Amoebae are protists that have complicated relationships with bacteria, which cover the whole spectrum of symbiosis. Amoeba-bacteria interactions contribute to the study of predation, symbiosis, pathogenesis, and human health. Given the complexity of their relationships, it is necessary to understand the ecology and evolution of their interactions. In this paper, we provide an updated review of the current understanding of amoeba-bacteria interactions. We start by discussing the diversity of amoebae and their bacterial partners. Besides, we define three types of ecological interactions between amoebae and bacteria and discuss their different outcomes. Finally, we focus on the implications of amoeba-bacteria interactions on human health, horizontal gene transfer, drinking water safety, and the evolution of symbiosis. In conclusion, amoeba-bacteria interactions are excellent model systems to investigate a wide range of scientific questions. Future studies should utilize advanced techniques to address research gaps such as detecting hidden diversity, lack of amoebae genome, and the impacts of amoeba predation on the microbiome.

BackgroundThe green algae Chlamydomonas reinhardtii and Volvox carteri are important models for studying light perception and response, expressing many different photoreceptors. More than 10 opsins were reported in C. reinhardtii, yet only two—the channelrhodopsins—were functionally characterized. Characterization of new opsins would help to understand the green algae photobiology and to develop new tools for optogenetics.ResultsHere we report the characterization of a novel opsin family from these green algae: light-inhibited guanylyl cyclases regulated through a two-component-like phosphoryl transfer, called “two-component cyclase opsins” (2c-Cyclops). We prove the existence of such opsins in C. reinhardtii and V. carteri and show that they have cytosolic N- and C-termini, implying an eight-transmembrane helix structure. We also demonstrate that cGMP production is both light-inhibited and ATP-dependent. The cyclase activity of Cr2c-Cyclop1 is kept functional by the ongoing phosphorylation and phosphoryl transfer from the histidine kinase to the response regulator in the dark, proven by mutagenesis. Absorption of a photon inhibits the cyclase activity, most likely by inhibiting the phosphoryl transfer. Overexpression of Vc2c-Cyclop1 protein in V. carteri leads to significantly increased cGMP levels, demonstrating guanylyl cyclase activity of Vc2c-Cyclop1 in vivo. Live cell imaging of YFP-tagged Vc2c-Cyclop1 in V. carteri revealed a development-dependent, layer-like structure at the immediate periphery of the nucleus and intense spots in the cell periphery.ConclusionsCr2c-Cyclop1 and Vc2c-Cyclop1 are light-inhibited and ATP-dependent guanylyl cyclases with an unusual eight-transmembrane helix structure of the type I opsin domain which we propose to classify as type Ib, in contrast to the 7 TM type Ia opsins. Overexpression of Vc2c-Cyclop1 protein in V. carteri led to a significant increase of cGMP, demonstrating enzyme functionality in the organism of origin. Fluorescent live cell imaging revealed that Vc2c-Cyclop1 is located in the periphery of the nucleus and in confined areas at the cell periphery.Electronic supplementary materialThe online version of this article (10.1186/s12915-018-0613-5) contains supplementary material, which is available to authorized users.

It is since many years textbook knowledge that the concentration of the second messenger cGMP is regulated in animal rod and cone cells by type II rhodopsins via a G-protein signaling cascade. Microbial rhodopsins with enzymatic activity for regulation of cGMP concentration were only recently discovered: in 2014 light-activated guanylyl-cyclase opsins in fungi and in 2017 a novel rhodopsin phosphodiesterase (RhoPDE) in the protist (RhoPDE). The light regulation of RhoPDE, however, seemed very weak or absent. Here, we present strong evidence for light regulation by studyingRhoPDE, expressed in oocytes, at different substrate concentrations. Hydrolysis of cGMP shows an ∼100-fold higher turnover than that of cAMP. Light causes a strong decrease in the value for cGMP from 80 to 13 µM but increases the maximum turnover only by ∼30%. The PDE activity for cAMP is similarly enhanced by light at low substrate concentrations. Illumination does not affect the cGMP degradation of Lys296 mutants that are not able to form a covalent bond of Schiff base type to the chromophore retinal. We demonstrate that RhoPDE shows cytosolic N- and C-termini, most likely via an eight-transmembrane helix structure.RhoPDE is a new optogenetic tool for light-regulated cGMP manipulation which might be further improved by genetic engineering.

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Soil protists are the invisible majority of soil eukaryotes, which are essential but often forgotten parts of the soil ecosystem. They play key roles in microbial food webs by predating on other soil microbes. However, it is not clear how dormant soil protists sense, recognize and feed on diverse microbial prey. In this study, we used a soil amoeba, Dictyostelium discoideum, to study selective discrimination and predation of 14 different bacteria. We found that discrimination and sensing of prey in D. discoideum started as early as resting spores. Dictyostelium discoideum had higher hatching rates, formed bigger amoeba plaques and preferred high nutritional value bacteria. The feeding speed of amoeba on various bacteria was constant and was not linked with sensing of prey or bacterial nutritional value. We also found that higher bacterial density decreased predation efficiency, and one species, P. fluorescens, induced a strong density‐dependent inhibition of amoeba spore production. In conclusion, we find that dormant D. discoideum can selectively sense and predate on different soil bacteria, a process that is likely mediated through active amoeba preference as well as bacterial inhibition. This study provides new insights into the role of protists in shaping soil bacterial communities, and future study needs to assess this in natural soil environments.