The Filter-Feeding Ciliates Colpidium striatum and Tetrahymena pyriformis Display Selective Feeding Behaviours in the Presence of Mixed, Equally-Sized, Bacterial Prey

In situ cell division and mortality rates of SAR11, SAR86, Bacteroidetes, and Aurantivirga during phytoplankton blooms reveal differences in population controls

Net growth of microbial populations, that is, changes in abundances over time, can be studied using 16S rRNA fluorescence in situ hybridization (FISH). However, this approach does not differentiate between mortality and cell division rates. We used FISH-based image cytometry in combination with dilution culture experiments to study net growth, cell division, and mortality rates of four bacterial taxa over two distinct phytoplankton blooms: the oligotrophs SAR11 and SAR86, and the copiotrophic phylum Bacteroidetes, and its genus Aurantivirga. Cell volumes, ribosome content, and frequency of dividing cells (FDC) co-varied over time. Among the three, FDC was the most suitable predictor to calculate cell division rates for the selected taxa. The FDC-derived cell division rates for SAR86 of up to 0.8/day and Aurantivirga of up to 1.9/day differed, as expected for oligotrophs and copiotrophs. Surprisingly, SAR11 also reached high cell division rates of up to 1.9/day, even before the onset of phytoplankton blooms. For all four taxonomic groups, the abundance-derived net growth (-0.6 to 0.5/day) was about an order of magnitude lower than the cell division rates. Consequently, mortality rates were comparably high to cell division rates, indicating that about 90% of bacterial production is recycled without apparent time lag within 1 day. Our study shows that determining taxon-specific cell division rates complements omics-based tools and provides unprecedented clues on individual bacterial growth strategies including bottom-up and top-down controls. IMPORTANCE The growth of a microbial population is often calculated from their numerical abundance over time. However, this does not take cell division and mortality rates into account, which are important for deriving ecological processes like bottom-up and top-down control. In this study, we determined growth by numerical abundance and calibrated microscopy-based methods to determine the frequency of dividing cells and subsequently calculate taxon-specific cell division rates in situ. The cell division and mortality rates of two oligotrophic (SAR11 and SAR86) and two copiotrophic (Bacteroidetes and Aurantivirga) taxa during two spring phytoplankton blooms showed a tight coupling for all four taxa throughout the blooms without any temporal offset. Unexpectedly, SAR11 showed high cell division rates days before the bloom while cell abundances remained constant, which is indicative of strong top-down control. Microscopy remains the method of choice to understand ecological processes like top-down and bottom-up control on a cellular level.

Temperature and nutrients drive eco-phenotypic dynamics in a microbial food web

Anthropogenic increases in temperature and nutrient loads will likely impact food web structure and stability. Although their independent effects have been reasonably well studied, their joint effects-particularly on coupled ecological and phenotypic dynamics-remain poorly understood. Here we experimentally manipulated temperature and nutrient levels in microbial food webs and used time-series analysis to quantify the strength of reciprocal effects between ecological and phenotypic dynamics across trophic levels. We found that (1) joint-often interactive-effects of temperature and nutrients on ecological dynamics are more common at higher trophic levels, (2) temperature and nutrients interact to shift the relative strength of top-down versus bottom-up control, and (3) rapid phenotypic change mediates observed ecological responses to changes in temperature and nutrients. Our results uncover how feedback between ecological and phenotypic dynamics mediate food web responses to environmental change. This suggests important but previously unknown ways that temperature and nutrients might jointly control the rapid eco-phenotypic feedback that determine food web dynamics in a changing world.

Protists' microbiome: A fine-scale, snap-shot field study on the ciliate Euplotes

Host-microbiome relationships play a fundamental role in the evolution and ecology of any living being. As unicellular organisms, protists represent a unique eukaryotic model to investigate selection mechanisms of the prokaryotic microbiome at the cellular level. Field investigations are central to disentangle relative importance of selective drivers in nature. Here we performed an analysis on data from a snap-shot field study reported previously on bacterial microbiomes associated to natural populations of protist ciliates of the genus Euplotes to detect at a fine scale any influence of habitat and/or host identity in microbiome selection. Comparative analyses revealed environment at a relatively large scale (sampling area) as the main driving factor in shaping prokaryotic communities' structures. No evidence of habitat as key-factor emerged when a smaller spatial scale was considered (pond/channel or site). When only microbiomes of ciliates from the same site were compared, a clear assessment on the influence of host identity at the species level was not achieved, probably due to the small and unbalanced number of individuals for the two considered host species. Starting from this point, wider sampling campaigns will contribute in the future to depict a general view of the drivers influencing the prokaryotic microbiomes of natural protist populations.

Predator dispersal influences predator distribution but not prey diversity in pitcher plant microbial metacommunities

The spatial distribution of predators can affect both the distribution and diversity of their prey. Therefore, differences in predator dispersal ability that affect their spatial distribution, could also affect prey communities. Here, we use the microbial communities within pitcher plant leaves as a model system to test the relationship between predator (protozoa) dispersal ability and distribution, and its consequences for prey (bacteria) diversity and composition. We hypothesized that limited predator dispersal results in clustered distributions and heterogeneous patches for prey species, whereas wide predator dispersal and distribution could homogenize prey metacommunities. We analyzed the distribution of two prominent bacterivore protozoans from a 2-year survey of an intact field of Sarracenia purpurea pitcher plants, and found a clustered distribution of Tetrahymena and homogeneous distribution of Poterioochromonas. We manipulated the sources of protozoan colonists and recorded protozoan recruitment and bacterial diversity in target leaves in a field experiment. We found the large ciliate, Tetrahymena, was dispersal limited and occupied few leaves, whereas the small flagellate Poterioochromonas was widely dispersed. However, the bacterial communities these protozoans feed on was unaffected by clustering of Tetrahymena, but likely influenced by Poterioochromonas and other bacterivores dispersing in the field. We propose that bacterial communities in this system are structured by a combination of well dispersed bacterivores, bacterial dispersal, and bottom-up mechanisms. Clustered predators could become strong drivers of prey communities if they were specialists or keystone predators, or if they exerted a dominant influence on other predators in top-down controlled systems. Linking dispersal ability within trophic levels and its consequences for trophic dynamics can lead to a more robust perspective on trophic metacommunities.

Experimental evaluation of microplastic consumption by using a size-fractionation approach in the planktonic communities

The increasing amount of plastic particles introduced into continental aquatic environments has drawn the attention of researchers around the globe. These particles can be assimilated by a wide range of aquatic organisms, from microorganisms to fish, causing detrimental effects on trophic webs. Using an experimental approach, we investigated the effect of microplastic particles of different sizes on the planktonic trophic chain by sampling natural plankton communities from a lake located in the Upper Paraná River floodplain, Brazil. Zooplankton samples were collected at the beginning of the experiment and after 36 h of incubation. Microplastic particles (MP) samples were taken every 12 h. The effect of MP particle consumption from the control and treatment groups indicates significant effects by all plankton size fractions (p < 0.05). We demonstrated that the presence of MP particles can significantly affect the trophic web, furthermore, we detected the effect of higher consumption effect of smaller size MP particles. This study suggest that the largest MP consumption effects come from the lower trophic levels of the trophic chain, such as protists. The competitive effect of large predators is a crucial factor in controlling the abundance of populations, and although they did not directly consume MP particles, they ingest them indirectly through prey capable of absorbing these compounds in the environment. Our findings warn that MP particles enter the food webs of tropical regions when exposed to these pollutants, and that the presence of these particles should not be neglected when studying freshwater ecosystems.

Removal of Waterborne Viruses by Tetrahymena pyriformis Is Virus-Specific and Coincides with Changes in Protist Swimming Speed

Biological treatment of waterborne viruses, specifically grazing of viruses by protists, can enhance microbial water quality while avoiding the production of toxic byproducts and high energy costs. However, tangible applications are limited by the lack of understanding of the underlying mechanisms. Here, we examined the feeding behavior of Tetrahymena pyriformis ciliates on 13 viruses, including bacteriophages, enteric viruses, and respiratory viruses. Significant differences in virus removal by T. pyriformis were observed, ranging from no removal (Qbeta, coxsackievirus B5) to ≥2.7 log₁₀ (JC polyomavirus) after 48 h of co-incubation of the protist with the virus. Removal rates were conserved even when protists were co-incubated with multiple viruses simultaneously. Video analysis revealed that the extent of virus removal was correlated with an increase in the protists' swimming speed, a behavioral trait consistent with the protists' response to the availability of food. Protistan feeding may be driven by a virus' hydrophobicity but was independent of virus size or the presence of a lipid envelope.

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.

Spatial distribution of the microzooplankton communities in the northern South China Sea: Insights into their function in microbial food webs

The spatial distribution of microzooplankton in the northern South China Sea was investigated in March 2016. Microzooplankton communities were dominated by cyclotrichids, aloricate oligotrichs, and choreotrichs within ciliates and the order Gymnodiniales within dinoflagellates. Microzooplankton abundance varied between 60 and 166,520 cells L^-1, with higher values in the coastal diluted water, and microzooplankton biomass exhibiting a similar pattern. High densities of Akashiwo cf. sanguinea were found in the upper waters along the coast, and mixotrophs dominated the communities in all the water masses. A canonical analysis of principal coordinates showed that the spatial patterns of microzooplankton communities could be clearly discriminated in the different water masses. Our findings provide insights into the functioning of microzooplankton and the potential risk of harmful Akashiwo cf. sanguinea algal blooms in coastal waters. In addition, our study provides evidence for using microzooplankton communities as potential indicators of water masses in complex marine systems.

Intra-guild predation (IGP) can increase or decrease prey density depending on the strength of IGP

In consumer communities, intra-guild predation (IGP) is a commonly observed interaction that is widely believed to increase resource density. However, some recent theoretical work predicts that resource density should first decrease, and then increase as the strength of IGP increases. This occurs because weak to intermediate IGP increases the IG predator density more than it reduces the IG prey density, so that weak to intermediate IGP leads to the lowest resource density compared to weak or strong IGP. We test this prediction that basal resource density would first decrease and then increase as the strength of IGP increase. We used a well-studied system with two protozoa species engaged in IGP and three bacteria species as the basal resources. We experimentally manipulated the percentage of the IG prey population that was available to an IG predator as a proxy for IGP strength. We found that bacterial density first decreased (by ~25%) and then increased (by ~30%) as the strength of IGP increased. Using a modified version of a published IGP model, we were able to explain ~70% of the variation in protozoa and bacterial density. Agreement of the empirical results with model predictions suggests that IGP first increased the IG predator density by consuming a small proportion of the IG prey population, which in turn increased the summed consumer density and decreased the bacterial resource density. As IGP strength increased further, the IG predator became satiated by the IG prey, which then freed the bacterial resource from predation and thus increased bacterial density. Consequently, our work shows that IGP can indeed decrease or increase basal resource density depending on its strength. Consequently, the impacts of IGP on resource density is potentially more complex than previously thought.

Detecting Associations Between Ciliated Protists and Prokaryotes with Culture-Independent Single-Cell Microbiomics: a Proof-of-Concept Study

Symbioses between prokaryotes and microbial eukaryotes, particularly ciliated protists, have been studied for a long time. Nevertheless, researchers have focused only on a few host genera and species, mainly due to difficulties in cultivating the hosts, and usually have considered a single symbiont at a time. Here, we present a pilot study using a single-cell microbiomic approach to circumvent these issues. Unicellular ciliate isolation followed by simultaneous amplification of eukaryotic and prokaryotic markers was used. Our preliminary test gave reliable and satisfactory results both on samples collected from different habitats (marine and freshwater) and on ciliates belonging to different taxonomic groups. Results suggest that, as already assessed for many macro-organisms like plants and metazoans, ciliated protists harbor distinct microbiomes. The applied approach detected new potential symbionts as well as new hosts for previously described ones, with relatively low time and cost effort and without culturing. When further developed, single-cell microbiomics for ciliates could be applied to a large number of studies aiming to unravel the evolutionary and ecological meaning of these symbiotic systems.

Bacterial Surface Traits Influence Digestion by Tetrahymena pyriformis and Alter Opportunity to Escape from Food Vacuoles

Endosymbiotic interactions are frequently found in nature, especially in the group of protists. Even though many endosymbioses have been studied in detail, little is known about the mechanistic origins and physiological prerequisites of endosymbiont establishment. A logical step towards the development of endocytobiotic associations is evading digestion and escaping from the host's food vacuoles. Surface properties of bacteria are probably involved in these processes. Therefore, we chemically modified the surface of a transformant strain of Escherichia coli prior to feeding to Tetrahymena pyriformis. N-(3-dimethylaminopropyl)-N'-ethylcarbodiimide allows any substance carrying amino- or carboxyl groups to be bound covalently to the bacterial surface by forming a peptide bond, thus, altering its properties biochemically and biophysically in a predictable manner. The effect of different traits on digestion of T. pyriformis was examined by fluorescence and transmission electron microscopy. The efficiency of digestion differs considerably depending on the coupled substances. Alkaline substances inhibit digestion partially, resulting in incomplete digestion and slightly enhanced escape rates. Increasing hydrophobicity leads to much higher escape frequencies. Both results point to possible mechanisms employed by pathogenic bacteria or potential endosymbionts in evading digestion and transmission to the host's cytoplasm.

Ingestion and digestion studies in Tetrahymena pyriformis based on chemically modified microparticles

Recognition of food and, in consequence, ingestion of digestible particles is a prerequisite for energy metabolism in Tetrahymena pyriformis. Understanding why some particles are ingested and digested, whereas others are not, is important for many fields of research, e.g. survival of pathogens in single-celled organisms or establishment of endosymbiotic relationships. We offered T. pyriformis synthetical bovine-serum-albumin (BSA)-methacrylate microparticles of approximately 5.5 μm diameter and studied the ciliates' ingestion and digestion behaviour. Different staining techniques as well as co-feeding with a transformant strain of Escherichia coli revealed that T. pyriformis considers these particles as natural food source and shows no feeding preference. Further, they are ingested at normal rates and may serve as sole food source. A pivotal advantage of these particles is the convenient modification of their surface by binding different ligands resulting in defined surface properties. Ingestion rate of modified microparticles either increased (additional BSA, enzymes) or decreased (amino acids). Furthermore, we investigated glycosylation patterns by lectin binding. By binding different substances to the surface in combination with various staining techniques, we provide a versatile experimental tool for elucidating details on food recognition and digestion that may allow to study evading digestion by pathogens or potential endosymbionts, too.

Single gene locus changes perturb complex microbial communities as much as apex predator loss

Many bacterial species are highly social, adaptively shaping their local environment through the production of secreted molecules. This can, in turn, alter interaction strengths among species and modify community composition. However, the relative importance of such behaviours in determining the structure of complex communities is unknown. Here we show that single-locus changes affecting biofilm formation phenotypes in Bacillus subtilis modify community structure to the same extent as loss of an apex predator and even to a greater extent than loss of B. subtilis itself. These results, from experimentally manipulated multitrophic microcosm assemblages, demonstrate that bacterial social traits are key modulators of the structure of their communities. Moreover, they show that intraspecific genetic variability can be as important as strong trophic interactions in determining community dynamics. Microevolution may therefore be as important as species extinctions in shaping the response of microbial communities to environmental change.

Some species of social bacteria can chemically modify their nutrient environments, which may influence community interactions. Here, McClean et al. show that changes at a single gene locus in a biofilm-forming bacteria can perturb community structure to the same extent as the loss of an apex predator.

Mechanisms involved in Escherichia coli and Serratia marcescens removal during activated sludge wastewater treatment

Wastewater treatment reduces environmental contamination by removing gross solids and mitigating the effects of pollution. Treatment also reduces the number of indicator organisms and pathogens. In this work, the fates of two coliform bacteria, Escherichia coli and Serratia marcescens, were analyzed in an activated sludge process to determine the main mechanisms involved in the reduction of pathogenic microorganisms during wastewater treatment. These bacteria, modified to express green fluorescent protein, were inoculated in an activated sludge unit and in batch systems containing wastewater. The results suggested that, among the different biological factors implied in bacterial removal, bacterivorous protozoa play a key role. Moreover, a representative number of bacteria persisted in the system as free-living or embedded cells, but their distribution into liquid or solid fractions varied depending on the bacterium tested, questioning the real value of bacterial indicators for the control of wastewater treatment process. Additionally, viable but nonculturable cells constituted an important part of the bacterial population adhered to solid fractions, what can be derived from the competition relationships with native bacteria, present in high densities in this environment. These facts, taken together, emphasize the need for reliable quantitative and qualitative analysis tools for the evaluation of pathogenic microbial composition in sludge, which could represent an undefined risk to public health and ecosystem functions when considering its recycling.

Microbial dynamics and flagellate grazing during transition to winter in Lakes Hoare and Bonney, Antarctica

The planktonic microbial communities of Lakes Hoare and Bonney were investigated during transition into winter. We hypothesized that the onset of darkness induces changes in the functional role of autotrophic and heterotrophic microplankton. Bacteria decreased in Lake Hoare during March-April, while in Lake Bonney bacterial abundances varied. Heterotrophic nanoflagellates (HNAN), phototrophic nanoflagellates (PNAN) and ciliates showed no marked decline with the onset of winter. PNAN outnumbered HNAN in both lakes. Grazing rates of HNAN in Lake Hoare ranged up to 30.8 bacteria per cell day(-1). The HNAN community grazed between 3.74 and 36.6 ng of bacterial carbon day(-1). Mixotrophic PNAN had grazing rates up to 15.2 bacteria per cell day(-1), and their daily community grazing exceeded bacterial production. In Lake Bonney East, PNAN grazing rates ranged up to 12.48 bacteria per cell day(-1) and in Lake Bonney West up to 8.16 bacteria per cell day(-1). As in Lake Hoare, the mixotrophic PNAN grazing rates (up to 950 ng C day(-1)) usually exceeded bacterial production. HNAN grazing rates were generally similar to those in Lake Hoare. As winter encroaches, these lakes move progressively towards heterotrophy and probably function during the winter, enabling populations to enter the short austral summer with actively growing populations.

Preferential feeding by the ciliates Chilodonella and Tetrahymena spp. and effects of these protozoa on bacterial biofilm structure and composition

Protozoa are important components of microbial food webs, but protozoan feeding preferences and their effects in the context of bacterial biofilms are not well understood. The feeding interactions of two contrasting ciliates, the free-swimming filter feeder Tetrahymena sp. and the surface-associated predator Chilodonella sp., were investigated using biofilm-forming bacteria genetically modified to express fluorescent proteins. According to microscopy, both ciliates readily consumed cells from both Pseudomonas costantinii and Serratia plymuthica biofilms. When offered a choice between spatially separated biofilms, each ciliate showed a preference for P. costantinii biofilms. Experiments with bacterial cell extracts indicated that both ciliates used dissolved chemical cues to locate biofilms. Chilodonella sp. evidently used bacterial chemical cues as a basis for preferential feeding decisions, but it was unclear whether Tetrahymena sp. did also. Confocal microscopy of live biofilms revealed that Tetrahymena sp. had a major impact on biofilm morphology, forming holes and channels throughout S. plymuthica biofilms and reducing P. costantinii biofilms to isolated, grazing-resistant microcolonies. Grazing by Chilodonella sp. resulted in the development of less-defined trails through S. plymuthica biofilms and caused P. costantinii biofilms to become homogeneous scatterings of cells. It was not clear whether the observed feeding preferences for spatially separated P. costantinii biofilms over S. plymuthica biofilms resulted in selective targeting of P. costantinii cells in mixed biofilms. Grazing of mixed biofilms resulted in the depletion of both types of bacteria, with Tetrahymena sp. having a larger impact than Chilodonella sp., and effects similar to those seen in grazed single-species biofilms.