Phages as vectors and indicators for biological information: Phage transport and phage-mycosphere interactions

Bacterial viruses, also known as phages, are intrinsic components of the Earth’s Critical Zone (CZ). Together with diverse communities of bacteria and fungi, they occupy habitats of the CZ extending from the vegetation canopy, through the soils and into the aquifers. In this thesis, I aimed to study the transport of phages in the upper CZ and their interactions with non-host soil bacteria and fungi to reveal their role in regulating the CZ microbial life. To reflect transport processes of CZ-inhabiting phages in soil tracers are highly useful. Thus, in the first study, I evaluated the transport efficiency and particle intactness of marine tracer phages passing through soil. Marine phages were selected as tracer, because they are non-pathogenic, non-toxic, naturally absent and thus non-multiplying in the terrestrial subsurface. I found that the marine phages PSA-HM1 and PSA-HS2 retained high phage particle intactness in contrast to commonly used Escherichia virus T4. This suggests their potential as particle tracers to mimic the transport of (bio-) colloids of similar traits in soil. Soil in the CZ is often unsaturated and restricts mobility of microorganisms. Fungi bridge unsaturated zones in soil and hence provide network for microbial transport. In the second study, I developed a hyphosphere model system mimicking unsaturated soil environment, and reported on the ability of hyphal-riding bacteria to co-transport lytic phages and to utilize phages as “weapons” for improved colonization of water-unsaturated habitats. As the findings emphasize the importance of hyphal transport of bacteria and associated phages, in the third study, I developed a hyphae-assisted approach and isolated five soil bacteria able to co-transport phages. In analogy to invasion frameworks in macroecology, the hyphosphere model system with bacteria and co-transported phages can be useful models to simulate processes of biological invasion at micro-scale. In the fourth study, I investigated dormant phages (i.e. prophages) that are widespread in the CZ and can be induced under environmental stress. I found that volatile fungal metabolites can act as triggers for prophage induction and may exert long-distance manipulation of prophage activity thereby affecting microbial community and nutrient cycling in soil. Altogether, the findings may help to elucidate transport processes of phages in the CZ and to reveal the role of phages in the CZ microbial ecosystem. Approaches (e.g. phage as tracers) and findings (e.g. phage-bacterial co-transport) may also serve as useful tools for testing hypothesis in other disciplines, such as hydrogeology, invasion ecology and chemical ecology

Gluon contribution to open heavy-meson production in heavy-ion collisions

A sizable contribution to heavy quark production in high-energy hadronic and nuclear collisions comes from heavy quark-antiquark pair production from gluon splitting during the parton shower evolution. We investigate the effect of gluon-medium interaction on open heavy flavor spectra in ultra-relativistic heavy-ion collisions. The interaction of hard gluons and heavy quarks with the hot QCD medium is simulated by utilizing a Langevin transport model that simultaneously incorporates contributions from collisional and radiative processes. It is found that while the gluon splitting channel has quite an important contribution to the single $D$ meson production cross section, its influence on the final heavy meson nuclear modification turns out to be quite modest because the average lifetime of hard gluons is short before splitting into heavy quark-antiquark pairs during the evolution and propagation of the parton shower.Comment: 5 pages, 6 figure

Parton Energy Loss and the Generalized Jet Transport Coefficient

We revisit radiative parton energy loss in deeply inelastic scattering (DIS) off a large nucleus within the perturbative QCD approach. We calculate the gluon radiation spectra induced by double parton scattering in DIS without collinear expansion in the transverse momentum of initial gluons as in the original high-twist approach. The final radiative gluon spectrum can be expressed in terms of the convolution of hard partonic parts and unintegrated or transverse momentum dependent (TMD) quark-gluon correlations. The TMD quark-gluon correlation can be factorized approximately as a product of initial quark distribution and TMD gluon distribution which can be used to define the generalized or TMD jet transport coefficient. Under the static scattering center and soft radiative gluon approximation, we recover the result by Gylassy-Levai-Vitev (GLV) in the first order of the opacity expansion. The difference as a result of the soft radiative gluon approximation is investigated numerically under the static scattering center approximation.Comment: 33 pages in RevTeX with 30 figures, final version appeared in PRD with additional typos correcte

Optical isolation with nonlinear topological photonics

It is shown that the concept of topological phase transitions can be used to design nonlinear photonic structures exhibiting power thresholds and discontinuities in their transmittance. This provides a novel route to devising nonlinear optical isolators. We study three representative designs: (i) a waveguide array implementing a nonlinear 1D Su-Schrieffer-Heeger (SSH) model, (ii) a waveguide array implementing a nonlinear 2D Haldane model, and (iii) a 2D lattice of coupled-ring waveguides. In the first two cases, we find a correspondence between the topological transition of the underlying linear lattice and the power threshold of the transmittance, and show that the transmission behavior is attributable to the emergence of a self-induced topological soliton. In the third case, we show that the topological transition produces a discontinuity in the transmittance curve, which can be exploited to achieve sharp jumps in the power-dependent isolation ratio.Comment: 11 pages, 7 figure