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Concept: Protist


Leeuwenhoek’s 1677 paper, the famous ‘letter on the protozoa’, gives the first detailed description of protists and bacteria living in a range of environments. The colloquial, diaristic style conceals the workings of a startlingly original experimental mind. Later scientists could not match the resolution and clarity of Leeuwenhoek’s microscopes, so his discoveries were doubted or even dismissed over the following centuries, limiting their direct influence on the history of biology; but work in the twentieth century confirmed Leeuwenhoek’s discovery of bacterial cells, with a resolution of less than 1 µm. Leeuwenhoek delighted most in the forms, interactions and behaviour of his little ‘animalcules’, which inhabited a previously unimagined microcosmos. In these reflections on the scientific reach of Leeuwenhoek’s ideas and observations, I equate his questions with the preoccupations of our genomic era: what is the nature of Leeuwenhoek’s animalcules, where do they come from, how do they relate to each other? Even with the powerful tools of modern biology, the answers are far from resolved-these questions still challenge our understanding of microbial evolution. This commentary was written to celebrate the 350th anniversary of the journal Philosophical Transactions of the Royal Society.

Concepts: Bacteria, Organism, Microbiology, Eukaryote, Science, Microorganism, Protist, Royal Society


Learning, defined as a change in behaviour evoked by experience, has hitherto been investigated almost exclusively in multicellular neural organisms. Evidence for learning in non-neural multicellular organisms is scant, and only a few unequivocal reports of learning have been described in single-celled organisms. Here we demonstrate habituation, an unmistakable form of learning, in the non-neural organism Physarum polycephalum In our experiment, using chemotaxis as the behavioural output and quinine or caffeine as the stimulus, we showed that P. polycephalum learnt to ignore quinine or caffeine when the stimuli were repeated, but responded again when the stimulus was withheld for a certain time. Our results meet the principle criteria that have been used to demonstrate habituation: responsiveness decline and spontaneous recovery. To distinguish habituation from sensory adaptation or motor fatigue, we also show stimulus specificity. Our results point to the diversity of organisms lacking neurons, which likely display a hitherto unrecognized capacity for learning, and suggest that slime moulds may be an ideal model system in which to investigate fundamental mechanisms underlying learning processes. Besides, documenting learning in non-neural organisms such as slime moulds is centrally important to a comprehensive, phylogenetic understanding of when and where in the tree of life the earliest manifestations of learning evolved.

Concepts: Psychology, Cell, Bacteria, Organism, Species, Microorganism, Protist, Physarum polycephalum


The dinoflagellates are an important group of eukaryotic, single celled algae. They are the sister group of the Apicomplexa, a group of intracellular parasites and photosynthetic algae including the malaria parasite Plasmodium. Many apicomplexan mitochondria have a number of unusual features, including the lack of a pyruvate dehydrogenase and the existence of a branched TCA cycle. Here, we analyse dinoflagellate EST (expressed sequence tag) data to determine whether these features are apicomplexan-specific, or if they are more widespread. We show that dinoflagellates have replaced a key subunit (E1) of pyruvate dehydrogenase with a subunit of bacterial origin and that transcripts encoding many of the proteins that are essential in a conventional ATP synthase/Complex V are absent, as is the case in Apicomplexa. There is a pathway for synthesis of starch or glycogen as a storage carbohydrate. Transcripts encoding isocitrate lyase and malate synthase are present, consistent with ultrastructural reports of a glyoxysome. Finally, evidence for a conventional haem biosynthesis pathway is found, in contrast to the Apicomplexa, Chromera and early branching dinoflagellates (Perkinsus, Oxyrrhis).

Concepts: Algae, Photosynthesis, Bacteria, Metabolism, Plastid, Apicomplexa, Citric acid cycle, Protist


In spite of the ecological importance of protists, few data are available on their distribution in soil. This investigation is the first of its kind on what could be the major components of the soil protistan community, the Myxomycetes or plasmodial slime-moulds, a monophyletic class in the phylum Amoebozoa. Myxomycetes have a complex life cycle culminating in the formation of mainly macroscopic fruiting bodies, highly variable in shape and colour, that can be found in every terrestrial biome. Despite their prevalence, they are paradoxically absent from environmental DNA sampling studies. We obtained myxomycete SSU rRNA gene sequences from soil-extracted RNAs by using specific primers. Soil samples were collected in three mountain ranges (France, Scotland and Japan). Our study revealed an unexpectedly high diversity of dark-spored Myxomycetes with the recovery of 74 phylotypes. Of these, 74 % had less than 98 % identity with known sequences, thus showing a hidden diversity; there was little overlap between localities, implying biogeographical patterns. Few phylotypes were dominant and many were unique, consistent with the “rare biosphere” phenomenon. Our study provides first detailed insight into community composition of this ecologically important group of protists, establishing means for future studies of their distribution, abundance and ecology. © 2012 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd.All rights reserved.

Concepts: Biodiversity, RNA, Ribosomal RNA, Ecology, Ecosystem, Slime mold, Protist, Physarum polycephalum


A retrospective study of the pathologic findings in weedy (Phyllopteryx taeniolatus) and leafy (Phycodurus eques) seadragons was performed on specimens submitted to 2 reference laboratories from 1994 to 2012 to determine the range and occurrence of diseases affecting aquarium-held populations. One hundred two and 94 total diagnoses were recorded in weedy and leafy seadragons, respectively. Two of the more common etiologic diagnoses in both species were mycobacteriosis and scuticociliatosis, whereas myxozoanosis was common in weedy seadragons. Metazoan parasite infections were less common etiologic diagnoses. There were no correlations between mycobacteriosis and ciliate protozoan infections in either species. Myxozoanosis was usually found in combination with other diseases and, except for 1 case, was restricted to weedy seadragons. Phaeohyphomycosis, nonmycobacterial bacterial infections, and trauma were also important but less frequent diagnoses. Intestinal coccidiosis was found in weedy but not leafy seadragons. Mineralization of the swim bladder was detected in 26 of 197 leafy seadragons and only 2 of 257 weedy seadragons. Although weedy and leafy seadragons share certain diseases of significance to exhibit populations, there are diseases unique to each species about which the veterinary pathologist, clinician, or diagnostician should be aware.

Concepts: Bacteria, Eukaryote, Pathology, Protozoa, Protist, Ciliate, Syngnathidae, Leafy sea dragon


Acanthamoeba castellanii is a free-living amoeba widely found in environmental matrices such as soil and water. Arcobacter butzleri is an emerging potential zoonotic pathogen that can be isolated from environmental water sources, where they can establish endosymbiotic relationships with amoebas. The aim of this study was to describe the implication of mannose-binding proteins and membrane-associated receptors of glucose and galactose present in the amoebic membrane, during the attachment of Arcobacter butzleri by blocking with different saccharides. Another objective was to describe the signaling pathways involved in phagocytosis of these bacteria using specific inhibitors and analyze the implication of phagolysosome formation on the survival of Arcobacter butzleri inside the amoeba. We infer that the attachment of Arcobacter butzleri to the amoeba is a process which involves the participation of mannose-binding proteins and membrane-associated receptors of glucose and galactose present in the amoeba. We also demonstrated an active role of protozoan actin polymerization in the phagocytosis of Arcobacter butzleri and a critical involvement of PI3K and RhoA pathways. Further, we demonstrated that the tyrosine kinase-induced actin polymerization signal is essential in Acanthamoeba-mediated bacterial uptake. Through phagolysosomal formation analysis, we conclude that the survival of Arcobacter butzleri inside the amoeba could be related with the ability to remain inside vacuoles not fused with lysosomes, or with the ability to retard the fusion between these structures. All these results help the understanding of the bacterial uptake mechanisms used by Acanthamoeba castellanii and contribute to evidence of the survival mechanisms of Arcobacter butzleri.

Concepts: Protein, Cell, Signal transduction, Protist, Amoeboid, Amoeba


Benthic habitats harbour a significant (yet unexplored) diversity of microscopic eukaryote taxa, including metazoan phyla, protists, algae and fungi. These groups are thought to underpin ecosystem functioning across diverse marine environments. Coastal marine habitats in the Gulf of Mexico experienced visible, heavy impacts following the Deepwater Horizon oil spill in 2010, yet our scant knowledge of prior eukaryotic biodiversity has precluded a thorough assessment of this disturbance. Using a marker gene and morphological approach, we present an intensive evaluation of microbial eukaryote communities prior to and following oiling around heavily impacted shorelines. Our results show significant changes in community structure, with pre-spill assemblages of diverse Metazoa giving way to dominant fungal communities in post-spill sediments. Post-spill fungal taxa exhibit low richness and are characterized by an abundance of known hydrocarbon-degrading genera, compared to prior communities that contained smaller and more diverse fungal assemblages. Comparative taxonomic data from nematodes further suggests drastic impacts; while pre-spill samples exhibit high richness and evenness of genera, post-spill communities contain mainly predatory and scavenger taxa alongside an abundance of juveniles. Based on this community analysis, our data suggest considerable (hidden) initial impacts across Gulf beaches may be ongoing, despite the disappearance of visible surface oil in the region.

Concepts: Bacteria, Organism, Eukaryote, Species, Plant, Fungus, Animal, Protist


An amoeboid unicellular organism, a plasmodium of the true slime mold Physarum polycephalum, exhibits complex spatiotemporal oscillatory dynamics and sophisticated information processing capabilities while deforming its amorphous body. We previously devised an ‘amoeba-based computer (ABC),’ that implemented optical feedback control to lead this amoeboid organism to search for a solution to the traveling salesman problem (TSP). In the ABC, the shortest TSP route (the optimal solution) is represented by the shape of the organism in which the body area (nutrient absorption) is maximized while the risk of being exposed to aversive light stimuli is minimized. The shortness of the TSP route found by ABC, therefore, serves as a quantitative measure of the optimality of the decision made by the organism. However, it remains unclear how the decision-making ability of the organism originates from the oscillatory dynamics of the organism. We investigated the number of coexisting traveling waves in the spatiotemporal patterns of the oscillatory dynamics of the organism. We show that a shorter TSP route can be found when the organism exhibits a lower number of traveling waves. The results imply that the oscillatory dynamics are highly coordinated throughout the global body. Based on the results, we discuss the fact that the decision-making ability of the organism can be enhanced not by uncorrelated random fluctuations, but by its highly coordinated oscillatory dynamics.

Concepts: Operations research, Feedback, Microorganism, Slime mold, Protist, Travelling salesman problem, Physarum polycephalum, Function problem


Because microbial plankton in the ocean comprise diverse bacteria, algae, and protists that are subject to environmental forcing on multiple spatial and temporal scales, a fundamental open question is to what extent these organisms form ecologically cohesive communities. Here we show that although all taxa undergo large, near daily fluctuations in abundance, microbial plankton are organized into clearly defined communities whose turnover is rapid and sharp. We analyze a time series of 93 consecutive days of coastal plankton using a technique that allows inference of communities as modular units of interacting taxa by determining positive and negative correlations at different temporal frequencies. This approach shows both coordinated population expansions that demarcate community boundaries and high frequency of positive and negative associations among populations within communities. Our analysis thus highlights that the environmental variability of the coastal ocean is mirrored in sharp transitions of defined but ephemeral communities of organisms.

Concepts: Bacteria, Biology, Eukaryote, Species, Microorganism, Ocean, Protist, Plankton


Climate warming is accelerating the retreat of glaciers and recently, many ‘new’ glacial turbid lakes have been created. In the course of time, the loss of the hydrological connectivity to a glacier causes, however, changes in their water turbidity and turns these ecosystems into clear ones.To understand potential differences in the food-web structure between glacier-fed turbid and clear alpine lakes, we sampled ciliates, phyto-, bacterio- and zooplankton in one clear and one glacial turbid alpine lake, and measured key physicochemical parameters. In particular, we focused on the ciliate community and the potential drivers for their abundance distribution.In both lakes, the zooplankton community was similar and dominated by the copepod Cyclops abyssorum tatricus and rotifers including Polyarthra dolichoptera, Keratella hiemalis, Keratella cochlearis and Notholca squamula. The phytoplankton community structure differed and it was dominated by the planktonic diatom Fragilaria tenera and the cryptophyte alga Plagioselmis nannoplanctica in the glacial turbid lake, while chrysophytes and dinoflagellates were predominant in the clear one.Ciliate abundance and richness were higher in the glacial turbid lake (∼4000-27 800 Ind L(-1), up to 29 species) than in the clear lake (∼570-7150 Ind L(-1), up to eight species). The dominant species were Balanion planctonicum, Askenasia cf. chlorelligera, Urotricha cf. furcata and Mesodinium cf. acarus. The same species dominated in both lakes, except for Mesodinium cf. acarus and some particle-associated ciliates, which occurred exclusively in the glacial turbid lake. The relative underwater solar irradiance (i.e. percentage of PAR and UVR at depth) significantly explained their abundance distribution pattern, especially in the clear water lake. In the glacial turbid lake, the abundance of the dominating ciliate taxa was mainly explained by the presence of predatory zooplankton.Our results revealed an unexpected high abundance and richness of protists (algae, ciliates) in the glacial turbid lake. This type of lake likely offers more suitable environmental conditions and resource niches for protists than the clear and highly UV transparent lake.

Concepts: Algae, Lake, Phytoplankton, Protist, Dinoflagellate, Antarctica, Plankton, Turbidity