Emmy Noether Research Group "Viral Ecology"

Research Topics

Viruses, especially (bacterio)phages (viruses infecting bacteria), typically outnumber microbial cells ~10-fold in aquatic systems, recasting them from environmentally insignificant to the most abundant biological entities on Earth. Viruses are now considered as ubiquitous players that impact microbial communities through mortality and horizontal gene transfer to modulate microbial metabolism. During the last years diverse phenomena critical to the biology of microbes have been described to be driven by viruses, especially with respect to rapid environmental changes. The view that viruses are “only” parasites is no longer valid but viruses rather are able to transfer and store genetic information of their hosts and influence biogeochemical cycles in ecosystems. Consequently biogeochemical processes in microbial ecosystems and their potential for novel niche adaptation in response to changing environmental conditions can be understood only when this large dynamic gene pool carried by lytic and temporary viruses is recognized.

In our lab, we take an integrated approach to investigate microbes-viruses interactions by combining microcosm experiments employing model microbes and viruses, and culture-independent, high-throughput metagenomics. We are currently focusing on viruses from both environment (especially groundwater) and human (especially lung).


  1. The role of viruses in contaminant biodegradation

Contamination with organic pollutants, such as petroleum hydrocarbons, is widespread in groundwater and a notorious threat to our water resources. Biodegradation is the most important and sustainable process for contaminant breakdown. The biological activity that governed by numerous processes of which the current perspective is only evolving hydrology, biogeochemistry and environmental microbiology. One important piece of the puzzle, however, has been rarely touched: viruses.

We aim to elaborate a ground-breaking new perspective, the viral-driven degradation. We hypothesize that degradation of contaminants is greatly impacted by viruses through (i) horizontally transfer host metabolic genes related to contaminant degradation, and (ii) specifically lysing key bacterial degraders. In a cutting-edge and interdisciplinary research endeavor in the IGÖ, we seek to elaborate the role for viruses that is currently a “black box” and beyond our classical view of the stratification of microbial activities in redox gradients.


  1. Viruses – the hidden players in health-related microbial processes

The newly recognized key roles viruses play in the environment are hypothesized to be active in human-associate inner environments, such as lung and gut. Indeed, there is first evidence that, during antibiotic treatment, viruses in human gut temporarily store bacterial genetic information needed for the bacteria to recover later.

We seek to understand the overall impact of environmental factor driving the structure of viruses colonizing the lung surface and to investigate their impacts on human health and diseases development.

In the last year, we were able to identify major community members of human lung virome from both healthy and chronic obstructive pulmonary disease (COPD) patients in the framework of HMGU Environmental Health Project. Our preliminary data indicate (i) human lung virome are closely influenced by environment, especially by drinking water/groundwater; (ii) a surprisingly high abundance and diversity of human lung virome and suggesting viruses playing an important role to dramatically alter lung bacterial community structure and function; (iii) a close cross link between viruses and the bacterial quorum sensing system. The latter constitute a master regulator of bacterial activity and life style, thus are considered to play a major role in the mechanistic interaction of the microbiome within the lung, especially in the lung of cystic fibrosis and COPD patients (Deng et al., in prep). 

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