire it from their prey. We modelled phototrophy and phagotrophy of two mixotrophic protists as a function of irradiance and prey abundance. We hypothesised that differences in their physiology (constitutive versus non-constitutive mixotrophy) can result in different responses to light gradients. We fitted the models with primary production and bacterivory data from laboratory and field experiments with the nanoflagellate Chrysochromulina parva (CM) and the ciliate Ophrydium naumanni (NCM) from north Andean Patagonian lakes. We found a non-monotonic response of phototrophy and phagotrophy to irradiance in both mixotrophs, which was successfully represented by our models. Maximum values for phototrophy and phagotrophy were found at intermediate irradiance coinciding with the light at the deep chlorophyll maxima in these lakes. At lower and higher irradiances, we found a decoupling between phototrophy and phagotrophy in the NCM while these functions were more coupled in the CM. Our modelling approach revealed the difference between both mixotrophic functional types on the balance between their nutritional strategies under different light scenarios. Thus, our proposed models can be applied to account how changing environmental conditions affect both primary and secondary production within the planktonic microbial food web.

Genome architecture used to supplement species delineation in two cryptic marine ciliates

The purpose of this study is to determine which taxonomic methods can elucidate clear and quantifiable differences between two cryptic ciliate species, and to test the utility of genome architecture as a new diagnostic character in the discrimination of otherwise indistinguishable taxa. Two cryptic tintinnid ciliates, Schmidingerella arcuata and Schmidingerella meunieri, are compared via traditional taxonomic characters including lorica morphometrics, ribosomal RNA (rRNA) gene barcodes and ecophysiological traits. In addition, single-cell 'omics analyses (single-cell transcriptomics and genomics) are used to elucidate and compare patterns of micronuclear genome architecture between the congeners. The results include a highly similar lorica that is larger in S. meunieri, a 0%-0.5% difference in rRNA gene barcodes, two different and nine indistinguishable growth responses among 11 prey treatments, and distinct patterns of micronuclear genomic architecture for genes detected in both ciliates. Together, these results indicate that while minor differences exist between S. arcuata and S. meunieri in common indices of taxonomic identification (i.e., lorica morphology, DNA barcode sequences and ecophysiology), differences exist in their genomic architecture, which suggests potential genetic incompatibility. Different patterns of micronuclear architecture in genes shared by both isolates also enable the design of species-specific primers, which are used in this study as unique "architectural barcodes" to demonstrate the co-occurrence of both ciliates in samples collected from a NW Atlantic estuary. These results support the utility of genomic architecture as a tool in species delineation, especially in ciliates that are cryptic or otherwise difficult to differentiate using traditional methods of identification.

Paleoreconstructions of ciliate communities reveal long-term ecological changes in temperate lakes

Ciliates are unicellular heterotrophic organisms that play a key role in aquatic planktonic and benthic food webs. Advances in sedimentary DNA (sed-DNA) analysis offer the possibility to integrate these bioindicators in paleoenvironmental reconstructions. In this study, we used the top–bottom paleolimnological approach and metabarcoding techniques applied to sed-DNA to compare the recent and past (i.e. prior to major anthropogenic impacts) ciliate communities of 48 lakes located along an elevation gradient. Our results show an overall decline in the β-diversity in recent time, especially in lowland lakes, which are more strongly exposed to local human pressures. Analyses of the functional groups indicate important restructuration of the food web, including the recent increase in mixotrophs. Moreover, changes in the benthic ciliates were consistent with the widespread increase in deep water anoxia. Our results provided evidence that sed-DNA can uncover information about past ciliate communities on a wide variety of lakes. Overall, our study demonstrates the potential of using ciliates as new paleoindicators, integrating information from the pelagic to the benthic zones, and providing valuable insights into ecosystem functioning through a trait-based functional community approach. As paleoindicator, they thus offer a more holistic view on the long-term changes of aquatic ecosystems.

Bacterial and Protistan Community Variation across the Changjiang Estuary to the Ocean with Multiple Environmental Gradients

Plankton microorganisms play central roles in the marine food web and global biogeochemical cycles, while their distribution and abundance are affected by environmental variables. The determinants of microbial community composition and diversity in estuaries and surrounding waters with multiple environmental gradients at a fine scale remain largely unclear. Here, we investigated bacterial and protistan community assembly in surface waters from 27 stations across the Changjiang Estuary to the ocean, with salinity ranging from 0 to 32.1, using 16S rRNA and 18S rRNA gene amplicon sequencing. Statistical analyses revealed that salinity is the major factor structuring both bacterial and protistan communities. Salinity also acted as a significant environmental determinant influencing alpha-diversity patterns. Alpha diversity indices for bacterial and protistan communities revealed a species minimum in higher-salinity waters (22.1–32.1). Contrary to the protistan community, the highest bacterial diversity was identified in medium-salinity waters (2.8–18.8), contrasting Remane’s Artenminimum concept. The distribution of major planktonic taxa followed the expected pattern, and the salinity boundary for Syndiniales was specifically identified. These findings revealed the significant effects of salinity on the microbial community across an estuary to ocean transect and the distinct response to salinity between bacterial and protistan communities.

A novel membrane complex is required for docking and regulated exocytosis of lysosome-related organelles in Tetrahymena thermophila

In the ciliate Tetrahymena thermophila, lysosome-related organelles called mucocysts accumulate at the cell periphery where they secrete their contents in response to extracellular events, a phenomenon called regulated exocytosis. The molecular bases underlying regulated exocytosis have been extensively described in animals but it is not clear whether similar mechanisms exist in ciliates or their sister lineage, the Apicomplexan parasites, which together belong to the ecologically and medically important superphylum Alveolata. Beginning with a T. thermophila mutant in mucocyst exocytosis, we used a forward genetic approach to uncover MDL1 (Mucocyst Discharge with a LamG domain), a novel gene that is essential for regulated exocytosis of mucocysts. Mdl1p is a 40 kDa membrane glycoprotein that localizes to mucocysts, and specifically to a tip domain that contacts the plasma membrane when the mucocyst is docked. This sub-localization of Mdl1p, which occurs prior to docking, underscores a functional asymmetry in mucocysts that is strikingly similar to that of highly polarized secretory organelles in other Alveolates. A mis-sense mutation in the LamG domain results in mucocysts that dock but only undergo inefficient exocytosis. In contrast, complete knockout of MDL1 largely prevents mucocyst docking itself. Mdl1p is physically associated with 9 other proteins, all of them novel and largely restricted to Alveolates, and sedimentation analysis supports the idea that they form a large complex. Analysis of three other members of this putative complex, called MDD (for Mucocyst Docking and Discharge), shows that they also localize to mucocysts. Negative staining of purified MDD complexes revealed distinct particles with a central channel. Our results uncover a novel macromolecular complex whose subunits are conserved within alveolates but not in other lineages, that is essential for regulated exocytosis in T. thermophila.

Taxonomic and Functional Metrics of Ciliates and Amoeboid Protists in Response to Stream Revitalization

Tufa-depositing streams provide great microhabitat complexity and are therefore inhabited by various periphytic phagotrophic organisms such as ciliates and amoeboid protists. Recent removal of invasive plant species Ailanthus altissima (Mill.) Swinge from the Skradinski buk tufa barrier (Krka National Park, Croatia) resulted in changes in the barrier hydromorphology including the reactivation (revitalization) of dry streams. The objective of this study was to investigate: (1) the taxonomic and functional response of periphytic ciliates and amoeboid protists to stream revitalization by comparing taxonomic (i.e., abundance, species richness and diversity) and functional (i.e., functional diversity) metrics between revitalized (N) and control sites (C) during 1 and 2-months immersion period; (2) which environmental and (3) periphyton-associated factors shape the taxonomic and functional metrics and to what extent; (4) how duration of immersion affects taxonomic and functional metrics at revitalized sites. Our results showed that taxonomic and functional metrics of ciliates and amoeboid protists responded to the prevailing conditions characteristic of revitalized tufa-depositing streams: changing hydrology (occasional high flow or drought), soil drainage, and extensive inorganic matter, i.e., tufa deposition, although their responses were somewhat different. The two assemblages also showed different responses of taxonomic and functional metrics with respect to immersion duration: while the taxonomic and functional diversity of ciliates at N sites increased with longer immersion, indicating niche diversification, those of amoeboid protists hardly changed with time. Our results suggest that a comprehensive analysis of taxonomic and functional metrics of ciliates and amoeboid protists could be a good proxy for assessing revitalization of tufa-depositing streams. However, the temporal component should always be considered when conducting such studies, as the colonization processes of ciliates and amoeboid protists are quite complex, especially in tufa-depositing streams.

Periphytic Ciliate Communities in Lake Ecosystem of Temperate Riverine Floodplain: Variability in Taxonomic and Functional Composition and Diversity with Seasons and Hydrological Changes

Periphytic ciliate communities of riverine floodplains have hardly been studied, although they play an important role in aquatic food webs and contribute to the overall ecosystem functioning. In this study we analyzed the taxonomic and functional composition and diversity of these communities across all seasons and hydrological phases. The study was conducted in a floodplain lake, a part of the large natural Danube floodplain, from February 2015 to September 2016. We found that higher temperature and hydrologically stable conditions during the lake isolation phase, when a high amount of suspended food is available, result in the highest ciliate abundances and dominance of relatively large suspension-feeding ciliates, mainly peritrichs, which could serve as good bioindicators for detecting disturbances in river-floodplain ecosystems. During the flow pulse phase, associated with lower temperatures, and during the phase of extreme floods, when the availability of suspended food was largely reduced, small surface-feeding ciliates prevailed in the periphyton. Further, while the total ciliate abundance was the lowest, the highest taxonomic and functional diversity was found, especially during an intermediate level of hydrological connectivity (flow pulse). Our results confirm the importance of different levels of hydrological connectivity for maintaining biodiversity in riverine floodplains and add to a growing awareness of the need to preserve the natural hydrological regimes of large rivers.

Distribution of Membrane Trafficking System Components Across Ciliate Diversity Highlights Heterogenous Organelle-Associated Machinery

The ciliate phylum is a group of protists noted for their unusual membrane trafficking system and apparent environmental ubiquity; as highly successful microbial predators, they are found in all manner of environments and the ability for specific species to adapt to extremely challenging conditions makes them valued as bioindicators. Ciliates have also been used for many years as cell biological models due to their large cell size and ease of culturing, and for many fundamental cell structures, particularly membrane-bound organelles, ciliates were some of the earliest organisms in which these were observed via microscopy. In this study, we carried out a comparative genomic survey of selected membrane trafficking proteins in a pan-ciliate transcriptome and genome dataset. We observed considerable loss of membrane trafficking system (MTS) proteins that would indicate a loss of machinery that is generally conserved across eukaryotic diversity, even after controlling for potentially incomplete genome representation. In particular, the DSL1 complex was missing in all surveyed ciliates. This protein complex has been shown as involved in peroxisome biogenesis in some model systems, and a paucity of DSL1 components has been indicative of degenerate peroxisome. However, Tetrahymena thermophila (formerly Tetrahymena pyroformis) was one of the original models for visualising peroxisomes. Conversely, the AP3 complex essential for mucocyst maturation in T. thermophila, is poorly conserved despite the presence of secretory lysosome-related organelles across ciliate diversity. We discuss potential resolutions for these apparent paradoxes in the context of the heterogenous distribution of MTS machinery across the diversity of ciliates.

Impacts of UV-C irradiation on marine biofilm community succession

Marine biofilms are diverse microbial communities and important ecological habitats forming on surfaces submerged in the ocean. Biofilm communities resist environmental disturbance, making them a nuisance to some human activities ('biofouling'). Anti-fouling solutions rarely address the underlying stability or compositional responses of these biofilms. Using bulk measurements and molecular analyses, we examined temporal and UV-C antifouling-based shifts in marine biofilms in the coastal Western North Atlantic Ocean during early fall. Over a 24-d period, bacterial communities shifted from early dominance of Gammaproteobacteria to increased proportions of Alphaproteobacteria, Bacteroidia and Acidimicrobiia. In a network analysis based on temporal covariance, Rhodobacteraceae (Alphaproteobacteria) nodes were abundant and densely connected with generally positive correlations. In the eukaryotic community, persistent algal, protistan, and invertebrate groups were observed, although consistent temporal succession was not detected. Biofilm UV-C treatment at 13 and 20 days resulted in losses of chlorophyll a and transparent exopolymer particles, indicating biomass disruption. Bacterial community shifts suggested that UV-C treatment decreased biofilm maturation rate and was associated with proportional shifts among diverse bacterial taxa. UV-C treatment was also associated with increased proportions of protists potentially involved in detritivory and parasitism. Older biofilm communities had increased resistance to UV-C, suggesting that early biofilms are more susceptible to UV-C based antifouling. The results suggest that UV-C irradiation is potentially an effective antifouling method in marine environments in terms of biomass removal and in slowing maturation. However, as they mature, biofilm communities may accumulate microbial members that are tolerant or resilient under UV-treatment. Importance Marine biofilms regulate processes from organic matter and pollutant turnover to eukaryotic settlement and growth. Biofilm growth and eukaryotic settlement interfering with human activities via growth on ship hulls, aquaculture operations, or other marine infrastructure are called 'biofouling'. There is a need to develop sustainable anti-fouling techniques by minimizing impacts to surrounding biota. We use the biofouling-antifouling framework to test hypotheses about marine biofilm succession and stability in response to disturbance, using a novel UV-C LED device. We demonstrate strong bacterial biofilm successional patterns and detect taxa potentially contributing to stability under UV-C stress. Despite UV-C-associated biomass losses and varying UV susceptibility of microbial taxa, we detected high compositional resistance among biofilm bacterial communities, suggesting decoupling of disruption in biomass and community composition following UV-C irradiation. We also report microbial covariance patterns over 24 days of biofilm growth, pointing to areas for study of microbial interactions and targeted antifouling.

In situ Prokaryotic and Eukaryotic Communities on Microplastic Particles in a Small Headwater Stream in Germany

The ubiquitous use of plastic products in our daily life is often accompanied by improper disposal. The first interactions of plastics with organisms in the environment occur by overgrowth or biofilm formation on the particle surface, which can facilitate the ingestion by animals. In order to elucidate the colonization of plastic particles by prokaryotic and eukaryotic microorganisms in situ, we investigated microbial communities in biofilms on four different polymer types and on mineral particles in a small headwater stream 500 m downstream of a wastewater treatment plant in Germany. Microplastic and mineral particles were exposed to the free-flowing water for 4 weeks in spring and in summer. The microbial composition of the developing biofilm was analyzed by 16S and 18S amplicon sequencing. Despite the expected seasonal differences in the microbial composition of pro- and eukaryotic communities, we repeatedly observed polymer type-specific differentiation in both seasons. The order of polymer type-specific prokaryotic and eukaryotic community distances calculated by Robust Aitchison principal component analysis (PCA) was the same in spring and summer samples. However, the magnitude of the distance differed considerably between polymer types. Prokaryotic communities on polyethylene particles exhibited the most considerable difference to other particles in summer, while eukaryotic communities on polypropylene particles showed the most considerable difference to other spring samples. The most contributing bacterial taxa to the polyethylene-specific differentiation belong to the Planctomycetales, Saccharimonadales, Bryobacterales, uncultured Acidiomicrobia, and Gemmatimonadales. The most remarkable differences in eukaryotic microorganism abundances could be observed in several distinct groups of Ciliophora (ciliates) and Chlorophytes (green algae). Prediction of community functions from taxonomic abundances revealed differences between spring and summer, and – to a lesser extent – also between polymer types and mineral surfaces. Our results show that different microplastic particles were colonized by different biofilm communities. These findings may be used for advanced experimental designs to investigate the role of microorganisms on the fate of microplastic particles in freshwater ecosystems.

Freshwater protists: unveiling the unexplored in a large floodplain system

Protists play a fundamental role in all ecosystems, but we are still far from estimating the total diversity of many lineages, in particular in highly diverse environments, such as freshwater. Here, we survey the protist diversity of the Paraná River using metabarcoding, and we applied an approach that includes sequence similarity and phylogeny to evaluate the degree of genetic novelty of the protists' communities against the sequences described in the reference database PR² . We observed that ~28% of the amplicon sequence variants were classified as novel according to their similarity with sequences from the reference database; most of them were related to heterotrophic groups traditionally overlooked in freshwater systems. This lack of knowledge extended to those groups within the green algae (Archaeplastida) that are well documented such as Mamiellophyceae, and also to the less studied Pedinophyceae, for which we found sequences representing novel deep-branching clusters. Among the groups with potential novel protists, Bicosoecida (Stramenopiles) were the best represented, followed by Codosiga (Opisthokonta), and the Perkinsea (Alveolata). This illustrates the lack of knowledge on freshwater planktonic protists and also the need for isolation and/or cultivation of new organisms to better understand their role in ecosystem functioning.

Functionally similar species of ciliates have similar dynamics: A biennial survey study in a large eutrophic lake

The spatial and temporal planktonic ciliate community structure of a large shallow eutrophic lake was described in detail based on a monthly monitoring campaign over 2 years using the quantitative protargol stain approach. We found that there was a large variety and low constancy of ciliate plankton and a clear advantage of several small species. Balanion planctonicum, Rimostrombidium brachykinetum, and Urotricha farcta contributed 19.7%, 13.4%, and 10.7% to the total abundance, respectively. The ciliate community was significantly varied in different lake regions of different eutrophication levels, and the distribution of some of the main species, especially prostomatids and scuticociliatids, might be closely related to the nutrient level of the lake regions. The seasonal dynamics of ciliate taxa with similar functional feeding habits across regions at different trophic levels are more convergent than those of species with very different functions, and the top-down effect (cladocerans, rotifers), nutrition, and water temperature were the key factors shaping ciliate community structure. The results of this study accentuate the important effects of species functional diversity on community differences and may improve our knowledge of ciliate diversity and functional ecology in shallow eutrophic lakes.

Wild ciliates differ in susceptibility to Legionella pneumophila JR32

We investigated how Legionella pneumophila (Lp) JR32 interacts with Anteglaucoma CS11A and Colpoda E6, two ciliates that we isolated from sewage and sink trap sludge, respectively, using a handmade maze device containing a 96-well crafting plate. Our 18S rDNA-based phylogenetic analysis showed that Anteglaucoma CS11A and Colpoda E6 formed distinct clades. Scanning electron microscopy showed that Anteglaucoma CS11A had a bigger-sized body than Colpoda E6 and, unlike Tetrahymena IB (the reference strain), neither ciliate produced pellets, which are extracellular vacuoles. Fluorescence microscopic observations revealed that although the intake amounts differed, all three ciliates rapidly ingested LpJR32 regardless of the presence or absence of the icm/dot virulence genes, indicating that they all interacted with LpJR32. In co-cultures with Anteglaucoma CS11A, the LpJR32 levels were maintained but fell dramatically when the co-culture contained the LpJR32 icm/dot deletion mutant instead. Anteglaucoma CS11A died within 2 days of co-culture with LpJR32, but survived co-culture with the deletion mutant. In co-cultures with Colpoda E6, LpJR32 levels were maintained but temporarily decreased independently of the virulence gene. Concurrently, the Colpoda E6 ciliates survived by forming cysts, which may enable them to resist harsh environments, and by diminishing the sensitivity of trophozoites to Lp. In the Tetrahymena IB co-cultures with LpJR32 or Δicm/dot, the Lp levels were maintained, albeit with temporal decreases, and the Tetrahymena IB levels were also maintained. We conclude that unlike Tetrahymena IB with pellet production, Anteglaucoma CS11A can be killed by LpJR32 infection, and Colpoda E6 can resist LpJR32 infection through cyst formation and the low sensitivity of trophozoites to Lp. Thus, the two ciliates that we isolated had different susceptibilities to LpJR32 infection.

Biogeographic Role of the Kuroshio Current Intrusion in the Microzooplankton Community in the Boundary Zone of the Northern South China Sea

Kuroshio Current intrusion (KCI) has significant impacts on the oceanographic conditions and ecological processes of the Pacific-Asian marginal seas. Little is known to which extent and how, specifically, the microzooplankton community can be influenced through the intrusion. Here, we focused on ciliates that often dominated the microzooplankton community and investigated their communities using high-throughput sequencing of 18S rRNA gene transcripts in the northern South China Sea (NSCS), where the Kuroshio Current (KC) intrudes frequently. We first applied an isopycnal mixing model to assess the fractional contribution of the KC to the NSCS. The ciliate community presented a provincial distribution pattern corresponding to more and less Kuroshio-influenced stations. Structural equation modeling revealed a significant impact of the KCI on the community, while environmental variables had a marginal impact. KCI-sensitive OTUs were taxonomically diverse but mainly belonged to classes Spirotrichea and Phyllopharyngea, suggesting the existence of core ciliates responding to the KCI. KCI-sensitive OTUs were grouped into two network modules that showed contrasting abundance behavior with the KC fraction gradient, reflecting differential niches (i.e., winner and loser) in the ciliate community during the Kuroshio intrusion scenarios. Our study showed that the Kuroshio intrusion, rather than environmental control, was particularly detrimental to the oligotrophic microzooplankton community.

Cascading effects in freshwater microbial food webs by predatory Cercozoa, Katablepharidacea and ciliates feeding on aplastidic bacterivorous cryptophytes

Heterotrophic nanoflagellates (HNF) are considered as major planktonic bacterivores, however, larger HNF taxa can also be important predators of eukaryotes. To examine this trophic cascading, natural protistan communities from a freshwater reservoir were released from grazing pressure by zooplankton via filtration through 10- and 5-µm filters, yielding microbial food webs of different complexity. Protistan growth was stimulated by amendments of five Limnohabitans strains, thus yielding five prey-specific treatments distinctly modulating protistan communities in 10- versus 5-µm fractions. HNF dynamics was tracked by applying five eukaryotic fluorescence in situ hybridization probes covering 55-90% of total flagellates. During the first experimental part, mainly small bacterivorous Cryptophyceae prevailed, with significantly higher abundances in 5-µm treatments. Larger predatory flagellates affiliating with Katablepharidacea and one Cercozoan lineage (increasing to up to 28% of total HNF) proliferated towards the experimental endpoint, having obviously small phagocytized HNF in their food vacuoles. These predatory flagellates reached higher abundances in 10-µm treatments, where small ciliate predators and flagellate hunters also (Urotricha spp., Balanion planctonicum) dominated the ciliate assemblage. Overall, our study reports pronounced cascading effects from bacteria to bacterivorous HNF, predatory HNF and ciliates in highly treatment-specific fashions, defined by both prey-food characteristics and feeding modes of predominating protists.

Microbial Grazers May Aid in Controlling Infections Caused by the Aquatic Zoosporic Fungus Batrachochytrium dendrobatidis

Free-living eukaryotic microbes may reduce animal diseases. We evaluated the dynamics by which micrograzers (primarily protozoa) apply top-down control on the chytrid Batrachochytrium dendrobatidis (Bd) a devastating, panzootic pathogen of amphibians. Although micrograzers consumed zoospores (∼3 μm), the dispersal stage of chytrids, not all species grew monoxenically on zoospores. However, the ubiquitous ciliate Tetrahymena pyriformis, which likely co-occurs with Bd, grew at near its maximum rate (r = 1.7 d-1). A functional response (ingestion vs. prey abundance) for T. pyriformis, measured using spore-surrogates (microspheres) revealed maximum ingestion (I max ) of 1.63 × 103 zoospores d-1, with a half saturation constant (k) of 5.75 × 103 zoospores ml-1. Using these growth and grazing data we developed and assessed a population model that incorporated chytrid-host and micrograzer dynamics. Simulations using our data and realistic parameters obtained from the literature suggested that micrograzers could control Bd and potentially prevent chytridiomycosis (defined as 104 sporangia host-1). However, simulated inferior micrograzers (0.7 × I max and 1.5 × k) did not prevent chytridiomycosis, although they ultimately reduced pathogen abundance to below levels resulting in disease. These findings indicate how micrograzer responses can be applied when modeling disease dynamics for Bd and other zoosporic fungi.

The mechanism of species coexistence and diversity maintenance along aspects in the northeast of the Qinghai–Tibetan plateau

To examine the role of plant functional traits and phylogenetic relationships in predicting plant community species coexistence and diversity maintenance, we measured 73 species and six functional traits along a slope aspect gradient on the Qinghai–Tibetan plateau. We calculated the net relatedness index (NRI), the nearest taxon index (NTI), phylogenetic diversity (PD), functional diversity, and analysed phylogenetic signals. The results show that the species richness, plant composition, and PD changed substantially from northern to southern aspects, and the phylogenetic structure of the community changed from clustering to over-dispersion. Weak phylogenetic signals in plant height, leaf nitrogen content, and leaf potassium content were recorded. We conclude that the influencing factor(s) of species coexistence on northern and north-western aspects is limiting similarity (interspecific competition), whereas on southern and south-western aspects, habitat filtering (environmental effect) is predominant. On western aspects, the influencing factors are driven by three processes: limiting similarity, habitat filtration, and random processes. Results suggest that niche processes (including habitat filtration and limiting similarity) are the main mechanisms for species coexistence and diversity maintenance on aspects of the alpine meadow in the northeast of the Qinghai–Tibetan plateau, while random processes appear at the transitional zone (the western aspect in our study) between aspects.

Aquatic food webs in deep temperate lakes: Key species establish through their autecological versatility

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 (12 months, biweekly sampling) of protistan plankton communities in surface layers (epilimnion) and bottom waters (hypolimnion) of two temperate deep lakes, Lake Mondsee (Austria) and Lake Zurich (Switzerland). Lake Zurich plankton communities were less tightly connected, more fragmented and had a higher susceptibility to a species extinction scenario compared to Lake Mondsee communities. We interpret these results as a lower robustness of Lake Zurich protistan plankton to environmental stressors, especially stressors resulting from climate change. In all networks, the phylum Ciliophora contributed the highest number of nodes, among them several in key positions of the networks. Associations in ciliate-specific subnetworks resembled autecological species-specific traits that indicate adaptions to specific environmental conditions. We demonstrate the strength of co-occurrence network analyses to deepen our understanding of plankton community dynamics in lakes and indicate biotic relationships, which resulted in new hypotheses that may guide future research in climate-stressed ecosystems.

Functional Ecology of Two Contrasting Freshwater Ciliated Protists in Relation to Temperature

We conducted microcosm experiments with two contrasting freshwater ciliates on functional traits (FTs) related to their growth rate (numerical response, NR) and ingestion rate (functional response, FR) over a range of ecologically relevant temperatures. Histiobalantium bodamicum and Vorticella natans are common planktonic ciliates but their abundance, swimming behavior, and temperature tolerance are different. In contrast to most sessile peritrich species, the motile V. natans is not strictly bacterivorous but also voraciously feeds upon small algae. We observed three main alterations in the shape of NR of both species with temperature, that is, change in the maximum growth rate, in the initial slope and in the threshold food level needed to sustain the population. Similarly, maximum ingestion rate, gross growth efficiency (GGE), and cell size varied with temperature and species. These findings caution against generalizing ciliate performance in relation to the ongoing global warming. Our results suggest that V. natans is the superior competitor to H. bodamicum in terms of temperature tolerance and bottom-up control. However, the abundance of V. natans is usually low compared to H. bodamicum and other common freshwater ciliates, suggesting that V. natans is more strongly top-down controlled via predation than H. bodamicum. The taxonomic position of V. natans has been debated. Therefore, to confirm species and genus affiliation of our study objects, we sequenced their small subunit ribosomal RNA (SSU rDNA) gene.

Anthropogenic impact on the historical phytoplankton community of Lake Constance reconstructed by multimarker analysis of sediment-core environmental DNA

During the 20th century, many lakes in the Northern Hemisphere were affected by increasing human population and urbanization along their shorelines and catchment, resulting in aquatic eutrophication. Ecosystem monitoring commenced only after the changes became apparent, precluding any examination of timing and dynamics of initial community change in the past and comparison of pre- and postimpact communities. Peri-Alpine Lake Constance (Germany) underwent a mid-century period of eutrophication followed by re-oligotrophication since the 1980s and is now experiencing warm temperatures. We extended the period for which monitoring data of indicator organisms exist by analysing historical environmental DNA (eDNA) from a sediment core dating back some 110 years. Using three metabarcoding markers-for microbial eukaryotes, diatoms and cyanobacteria-we revealed two major breakpoints of community change, in the 1930s and the mid-1990s. In our core, the latest response was exhibited by diatoms, which are classically used as palaeo-bioindicators for the trophic state of lakes. Following re-oligotrophication, overall diversity values reverted to similar ones of the early 20th century, but multivariate analysis indicated that the present community is substantially dissimilar. Community changes of all three groups were strongly correlated to phosphorus concentration changes, whereas significant relationships to temperature were only observed when we did not account for temporal autocorrelation. Our results indicate that each microbial group analysed exhibited a unique response, highlighting the particular strength of multimarker analysis of eDNA, which is not limited to organisms with visible remains and can therefore discover yet unknown responses and abiotic-biotic relationships.

Spatiotemporal Patterns in Diversity and Assembly Process of Marine Protist Communities of the Changjiang (Yangtze River) Plume and Its Adjacent Waters

Marine protists are highly heterogeneous and play key roles in the structure and functioning of marine ecosystems. However, little is known on the underlying biogeographic processes and seasonal diversity patterns that shape their community assembly in a regional scale in marginal sea. In this study, we conducted high-throughput sequencing of 18S rRNA gene to survey the protist community compositions (PCCs) of the Changjiang (Yangtze River) plume, an intensely human-affected coastal area, to the adjacent continental shelf waters over three seasons. Furthermore, the different impacts of environmental and spatial factors on marine PCCs were examined. The results revealed significant dissimilarities of PCC’s diversity among seasons and habitats, with more obvious seasonal variations in the Changjiang plume. Procrustes analysis showed better consistency of the community-environment relationship in shelf area, further supported by stronger correlation coefficients computed in the Mantel tests. This might be explained by seasonal dynamics of Changjiang Diluted Waters (i.e., the mixing of the Changjiang runoff with inshore water of the East China Sea) that changed the environmental conditions of coastal area dramatically, resulting in lower importance of spatial factors (dispersal limitation) on PCCs compared with environmental filters, including physicochemical properties (e.g., water temperature, salinity, dissolved oxygen, and nutrients), as well as biotic factors (e.g., Chl a and food abundance). This was further explained by higher immigration rate and fitness to neutral model, which suggested a predominant role of neutral process in shaping the PCCs in coastal area. Different richness, diversity, and taxonomic compositions but comparable biogeographic patterns were observed among abundant and rare sub-communities. In general, the abundant sub-communities exhibited higher dispersal ability which tend to respond to environmental selection during dispersal, whereas the rare sub-communities appeared to be present only in few samples due to dispersal limitation. Co-occurrence network further indicated the importance of biotic interactions in community assembly and potential roles of rare taxa in maintaining the community structure. Overall, this study suggests the dynamic in the biogeographic patterns of PCCs of the Changjiang plume to the adjacent waters in the ECS responding with the changing environmental conditions and geographical factors.

Ciliates as model organisms for the ecotoxicological risk assessment of heavy metals: A meta-analysis

Ciliates are key components of aquatic ecosystems, significantly contributing to the decomposition of organic matter and energy transfer to higher trophic levels. They are considered good biological indicators of chemical pollution and relatively sensitive to heavy metal contamination. In this study, we performed a meta-analysis of the available toxicity data of heavy metals and ciliates to assess: (1) the sensitivity of freshwater ciliates to different heavy metals, (2) the relative sensitivity of ciliates in comparison to the standard test species used in ecotoxicological risk assessment, and (3) the difference in sensitivity across ciliate taxa. Our study shows that the tolerance of ciliates to heavy metals varies notably, which is partly influenced by differences in methodological conditions across studies. Ciliates are, in general, sensitive to Mercury > Cadmium > Copper > Zinc > Lead > Chromium. Also, this study shows that most ciliates are more tolerant to heavy metal pollution than the standard test species used in ecotoxicological risk assessments, i.e., Raphidocelis subcapitata, Daphnia magna, and Onchornyncus mykiss. Threshold concentrations derived from toxicity data for these species is expected to confer sufficient protection for the vast majority of ciliate species. Our data analysis also shows that the most commonly tested ciliate species, Paramecium caudatum and Tetrahymena thermophila, are not necessarily the most sensitive ones to heavy metal pollution. Finally, this study stresses the importance of developing standard toxicity test protocols for ciliates, which could lead to a better comprehension of the toxicological impact of heavy metals and other contaminants to ciliate species.

Water mass-driven spatial effects and environmental heterogeneity shape microeukaryote biogeography in a subtropical, hydrographically complex ocean system - A case study of ciliates

The relative importance of geographic distance and depth in shaping microeukaryote community composition on a regional scale remains unclear, especially how that composition is related to the movement of water masses. Here, we collected 156 water samples across the Taiwan Strait, which is characterized by complex topography and dynamic circulation, to investigate the composition of the ciliate community with high-throughput sequencing of the 18S rRNA gene transcript. Ciliate alpha diversity exhibited strong correlations with water chemistry, food abundance, and geographic distance; approximately 50% of the variance of the diversity could be explained by dissolved oxygen concentrations, chlorophyll a concentrations, bacterial abundance, and latitude. The sampling sites could be divided into three provinces based on the compositions of the ciliate communities, which exhibited a distinctly nonuniform spatial distribution pattern on a regional scale (587 km). Geographic distance, environmental conditions, and depth were identified as principal determinants of the ciliate community within the Strait. Geographic distance was the most influential factor. The effect of geographic distance seems to mainly reflect the movement of water masses that strongly constrain dispersal and contribute to environmental heterogeneity that accounts for 86.0% and 5.5%, respectively, of community variance across the Strait. Overall, this study revealed that ciliate biogeography as a function of depth and environmental gradients is linked on a regional scale to the water masses that the ciliates inhabit. This result expands our knowledge of the drivers of microeukaryote community composition across regions within which there are water mass movements and strong spatial and environmental gradients.

Diversification of CORVET tethers facilitates transport complexity in Tetrahymena thermophila

In endolysosomal networks, two hetero-hexameric tethers called HOPS and CORVET are found widely throughout eukaryotes. The unicellular ciliate Tetrahymena thermophila possesses elaborate endolysosomal structures, but curiously both it and related protozoa lack the HOPS tether and several other trafficking proteins, while retaining the related CORVET complex. Here, we show that Tetrahymena encodes multiple paralogs of most CORVET subunits, which assemble into six distinct complexes. Each complex has a unique subunit composition and, significantly, shows unique localization, indicating participation in distinct pathways. One pair of complexes differ by a single subunit (Vps8), but have late endosomal versus recycling endosome locations. While Vps8 subunits are thus prime determinants for targeting and functional specificity, determinants exist on all subunits except Vps11. This unprecedented expansion and diversification of CORVET provides a potent example of tether flexibility, and illustrates how 'backfilling' following secondary losses of trafficking genes can provide a mechanism for evolution of new pathways.This article has an associated First Person interview with the first author of the paper.

Using Cilioplankton as an Indicator of the Ecological Condition of Aquatic Ecosystems

We assess the quality of surface water in water bodies located in the Middle Volga region (Russian Federation). The water quality is assessed using 19 chemical compounds and cilioplankton indicators, such as the total number of species, the abundance of each species, and, based on both of them, the saprobity index and the Shannon–Weaver diversity index (H). We classify the water quality from polluted to extremely dirty by using abiotic indicators, and from conditionally clean to dirty by means of biotic indicators. Using the logistic regression method, we are able to predict the water quality (clean or dirty) in correspondence with the species diversity index (H) and to clarify how the quality of the water is related to its physicochemical properties. The seven most significant chemical predictors of both natural origin (mineralization, hydro carbonates, and chlorides) and natural-anthropogenic origin (organic substances (according to BOD5), nitrates, total petroleum hydrocarbons, iron), identified during the stepwise selection procedure, have a substantial influence on the outcome of the model. Qualitative and quantitative indicators of development of ciliates, as well as indices calculated on their basis, allow assessing with a very high level of accuracy the water quality and the condition of aquatic ecosystems in general. The Shannon index calculated for the number of ciliates can be successfully used for ranking water bodies as “clean/dirty”.