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

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.

Ciliate Grazing on the Bloom-Forming Microalga Gonyostomum semen

The freshwater raphidophyte Gonyostomum semen forms extensive summer blooms in northern European humic lakes. The development of these blooms might be facilitated by a lack of natural top-down control, as few zooplankton species are able to prey on these large algal cells (up to 100 μm) that expel trichocysts upon physical stress. In this study, we describe a small ciliate species (< 17 μm) that preys on G. semen by damaging the cell membrane until cytoplasm and organelles spill out. Sequencing of clonal cultures of the ciliate tentatively identified it as the prostomatid species Urotricha pseudofurcata. Grazing experiments illustrated that feeding by U. cf. pseudofurcata can significantly reduce cell concentrations of the microalga. However, differences in cell size and growth rate between two investigated ciliate strains resulted in noticeably different grazing pressure. Environmental sequencing data from five different lakes supported potential interactions between the two species. Urotricha cf. pseudofurcata might, thus, play an important role in aquatic ecosystems that are regularly dominated by G. semen, reducing the abundance of this bloom-forming microalga and enabling transfer of organic carbon to higher trophic levels.

Global freshwater distribution of Telonemia protists

Telonemia are one of the oldest identified marine protists that for most part of their history have been recognized as a distinct incertae sedis lineage. Today, their evolutionary proximity to the SAR supergroup (Stramenopiles, Alveolates, and Rhizaria) is firmly established. However, their ecological distribution and importance as a natural predatory flagellate, especially in freshwater food webs, still remain unclear. To unravel the distribution and diversity of the phylum Telonemia in freshwater habitats, we examined over a thousand freshwater metagenomes from all over the world. In addition, to directly quantify absolute abundances, we analyzed 407 samples from 97 lakes and reservoirs using Catalyzed Reporter Deposition-Fluorescence in situ Hybridization (CARD-FISH). We recovered Telonemia 18S rRNA gene sequences from hundreds of metagenomic samples from a wide variety of habitats, indicating a global distribution of this phylum. However, even after this extensive sampling, our phylogenetic analysis did not reveal any new major clades, suggesting current molecular surveys are near to capturing the full diversity within this group. We observed excellent concordance between CARD-FISH analyses and estimates of abundances from metagenomes. Both approaches suggest that Telonemia are largely absent from shallow lakes and prefer to inhabit the colder hypolimnion of lakes and reservoirs in the Northern Hemisphere, where they frequently bloom, reaching 10%-20% of the total heterotrophic flagellate population, making them important predatory flagellates in the freshwater food web.

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.

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.

Widespread Occurrence of Two Planktonic Ciliate Species (Urotricha, Prostomatida) Originating from High Mountain Lakes

Ciliates of the genus Urotricha are widely distributed and occur in almost any freshwater body. Thus far, almost all species have been described from morphology only. Here, we applied an integrative approach on the morphology, molecular phylogeny and biogeography of two species isolated from high mountain lakes in the Central Alps, Austria. As these remote lakes are known to have water temperatures <15 °C, our hypothesis was that these urotrichs might prefer ‘cold’ environments. We studied the morphological details from living and silver-stained individuals, and their molecular sequences (ribosomal operon, ITS), and screened available datasets for their biogeography. The two Urotricha species resembled morphological features of several congeners. An accurate species assignment was difficult due to several overlapping characteristics. However, we tentatively attributed the investigated species to Urotricha nais and Urotricha globosa. The biogeographic analyses revealed their occurrence in Europe, Africa and Asia, and no correlations to (cold) temperatures were found. Our findings suggest that these two urotrichs, originating from two cold and remote habitats, are probably cryptic species well adapted to their harsh environment.

Mixing regime shapes the community assembly process, microbial interaction and proliferation of cyanobacterial species Planktothrix in a stratified lake

Lake mixing influences aquatic chemical properties and microbial community composition, and thus, we hypothesized that it would alter microbial community assembly and interaction. To clarify this issue, we explored the community assembly processes and cooccurrence networks in four seasons at two depths (epilimnion and hypolimnion) in a mesotrophic and stratified lake (Chenghai Lake), which formed stratification in the summer and turnover in the winter. During the stratification period, the epilimnion and hypolimnion went through contrary assembly processes but converged to similar assembly patterns in the mixing period. In a highly homogeneous selection environment, species with low niche breadth were filtered, resulting in decreased species richness. Water mixing in the winter homogenized the environment, resulting in a simpler microbial cooccurrence network. Interestingly, we observed a high abundance of the cyanobacterial genus Planktothrix in the winter, probably due to nutrient redistribution and Planktothrix adaptivity to the winter environment in which mixing played important roles. Our study provides deeper fundamental insights into how environmental factors influence microbial community structure through community assembly processes.

Molecular Data Reveal a Cryptic Diversity in the Genus Urotricha (Alveolata, Ciliophora, Prostomatida), a Key Player in Freshwater Lakes, With Remarks on Morphology, Food Preferences, and Distribution

Species of the ciliate genus Urotricha are key players in freshwater plankton communities. In the pelagial of lakes, about 20 urotrich species occur throughout an annual cycle, some of which play a pivotal role in aquatic food webs. For example, during the phytoplankton spring bloom, they consume a remarkable proportion of the algal production. In ecological studies, urotrich ciliates are usually merely identified to genus rank and grouped into size classes. This is unsatisfying considering the distinct autecological properties of individual species and their specific spatial and temporal distribution patterns. As a basis for future research, we characterized in detail four common urotrich morphotypes, i.e., specimens identified as U. furcata and tentatively as U. agilis, U. pseudofurcata, and U. castalia, using state-of-the-art methods. We used an integrative polyphasic approach, in which morphological studies (in vivo observation, silver staining methods, scanning electron microscopy) were linked with a molecular approach exploiting four different gene fragments as taxonomic DNA barcodes with different resolution potential (SSU rDNA, ITS-1, ITS-2, hypervariable V4 and V9 regions of the SSU rDNA). We shed light on the diversity of urotrich ciliates as well as on their global distribution patterns, and annual cycles. Additionally, we coupled individual species occurrences and environmental parameters, and subsequently modeled the distribution and occurrence, using logistic regressions. Furthermore, for one strain putatively identified as U. castalia, we ascertained the optimal cultivation media and food preferences. Thereby, our comprehensive view on these important freshwater ciliates that frequently occur in environmental high throughput sequencing datasets worldwide will allow future studies to better exploit protistan plankton data from lakes.

Nitrogen cycling processes and the role of multi-trophic microbiota in dam-induced river-reservoir systems

The nitrogen (N) cycle is one of the most important nutrient cycles in river systems, and it plays an important role in maintaining biogeochemical balance and global climate stability. One of the main ways that humans have altered riverine ecosystems is through the construction of hydropower dams, which have major effects on biogeochemical cycles. Most previous studies examining the effects of damming on N cycling have focused on the whole budget or flux along rivers, and the role of river as N sources or sinks at the global or catchment scale. However, so far there is still lack of comprehensive and systematic summarize on N cycling and the controlling mechanisms in reservoirs affected by dam impoundment. In this review, we firstly summarize N cycling processes along the longitudinal riverine-transition-lacustrine gradient and the vertically stratified epilimnion-thermocline-hypolimnion gradient. Specifically, we highlight the direct and indirect roles of multi-trophic microbiota and their interactions in N cycling and discuss the main factors controlling these biotic processes. In addition, future research directions and challenges in incorporating multi-trophic levels in bioassessment, environmental flow design, as well as reservoir regulation and restoration are summarized. This review will aid future studies of N fluxes along dammed rivers and provide an essential reference for reservoir management to meet ecological needs.

Phenotypic plasticity through disposable genetic adaptation in ciliates

Ciliates have an extraordinary genetic system in which each cell harbors two distinct kinds of nucleus, a transcriptionally active somatic nucleus and a quiescent germline nucleus. The latter undergoes classical, heritable genetic adaptation, while adaptation of the somatic nucleus is only short-term and thus disposable. The ecological and evolutionary relevance of this nuclear dimorphism have never been well formalized, which is surprising given the long history of using ciliates such as Tetrahymena and Paramecium as model organisms. We present a novel, alternative explanation for ciliate nuclear dimorphism which, we argue, should be considered an instrument of phenotypic plasticity by somatic selection on the level of the ciliate clone, as if it were a diffuse multicellular organism. This viewpoint helps to put some enigmatic aspects of ciliate biology into perspective and presents the diversity of ciliates as a large natural experiment that we can exploit to study phenotypic plasticity and organismality.

Lake Ecosystem Robustness and Resilience Inferred from a Climate-Stressed Protistan Plankton Network

Network analyses of biological communities allow for identifying potential consequences of climate change on the resilience of ecosystems and their robustness to resist stressors. Using DNA metabarcoding datasets from a three-year-sampling (73 samples), we constructed the protistan plankton co-occurrence network of Lake Zurich, a model lake ecosystem subjected to climate change. Despite several documentations of dramatic lake warming in Lake Zurich, our study provides an unprecedented perspective by linking changes in biotic association patterns to climate stress. Water temperature belonged to the strongest environmental parameters splitting the data into two distinct seasonal networks (October–April; May–September). The expected ecological niche of phytoplankton, weakened through nutrient depletion because of permanent thermal stratification and through parasitic fungi, was occupied by the cyanobacterium Planktothrix rubescens and mixotrophic nanoflagellates. Instead of phytoplankton, bacteria and nanoflagellates were the main prey organisms associated with key predators (ciliates), which contrasts traditional views of biological associations in lake plankton. In a species extinction scenario, the warm season network emerged as more vulnerable than the cold season network, indicating a time-lagged effect of warmer winter temperatures on the communities. We conclude that climate stressors compromise lake ecosystem robustness and resilience through species replacement, richness differences, and succession as indicated by key network properties.

CARD-FISH in the Sequencing Era: Opening a New Universe of Protistan Ecology

Phagotrophic protists are key players in aquatic food webs. Although sequencing-based studies have revealed their enormous diversity, ecological information on in situ abundance, feeding modes, grazing preferences, and growth rates of specific lineages can be reliably obtained only using microscopy-based molecular methods, such as Catalyzed Reporter Deposition-Fluorescence in situ Hybridization (CARD-FISH). CARD-FISH is commonly applied to study prokaryotes, but less so to microbial eukaryotes. Application of this technique revealed that Paraphysomonas or Spumella-like chrysophytes, considered to be among the most prominent members of protistan communities in pelagic environments, are omnipresent but actually less abundant than expected, in contrast to little known groups such as heterotrophic cryptophyte lineages (e.g., CRY1), cercozoans, katablepharids, or the MAST lineages. Combination of CARD-FISH with tracer techniques and application of double CARD-FISH allow visualization of food vacuole contents of specific flagellate groups, thus considerably challenging our current, simplistic view that they are predominantly bacterivores. Experimental manipulations with natural communities revealed that larger flagellates are actually omnivores ingesting both prokaryotes and other protists. These new findings justify our proposition of an updated model of microbial food webs in pelagic environments, reflecting more authentically the complex trophic interactions and specific roles of flagellated protists, with inclusion of at least two additional trophic levels in the nanoplankton size fraction. Moreover, we provide a detailed CARD-FISH protocol for protists, exemplified on mixo- and heterotrophic nanoplanktonic flagellates, together with tips on probe design, a troubleshooting guide addressing most frequent obstacles, and an exhaustive list of published probes targeting protists.