Effective removal of the rotifer Brachionus calyciflorus from a Chlorella vulgaris microalgal culture by homogeneous solar photo-Fenton at neutral pH.

In this study, a citrate-modified photo-Fenton process was successfully applied to decontaminate a Chlorella vulgaris microalgae culture spiked with the rotifer Brachionus calyciflorus (5 individuals mL-1). The applied treatment (1 mg L-1 Fe2+, 20 mg L-1 H2O2, 17.5 mg L-1 citric acid) had only moderate effects on viability and regrowth of the microalgae since, after a short post-treatment delay of a few days, they reached final cell densities similar to that obtained for microalgae cultures that were not spiked. The decontamination was effective as no regrowth of rotifers was observed in the microalgae cultures after treatment. The efficacy of the citrate-modified photo-Fenton treatment was also studied with a higher starting concentration of 20 rotifers mL-1 and was compared with a solar light/H2O2 treatment. Results show that both treatments had similar efficacies on the rotifer elimination, but that the citrate-modified photo-Fenton treatment had a lower negative impact on the regrowth of microalgae than the solar light/H2O2 treatment. However, when microalgae cultures were spiked with 20 rotifers mL-1, rotifers were only partially inactivated and post-treatment regrowth occurred, which highlights the importance to apply the photo-Fenton process at an early stage of a contamination to achieve full rotifer elimination. In any case, a contamination with 5 rotifers mL-1 is already a significant threat as numbers above 1000 rotifers mL-1 were reached after 14 days and caused the microalgae culture to fail. Overall, our treatment suggests that the citrate-modified solar photo-Fenton process is an environmentally friendly solution to support the maintenance of contaminant-free microalgal cultures.

When your PhD (almost) falls apart.

As a chance observation threatens to unravel several years of work, a PhD student must decide how to respond.

Co-transfer of functionally interdependent genes contributes to genome mosaicism in lambdoid phages.

Lambdoid (or Lambda-like) phages are a group of related temperate phages that can infect Escherichia coli and other gut bacteria. A key characteristic of these phages is their mosaic genome structure, which served as the basis for the 'modular genome hypothesis'. Accordingly, lambdoid phages evolve by transferring genomic regions, each of which constitutes a functional unit. Nevertheless, it is unknown which genes are preferentially transferred together and what drives such co-transfer events. Here we aim to characterize genome modularity by studying co-transfer of genes among 95 distantly related lambdoid (pro-)phages. Based on gene content, we observed that the genomes cluster into 12 groups, which are characterized by a highly similar gene content within the groups and highly divergent gene content across groups. Highly similar proteins can occur in genomes of different groups, indicating that they have been transferred. About 26 % of homologous protein clusters in the four known operons (i.e. the early left, early right, immunity and late operon) engage in gene transfer, which affects all operons to a similar extent. We identified pairs of genes that are frequently co-transferred and observed that these pairs tend to be near one another on the genome. We find that frequently co-transferred genes are involved in related functions and highlight interesting examples involving structural proteins, the cI repressor and Cro regulator, proteins interacting with DNA, and membrane-interacting proteins. We conclude that epistatic effects, where the functioning of one protein depends on the presence of another, play an important role in the evolution of the modular structure of these genomes.

MyFishCheck: A Model to Assess Fish Welfare in Aquaculture.

Welfare in animal husbandry includes considerations of biology, ethics, ecology, law and economics. These diverse aspects must be translated into common quantifiable parameters and applicable methods to objectively assess welfare in animals. To assist this process in the field of aquaculture, where such methods are largely missing, we developed a model to assess fish welfare. A network of information was created to link needs, i.e., fundamental requirements for welfare, with parameters, i.e., quantifiable aspects of welfare. From this ontology, 80 parameters that are relevant for welfare, have practicable assessment methods and deliver reliable results were selected and incorporated into a model. The model, named MyFishCheck, allows the evaluation of welfare in five distinct modules: farm management, water quality, fish group behaviour, fish external and fish internal appearance, thereby yielding five individual grades categorising welfare ranging from critical, to poor, to acceptable, and good. To facilitate the use of the model, a software application was written. With its adaptability to different fish species, farming systems, regulations and purposes as well as its user-friendly digital version, MyFishCheck is a next step towards improved fish welfare assessment and provides a basis for ongoing positive developments for the industry, the farmers and the fish.

Fitness benefits to bacteria of carrying prophages and prophage-encoded antibiotic-resistance genes peak in different environments.

Understanding the role of horizontal gene transfer (HGT) in adaptation is a key challenge in evolutionary biology. In microbes, an important mechanism of HGT is prophage acquisition (phage genomes integrated into bacterial chromosomes). Prophages can influence bacterial fitness via the transfer of beneficial genes (including antibiotic-resistance genes, ARGs), protection from superinfecting phages, or switching to a lytic lifecycle that releases free phages infectious to competitors. We expect these effects to depend on environmental conditions because of, for example, environment-dependent induction of the lytic lifecycle. However, it remains unclear how costs/benefits of prophages vary across environments. Here, studying prophages with/without ARGs in Escherichia coli, we disentangled the effects of prophages alone and adaptive genes they carry. In competition with prophage-free strains, benefits from prophages and ARGs peaked in different environments. Prophages were most beneficial when induction of the lytic lifecycle was common, whereas ARGs were more beneficial upon antibiotic exposure and with reduced prophage induction. Acquisition of prophage-encoded ARGs by competing strains was most common when prophage induction, and therefore free phages, were common. Thus, selection on prophages and adaptive genes they carry varies independently across environments, which is important for predicting the spread of mobile/integrating genetic elements and their role in evolution.

Phage-host population dynamics promotes prophage acquisition in bacteria with innate immunity.

Temperate bacteriophages integrate in bacterial genomes as prophages and represent an important source of genetic variation for bacterial evolution, frequently transmitting fitness-augmenting genes such as toxins responsible for virulence of major pathogens. However, only a fraction of bacteriophage infections are lysogenic and lead to prophage acquisition, whereas the majority are lytic and kill the infected bacteria. Unless able to discriminate lytic from lysogenic infections, mechanisms of immunity to bacteriophages are expected to act as a double-edged sword and increase the odds of survival at the cost of depriving bacteria of potentially beneficial prophages. We show that although restriction-modification systems as mechanisms of innate immunity prevent both lytic and lysogenic infections indiscriminately in individual bacteria, they increase the number of prophage-acquiring individuals at the population level. We find that this counterintuitive result is a consequence of phage-host population dynamics, in which restriction-modification systems delay infection onset until bacteria reach densities at which the probability of lysogeny increases. These results underscore the importance of population-level dynamics as a key factor modulating costs and benefits of immunity to temperate bacteriophages.

Tripartite species interaction: eukaryotic hosts suffer more from phage susceptible than from phage resistant bacteria.

BACKGROUND: Evolutionary shifts in bacterial virulence are often associated with a third biological player, for instance temperate phages, that can act as hyperparasites. By integrating as prophages into the bacterial genome they can contribute accessory genes, which can enhance the fitness of their prokaryotic carrier (lysogenic conversion). Hyperparasitic influence in tripartite biotic interactions has so far been largely neglected in empirical host-parasite studies due to their inherent complexity. Here we experimentally address whether bacterial resistance to phages and bacterial harm to eukaryotic hosts is linked using a natural tri-partite system with bacteria of the genus Vibrio, temperate vibriophages and the pipefish Syngnathus typhle. We induced prophages from all bacterial isolates and constructed a three-fold replicated, fully reciprocal 75 × 75 phage-bacteria infection matrix. RESULTS: According to their resistance to phages, bacteria could be grouped into three distinct categories: highly susceptible (HS-bacteria), intermediate susceptible (IS-bacteria), and resistant (R-bacteria). We experimentally challenged pipefish with three selected bacterial isolates from each of the three categories and determined the amount of viable Vibrio counts from infected pipefish and the expression of pipefish immune genes. While the amount of viable Vibrio counts did not differ between bacterial groups, we observed a significant difference in relative gene expression between pipefish infected with phage susceptible and phage resistant bacteria. CONCLUSION: These findings suggest that bacteria with a phage-susceptible phenotype are more harmful against a eukaryotic host, and support the importance of hyperparasitism and the need for an integrative view across more than two levels when studying host-parasite evolution.

Viruses at Solid-Water Interfaces: A Systematic Assessment of Interactions Driving Adsorption.

Adsorption to solid-water interfaces is a major process governing the fate of waterborne viruses in natural and engineered systems. The relative contributions of different interaction forces to adsorption and their dependence on the physicochemical properties of the viruses remain, however, only poorly understood. Herein, we systematically studied the adsorption of four bacteriophages (MS2, fr, GA, and Qß) to five model surfaces with varying surface chemistries and to three dissolved organic matter adlayers, as a function of solution pH and ionic strength, using quartz crystal microbalance with dissipation monitoring. The viruses were selected to have similar sizes and shapes but different surface charges, polarities, and topographies, as identified by modeling the distributions of amino acids in the virus capsids. Virus-sorbent interactions were governed by long-ranged electrostatics and favorable contributions from the hydrophobic effect, and shorter-ranged van der Waals interactions were of secondary importance. Steric effects depended on the topographic irregularities on both the virus and sorbent surfaces. Differences in the adsorption characteristics of the tested viruses were successfully linked to differences in their capsid surface properties. Besides identifying the major interaction forces, this work highlights the potential of computable virus surface charge and polarity descriptors to predict virus adsorption to solid-water interfaces.

Opportunities for Switzerland to Contribute to the Production of Algal Biofuels: the Hydrothermal Pathway to Bio-Methane.

Microalgae have a significant potential to be a sustainable source of fuel and thus are of interest in the transition to a sustainable energy system, in particular for resource-dependent countries such as Switzerland. Independence of fossil fuels, considerable reduction of CO(2) emissions, and abandoning nuclear energy may be possible with an integrated system approach including the sourcing of biofuels from different types of biomass. Today, a full carbon-to-fuel conversion is possible, and has been recently demonstrated with an advanced hydrothermal technology. The potential to develop algal biofuels is viewed as high thanks to the possibility they offer to uncouple bioenergy from food production. Nevertheless, technological breakthroughs must take place before commercial production becomes a reality, especially to meet the necessary cost savings and efficiency gains in the algae cultivation structure. In addition, an integrated management of waste resources to promote the nutrient recovery appears today as imperative to further improve the economic viability and the environmental sustainability of algal production. We provide here a review that includes the global technological status of both algae production and their conversion into biofuels in order to understand first the added value of algal energy in general before we focus on the potential of algae to contribute specifically to the Swiss energy system to the horizon 2050. In this respect, the hydrothermal conversion pathway of microalgal biomass into synthetic natural gas (SNG) is emphasized, as research into this technology has received considerable attention in Switzerland during the last decade. In addition, SNG is a particularly relevant fuel in the Swiss context due to the existing gas grid and to the opportunity it offers to cover a wide spectrum of energy applications, in particular cogeneration of heat and electricity or use as a transport fuel in the growing gas car fleet.

Evolution of a morphological novelty occurred before genome compaction in a lineage of extreme parasites.

Intracellular parasitism results in extreme adaptations, whose evolutionary history is difficult to understand, because the parasites and their known free-living relatives are so divergent from one another. Microsporidia are intracellular parasites of humans and other animals, which evolved highly specialized morphological structures, but also extreme physiologic and genomic simplification. They are suggested to be an early-diverging branch on the fungal tree, but comparisons to other species are difficult because their rates of molecular evolution are exceptionally high. Mitochondria in microsporidia have degenerated into organelles called mitosomes, which have lost a genome and the ability to produce ATP. Here we describe a gut parasite of the crustacean Daphnia that despite having remarkable morphological similarity to the microsporidia, has retained genomic features of its fungal ancestors. This parasite, which we name Mitosporidium daphniae gen. et sp. nov., possesses a mitochondrial genome including genes for oxidative phosphorylation, yet a spore stage with a highly specialized infection apparatus--the polar tube--uniquely known only from microsporidia. Phylogenomics places M. daphniae at the root of the microsporidia. A comparative genomic analysis suggests that the reduction in energy metabolism, a prominent feature of microsporidian evolution, was preceded by a reduction in the machinery controlling cell cycle, DNA recombination, repair, and gene expression. These data show that the morphological features unique to M. daphniae and other microsporidia were already present before the lineage evolved the extreme host metabolic dependence and loss of mitochondrial respiration for which microsporidia are well known.

Defying bacteriophages: Contrasting altruistic with individual-based resistance mechanisms in Escherichia coli.

Adaptations by hosts in response to parasitism are generally believed to reduce the susceptibility of the adapted individual. However, recent work on Escherichia coli showed that bacteria can fight deadly phage attacks by committing altruistic suicide upon infection, in order to prevent parasite transmission to nearby relatives. Here, we compare the efficiency of suicidal host defense with individual-based resistance. We show that in unstructured environments suicidal host defense is futile since suicide cannot preferentially protect relatives, whereas individual-based resistance is highly efficient in defying phages. In contrast, we found that in structured environments suicidal host defense and individual-based resistance were both efficient in withstanding phages, with the latter type performing slightly better. We propose that the putative lower efficiency of suicidal host defense might be compensated by the fact that suicidal systems usually do not bear pleiotropic costs of resistance, as it is usually the case for individual-based resistance mechanisms.

Altruism can evolve when relatedness is low: evidence from bacteria committing suicide upon phage infection.

High relatedness among interacting individuals has generally been considered a precondition for the evolution of altruism. However, kin-selection theory also predicts the evolution of altruism when relatedness is low, as long as the cost of the altruistic act is minor compared with its benefit. Here, we demonstrate evidence for a low-cost altruistic act in bacteria. We investigated Escherichia coli responding to the attack of an obligately lytic phage by committing suicide in order to prevent parasite transmission to nearby relatives. We found that bacterial suicide provides large benefits to survivors at marginal costs to committers. The cost of suicide was low, because infected cells are moribund, rapidly dying upon phage infection, such that no more opportunity for reproduction remains. As a consequence of its marginal cost, host suicide was selectively favoured even when relatedness between committers and survivors approached zero. Altogether, our findings demonstrate that low-cost suicide can evolve with ease, represents an effective host-defence strategy, and seems to be widespread among microbes. Moreover, low-cost suicide might also occur in higher organisms as exemplified by infected social insect workers leaving the colony to die in isolation.

Real-time quantitative PCR to discriminate and quantify lambdoid bacteriophages of Escherichia coli K-12.

Quantification of bacteriophages by real-time quantitative PCR (qPCR) is an interesting alternative to the traditional plaque assay. Importantly, the method should in principle be able to discriminate between closely related phages that are indistinguishable by most other means. Here, a method is presented that employs qPCR to discriminate and quantify ten closely related lambdoid phages of Escherichia coli str. K-12. It is shown that (1) treatment of samples with DNase efficiently removes non-encapsidated DNA, while the titer of plaque forming units is not affected, (2) individual phage types can be accurately quantified in mixed lysates, and (3) the detection limit corresponds to that of a plaque assay. The method is used to quantify individual phage types that are released from lysogens that carry up to three different prophages.

Within-host competition determines reproductive success of temperate bacteriophages.

Within-host competition between parasites is frequently invoked as a major force for parasite evolution, yet quantitative studies on its extent in an organismal group are lacking. Temperate bacteriophages are diverse and abundant parasites of bacteria, distinguished by their ability to enter a facultative dormant state in their host. Bacteria can accumulate multiple phages that may eventually abandon dormancy in response to host stress. Host resources are then converted into phage particles, whose release requires cell death. To study within-host competition between phages, I used the bacterium Escherichia coli and 11 lambdoid phages to construct single and double lysogens. Lysogenic bacterial cultures were then induced and time to host cell lysis and productivity of phages was measured. In double lysogens, this revealed strong competitive interactions as in all cases productivity of at least one phage declined. The outcome of within-host competition was often asymmetrical, and phages were found to vary hierarchically in within-host competitive ability. In double infections, the phage with the shorter lysis time determined the timing of cell lysis, which was associated with a competitive advantage when time differences were large. The results emphasize that within-host competition greatly affects phage fitness and that multiple infections should be considered an integral part of bacteriophage ecology.

Cytological and molecular description of Hamiltosporidium tvaerminnensis gen. et sp. nov., a microsporidian parasite of Daphnia magna, and establishment of Hamiltosporidium magnivora comb. nov.

We describe the new microsporidium Hamiltosporidium tvaerminnensis gen. et sp. nov. with an emphasis on its ultrastructural characteristics and phylogenetic position as inferred from the sequence data of SSU rDNA, alpha- and beta-tubulin. This parasite was previously identified as Octosporea bayeri Jírovec, 1936 and has become a model system to study the ecology, epidemiology, evolution and genomics of microsporidia - host interactions. Here, we present evidence that shows its differences from O. bayeri. Hamiltosporidium tvaerminnensis exclusively infects the adipose tissue, the ovaries and the hypodermis of Daphnia magna and is found only in host populations located in coastal rock pool populations in Finland and Sweden. Merogonial stages of H. tvaerminnensis have isolated nuclei; merozoites are formed by binary fission or by the cleaving of a plasmodium with a small number of nuclei. A sporogonial plasmodium with isolated nuclei yields 8 sporoblasts. Elongated spores are generated by the most finger-like plasmodia. The mature spores are polymorphic in shape and size. Most spores are pyriform (4·9-5·6×2·2-2·3 µm) and have their polar filament arranged in 12-13 coils. A second, elongated spore type (6·8-12·0×1·6-2·1 µm) is rod-shaped with blunt ends and measures 6·8-12·0×1·6-2·1 µm. The envelope of the sporophorous vesicle is thin and fragile, formed at the beginning of the sporogony. Cytological and molecular comparisons with Flabelliforma magnivora, a parasite infecting the same tissues in the same host species, reveal that these two species are very closely related, yet distinct. Moreover, both cytological and molecular data indicate that these species are quite distant from F. montana, the type species of the genus Flabelliforma. We therefore propose that F. magnivora also be placed in Hamiltosporidium gen. nov.

Tuning a genetic switch: experimental evolution and natural variation of prophage induction.

Genetic switches allow organisms to modulate their phenotype in response to environmental changes. Understanding the evolutionary processes by which switches are tuned is central to understanding how phenotypic variation is realized. Prophage induction by phage lambda is the classic example of a genetic switch and allows lambda to move between two different modes of transmission: as a lysogen it reproduces vertically as a component of the host genome; as a free phage it reproduces horizontally by infectious epidemic spread. We show that the lambda switch can respond rapidly to selection for alteration in sensitivity and threshold. Sequencing of candidate genes in the genetic circuitry underlying the switch revealed mutations of likely adaptive significance in some, but not all candidates, suggesting that the core genetic circuitry plays a limited role in the fine-tuning of the switch in vivo. The relative ease with which the switch could be tuned by selection was further indicated by extensive variation in sensitivity and threshold of its response function among wild lambdoid phages. Together, our findings emphasize the adaptive significance of a finely tuned switch and draw attention to the selective factors shaping prophage induction in natural phage populations.

Morphology, molecular phylogeny, and ecology of Binucleata daphniae n. g., n. sp. (Fungi: Microsporidia), a parasite of Daphnia magna Straus, 1820 (Crustacea: Branchiopoda).

We describe a new microsporidian species Binucleata daphniae, n. g., n. sp., that infects the integument cells lining the hemocoele cavity of the carapace and the postabdomen of the cladoceran Daphnia magna Straus. Infected cells filled with spores accumulate as large clusters in the carapace cavity and heavily infected hosts are detected by their opaque appearance. Despite the parasite's presence, infected Daphnia grow and molt, but have a reduced fecundity. During the parasite's life cycle, chain-like meronts with isolated nuclei are formed, giving rise to binucleate presporonts, the most frequently observed, characteristic developmental stage. In sporogony, the nuclei of the presporont separate, divide, and eight spores enclosed in a thin-walled sporophorous vesicle are formed. Spores are 4.9 x 2.5 microm in size (fresh) and have an anisofilar polar filament with eight coils. DNA sequence analysis places B. daphniae in a clade of microsporidians that parasitize crustaceans and mosquitoes and have assumed complex life cycles. Binucleata daphniae, however, has a simple and direct life cycle and can be transferred to naïve hosts and maintained as persistent infections in populations of its host D. magna. We propose that B. daphniae has simplified its life cycle by losing its secondary host, rendering it unique in this clade.

Reverse arrangement of rRNA subunits in the microsporidium Glugoides intestinalis.

The rRNA gene cluster of microsporidia is typically arranged in the order small subunit-internal transcribed spacer-large subunit, which conforms with the general arrangement of these genes in nearly all organisms. We found a rearrangement of the cluster in the microsporidium Glugoides intestinalis, where the large subunit precedes the small subunit. Such a rearrangement has already been reported for several species in the microsporidian genus Nosema, and we provide evidence that the arrangement reported here is a second, independent event.

Octosporea bayeri: fumidil B inhibits vertical transmission in Daphnia magna.

Microsporidia are a highly successful and ecologically diverse group of parasites, and thus represent interesting model systems for research on host-parasite interactions. However, such research often requires the ability to cure hosts of infections, a difficult task, given the short lifespan of most invertebrates and the efficient vertical transmission of some parasites. To our knowledge, few treatments are available to cure microsporidiosis in invertebrate hosts, and protocols have not yet been developed to inhibit vertical transmission and thereby cure host lines. We present a protocol for inhibiting vertical transmission of the microsporidian parasite Octosporea bayeri in the freshwater crustacean Daphnia magna. We used 100 mg/L Fumidil B dissolved in the culture medium of the host. This technique allowed Daphnia to survive and reproduce and inhibited vertical transmission of the parasite. The method presented here may be of general interest for other aquatic host-parasite systems involving microsporidia.