Molecular Ecology

Our Research

We focus on the diversity, structure and function of natural microbiomes in groundwater, as well as in related terrestrial aquatic, soil and subsurface habitats. The investigated microbial community functions directly relate to water quality, the turnover of water pollutants and nutrients, and to complex microbe-habitat interactions. We work in pristine and contaminated aquifers, in urban, engineered and drinking water systems, in plant and agricultural systems, as well as in some exotic habitats such as caves and springs. Groundwater is one of mankind's most important drinking water resources, and chemical and microbiological water quality is a central topic in all of our projects. Thus we contribute important fundamental understanding to the achievement of a central millennium target defined by the UN, the access to safe water for drinking purposes and daily use.

Much of the research in our group is based on the so-called "key population" concept, advocating that only defined components of the complex microbiota found in environmental systems are actually relevant for specific functions. Absence or loss of such key populations may cause a decline of functionality. At the same time, the targeted identification and characterisation of such foundation species is often pivotal to understand the controls of environmental processes, such as pollutant degradation or pathogen removal in groundwater.

To a large part, this research is driven by the development and application of advanced molecular 'omics' technologies in combination with targeted labelling, where my group hosts a distinctive and cutting-edge research expertise. The well-known "stable isotope probing" (SIP) of nucleic acids has been pioneered by my group not only for groundwater systems, and we continue to push the development of such technologies to grasp the functionalities of key microbial populations in water, soil, the rhizosphere, food webs and microbe-host systems. These targeted strategies are a crucial asset to the non-target 'omics' approaches often used in in environmental and health microbiome research, and we have a long-standing practice of availing this know-how to project partners e.g. at the Helmholtz Zentrum München and at national and international University partners.

Current Projects

The POLLOX Project (ERC CoG)

Two central paradigms are currently understood to control biodegradation in groundwater and sediments: (i) Redox gradients and interphases between compartments are 'hot-spots' of for contaminant breakdown, and (ii) biodegradation is primarily limited by local electron acceptor availability, in particular that of oxygen. My group has published leading contributions to this understanding in recent years, especially in elucidating the ecology of anaerobic toluene degraders in aquifers.

This project now aims to question these established paradigms and to elaborate a ground-breaking new perspective of the role of molecular oxygen in what is currently considered as pollutant degradation in anoxic compartments. POLLOX postulates that oxygen-dependent degradation of pollutants in anaerobic compartments is possible by two unrecognised physiological adaptations of microbes. In a cutting-edge and interdisciplinary research endeavour, we aim to verify the hypothesis that filamentous Desulfobulbaceae and other so-called "cable bacteria" can anaerobically oxidise pollutants via long-distance (1-2 cm) transfer of electrons to oxygen across redox gradients. Second, we postulate that oxygenase-dependent degraders and catabolic pathways, in absence of external oxygen, can still be active in reduced compartments via self-sustained oxygenesis by nitric oxide dismutation.

The objectives of POLLOX have the potential to revolutionise the current perception of the role and relevance of molecular oxygen as an agent in contaminant degradation groundwater, and of how microbes can circumvent physical limitations (e.g. of mixing) in porous media. Moreover, the investigated electromicrobiological mechanisms and "intra-aerobic" catabolic pathways are both nascent fields, which may span widely not only the degradation of contaminants of emerging concern, but also health-related anaerobic microbiology. 

Ecology of anaerobic Hydrocarbon Degraders

We focus on anaerobic toluene degradation as a model system. We have pioneered the development of a widely applicable catabolic marker gene assay targeting a fragment of the benzylsuccinate synthase alpha-subunit (bssA) gene, the key-enzyme of anaerobic toluene-oxidation. Such molecular assays are a viable tool to characterize intrinsic degrader communities in hydrocarbon contaminated aquifers. We seek to understand how the diversity in a given catabolic gene pool relates to the ecological niches potentially filled by local degraders, and to functional redundancy. Together with feedback mechanisms between hydraulic, geochemical and biotic habitat parameters, this promotes an enhanced ecological perspective of the anaerobic degradation of hydrocarbons, which must be incorporated into updated concepts for site monitoring and bioremediation.

Biofilms in the Water Cycle

Biofilms are a fundamental entity of microbial life in all aquatic systems and especially important for chemical and biological water quality also in source and drinking water systems. Our group has embarked on this topic in collaboration with local water suppliers where we investigate the functioning of polymicrobial biofilms in drinking water distribution systems. In collaboration with the Bavarian Landesamt für Umwelt in Hof, we are currently also investigating the massive biofilm formation discovered in a peculiar methane-fuelled, iodine-rich former medicinal spring in Southern Germany. We aim to elucidate the drivers of this biofilm formation and unravel potential couplings between biogeochemical methane- and iodine-cycling in this unique subsurface system. The impact of biofilm microbiota on hygienic water parameters and on possible health-impacts of the former medicinal spring are also considered.

Picture: T. Lüders

Microbiota-mediated Carbon Fluxes

Microbial interactions and food webs control the flow of carbon and energy in most habitats. While the controls of the fluxes are often still poorly understood, the unravelling of keystone microbial populations involved in these processes is an important prerequisite. Hence the identity and diversity of microbiota involved in given turnover process has a significant impact on the rate and fate of respective fluxes, together with the nature and quality of the carbon source and the biogeochemical habitat conditions. Our group has a well-defined profile in tackling such questions for complex environmental microbiota, i.E. for microbial food webs, for plant-derived carbon fluxes in soil, or for microbial carbon and energy sharing in pollutant degradation.

Nitrogen Cycling in Water Systems

Increasing anthropogenic nitrogen loading in catchments is a serious threat to our water resources. Yet while the ecophysiologies of reductive (denitrification) or oxidative (nitrification) nitrogen cycling are well understood on the microbe level, the controls of these processes and populations on the watershed level are still poorly understood. In a project within the Helmholtz WasserZentrum München, our group has embarked on the elucidation of hydraulic feedback mechanisms on the activity of N-cycling natural microbiota in sedimentary systems. This work is also currently extended towards detecting potentially overlooked microbial populations active in NO-dismutation within the POLLOX project. In a habitat perspective, we aim to apply labelling-assisted molecular approaches to localize and quantify natural N-cycling populations and to predict turnover processes at the catchment scale.

Labelling-assisted targeted Environmental ‘Omics’

Our group has a strong record in combining targeted stable isotope probing (SIP) approaches with advanced DNA- and rRNA-based 'omics'. We combine SIP with next generation sequencing and are constantly aiming to develop even more advanced labelling strategies for keystone microbiota. Currently, we are striving to combine SIP with targeted environmental transcriptomics, which will, for the first time, allow accessing the most important expressed functions related to given turnover processes in time and space within natural microbial communities. This methodological development is also embedded within the POLLOX ERC project, but will be widely applicable to microbial activities and interactions in environmental and host systems.