Outside-host phage therapy as a biological control against environmental infectious diseases

Background

Environmentally growing pathogens present an increasing threat for human health, wildlife and food production. Treating the hosts with antibiotics or parasitic bacteriophages fail to eliminate diseases that grow also in the outside-host environment. However, bacteriophages could be utilized to suppress the pathogen population sizes in the outside-host environment in order to prevent disease outbreaks. Here, we introduce a novel epidemiological model to assess how the phage infections of the bacterial pathogens affect epidemiological dynamics of the environmentally growing pathogens. We assess whether the phage therapy in the outside-host environment could be utilized as a biological control method against these diseases. We also consider how phage-resistant competitors affect the outcome, a common problem in phage therapy. The models give predictions for the scenarios where the outside-host phage therapy will work and where it will fail to control the disease. Parameterization of the model is based on the fish columnaris disease that causes significant economic losses to aquaculture worldwide. However, the model is also suitable for other environmentally growing bacterial diseases.

Results

Transmission rates of the phage determine the success of infectious disease control, with high-transmission phage enabling the recovery of the host population that would in the absence of the phage go asymptotically extinct due to the disease. In the presence of outside-host bacterial competition between the pathogen and phage-resistant strain, the trade-off between the pathogen infectivity and the phage resistance determines phage therapy outcome from stable coexistence to local host extinction.

Conclusions

We propose that the success of phage therapy strongly depends on the underlying biology, such as the strength of trade-off between the pathogen infectivity and the phage-resistance, as well as on the rate that the phages infect the bacteria. Our results indicate that phage therapy can fail if there are phage-resistant bacteria and the trade-off between pathogen infectivity and phage resistance does not completely inhibit the pathogen infectivity. Also, the rate that the phages infect the bacteria should be sufficiently high for phage-therapy to succeed.

     

Adaptation to fluctuations in temperature by nine species of bacteria

Rapid environmental fluctuations are ubiquitous in the wild, yet majority of experimental studies mostly consider effects of slow fluctuations on organism. To test the evolutionary consequences of fast fluctuations, we conducted nine independent experimental evolution experiments with bacteria. Experimental conditions were same for all species, and we allowed them to evolve either in fluctuating temperature alternating rapidly between 20°C and 40°C or at constant 30°C temperature. After experimental evolution, we tested the performance of the clones in both rapid fluctuation and in constant environments (20°C, 30°C and 40°C). Results from experiments on these nine species were combined meta‐analytically. We found that overall the clones evolved in the fluctuating environment had evolved better efficiency in tolerating fluctuations (i.e., they had higher yield in fluctuating conditions) than the clones evolved in the constant environment. However, we did not find any evidence that fluctuation‐adapted clones would have evolved better tolerance to any measured constant environments (20°C, 30°C, and 40°C). Our results back up recent empirical findings reporting that it is hard to predict adaptations to fast fluctuations using tolerance curves.     

Micro‐fungi and invertebrate herbivores on birch trees: fungal mediated plant–herbivore interactions or responses to host quality?

We studied interactions between microfungi and herbivores sharing a host tree. In a series of experiments and field observations over a 3‐year period, we compared phenotypic and genetic correlations of fungal frequencies and performance of invertebrate herbivores growing on mature half‐sib progenies of mountain birches (Betula pubescens ssp. czerepanovii) in two environments, a forested river valley and an adjacent higher‐elevation mountain birch woodland. We found little support for direct relation between fungal frequencies and performance of herbivore species. Instead, genetic correlations, particularly between autumnal moth (Epirrita autumnata) and rust fungus (Melampsoridium betulinum), suggest that herbivore performance may be caused by (1) genetic differences in plant quality for fungi and herbivores, or (2) genetic differences in responses to environmental conditions.     

The invasive herb <Emphasis Type="Italic">Lupinus polyphyllus</Emphasis> attracts bumblebees but reduces total arthropod abundance

Invasive plant species generally reduce the abundance and diversity of local plant species, which may translate into alterations at higher tropic levels, such as arthropods. Due to the diverse functional roles of arthropods in the ecosystems, it is critical to understand how arthropod communities are affected by plant invasions. Here, we investigated the impact of the invasive ornamental herb Lupinus polyphyllus (Lindl.) on arthropod communities during its main flowering period in southwestern Finland over two years. The total number of arthropods was about 46% smaller at the invaded sites than at the uninvaded sites in both study years, and this difference was mainly due to a lower abundance of beetles, Diptera, Lepidoptera, and ants. However, the number of bumblebees (particularly Bombus lucorum) was about twice as high at invaded sites compared with uninvaded sites, even though bumblebee richness did not differ between sites. There was no statistically significant difference between invaded and uninvaded sites in the abundances of the other arthropod groups considered (Hymenoptera (excluding bumblebees and ants), Hemiptera, and Arachnida). In addition, L. polyphyllus affected the relative abundance of four arthropod groups, with the order Lepidoptera being less common at invaded sites than at uninvaded sites, while the opposite was true for bumblebees, Hemiptera, and Arachnida. Overall, these results demonstrate that the negative impact of L. polyphyllus on biodiversity goes beyond its own trophic level, suggesting that this species has the potential to alter the abundance of different arthropod groups and, consequently, the structure of arthropod communities at a large scale.     

Maternal effects in vulnerability to eye‐parasites and correlations between behavior and parasitism in juvenile Arctic charr

Hatchery‐reared fish show high mortalities after release to the wild environment. Explanations for this include potentially predetermined genetics, behavioral, and physiological acclimation to fish farm environments, and increased vulnerability to predation and parasitism in the wild. We studied vulnerability to Diplostomum spp. parasites (load of eye flukes in the lenses), immune defense (relative spleen size) and antipredator behaviors (approaches toward predator odor, freezing, and swimming activity) in hatchery‐reared juvenile Arctic charr (Salvelinus alpinus) using a nested mating design. Fish were exposed to eye‐fluke larvae via the incoming water at the hatchery. Fish size was positively associated with parasite load, but we did not find any relationship between relative spleen size and parasitism. The offspring of different females showed significant variation in their parasite load within sires, implying a dam effect in the vulnerability to parasites. However, the family background did not have any effect on spleen size. In the mean sire level over dams, the fish from the bolder (actively swimming) families in the predator trials suffered higher loads of eye flukes than those from more cautiously behaving families. Thus, the results indicate potentially maternally inherited differences in vulnerability to eye‐fluke parasites, and that the vulnerability to parasites and behavioral activity are positively associated with each other at the sire level. This could lead to artificial and unintentional selection for increased vulnerability to both parasitism and predation if these traits are favored in fish farm environments.     

Comparison of 1D and 2D NMR spectroscopy for metabolic profiling

High-resolution, liquid state nuclear magnetic resonance (NMR) spectroscopy is a popular platform for metabolic profiling because the technique is nondestructive, quantitative, reproducible, and the spectra contain a wealth of biochemical information. Because of the large dynamic range of metabolite concentrations in biofluids, statistical analyses of one-dimensional (1D) proton NMR data tend to be biased toward selecting changes in more abundant metabolites. Although two-dimensional (2D) proton-proton experiments can alleviate spectral crowding, they have been mainly used for structural determination. In this study, 2D total correlation spectroscopy NMR was used to compare the global metabolic profiles of urine obtained from wild-type and Abcc6-knockout mice. The 2D data were compared to an improved 1D experiment in which signal contributions from macromolecules and the urea peak have been spectroscopically removed for more accurate quantitation of low-abundance metabolites. Although statistical models from both 1D and 2D data could differentiate samples acquired from the two groups of mice, only the 2D spectra allowed the characterization of statistically relevant changes in the low-abundance metabolites. While acquisition of the 2D data require more time, the data obtained resulted in a more meaningful and comprehensive metabolic profile, aided in metabolite identifications, and minimized ambiguities in peak assignments.     

Grouping PCBs with Minimum Feeder Changes

In printed circuit board (PCB) assembly, the majority of electronic components are inserted by high-speed placement machines. Although the efficient utilization of the machinery is important for a manufacturer, it is hard to fully realize in high-mix low-volume production environments. On the machine level, the component setup strategy adopted by the manufacturer has a significant impact on the overall production efficiency. Usually, the setup strategy is formulated as a part type grouping problem or a minimum setup problem. In this article, we consider a hybridization of these two problems for the single machine case: The object function to be minimized includes a weighted sum of the number of part type groups (giving the number of setup occasions) and the number of feeder changeovers. We present algorithms for the problem and compare their efficiency.     

Combined effects of loose wood ash and carbon on inorganic N and P, key organisms, and the growth of Norway spruce seedlings and grasses in a pot experiment

The effects of wood ash on the growth of Norway spruce seedlings and grasses, nitrogen and phosphorus leaching, and soil fauna were investigated at two levels of carbon availability in a greenhouse experiment simulating harvested boreal forest. While sucrose-C amendment reduced grass biomass regardless of wood ash by 88%, the shoot and root biomass of spruce seedlings increased by 38% and 370%, respectively. Despite the large variation in above-ground biomass, C addition did not alter the concentration of water extractable ammonium nitrogen in humus, but it counteracted the ash-induced increase in soil phosphate concentration. C addition reduced the proportion of bacterial-feeding nematodes in the nematode community. Wood ash reduced enchytraeid size, but their biomass was not affected. Carbon treatment was crucial for enchytraeids probably because amended pots were moister than controls. Small compensatory grass growth following harvest implied that soil fauna made little nitrogen available to plants in one growing season. The results support the hypothesis that C availability may be an important determinant of nutrient retention, and has the potential to control plant competition in intensively harvested forests.     

The non-ribosomal assembly and frequent occurrence of the protease inhibitors spumigins in the bloom-forming cyanobacterium Nodularia spumigena

Nodularia spumigena is a filamentous nitrogen-fixing cyanobacterium that forms toxic blooms in brackish water bodies worldwide. Spumigins are serine protease inhibitors reported from a single strain of N. spumigena isolated from the Baltic Sea. These linear tetrapeptides contain non-proteinogenic amino acids including a C-terminal alcohol derivative of arginine. However, very little is known about these compounds despite the ecological importance of N. spumigena . We show that spumigins are assembled by two non-ribosomal peptide synthetases encoded in a 21 kb biosynthetic gene cluster. The compact non-ribosomal peptide synthetase features a reductive loading and release mechanism. Our analyses demonstrate that the bulk of spumigins produced by N. spumigena are released as peptide aldehydes in contrast to earlier findings. The main spumigin E variant contains an argininal residue and is a potent trypsin inhibitor. Spumigins were present in all of the N. spumigena strains isolated from the Baltic Sea and comprised up to 1% of the dry weight of the cyanobacterium. Our results demonstrate that bloom-forming N. spumigena strains produce a cocktail of enzyme inhibitors, which may explain in part the ecological success of this cyanobacterium in brackish water bodies worldwide.