Current research project:
Investigating the microbial ecology of soils in Switzerland
This is a large scale project funded by the Swiss federal office for the environment and Agroscope to increase our knowledge on the microbial ecology of soils. Soils in Switzerland are very diverse in form and content, ranging from highly fertile arable land, over forests and pastures to low organic content and comparably thin soils above rocky beds in alpine areas. Soil ecosystems are extremely heterogeneous and complex, with a wide array of external influences and soil community interactions. Particularly in arable land, the soil quality is one of the fundamental factors for crop production and is of extreme importance. However, there is still a gap of knowledge on the microbial diversity in soils, on their interactions as well as the stability or vulnerability of soil ecosystems towards external influences. The first objective of this project is therefore to set up a genetic database of soil microbes and link it to soil characteristics and data on the above-ground ecosystem.
(Agroscope Swiss centre of excellence for agricultural research, Institute for Sustainability Sciences, Group of Molecular Ecology)
Previous research project (2014-2016):
Snow is more than frozen water – microbial ecology of the nival zone
(Post-doctoral fellowship at Inst. of Biological Sciences, Macquarie University, Sydney, Australia)
Snow environments are found in many regions on earth and harbor ecologically interesting organisms that have adapted to the extreme cold, little water and nutrients, high radiation and extreme wind conditions. In the last decades, alarming changes due to global warming (melting of glaciers, reduced snowfall) have been recorded both in polar and mountainous snow regions. Little is known about the microorganisms that are living in snow and we do not know their ability to adapt to a changing climate. In this study, a detailed inventory of microbial organisms found in snow will be undertaken via gene sequencing approaches. Our data will provide answers to the following questions: What is the diversity and functional array of snow microbes? Is there a difference between active and inactive microbial assemblages in the snow pack? Is there a global biogeographic pattern of snow microbes across different snow regions on Earth? What enzymatic and genetic tools do microbes have in order to survive in cold, dry and nutrient-poor environments?
Previous research project (2010-2014):
Diversity of endospore-forming bacteria in sediment as a proxy for environmental lake history
(PhD at Laboratory of Microbiology, University of Neuchâtel, Switzerland)
Freshwater systems are heavily subjected to anthropogenic pressure such as input of pollutants, overshing, changes in climate regime, and eutrophication (high nutrient input). For environmental management and the implementation of conservation measures, the dynamics of freshwater ecosystems need to be known and biological reference conditions have to be established against which future changes can be measured. Baseline knowledge about biodiversity and ecosystem responses to environmental perturbations in lakes can be obtained from the sediments that provide an ideal environmental archive of past conditions. The thesis presented research on the diversity detection of bacterial endospores, and its use as proxy to reconstruct the environmental history of the last 100 years of Lake Geneva at the border of France and Switzerland.
Endospores are resistant structures formed when bacteria are under stress. Once these endospores are deposited in the sediment they remain dormant and serve as natural biological time capsules, archiving the conditions at the time of sedimentation. To infer the diversity of endospores for this work, two specic methods for targeted metagenomics were developed and validated in sediments. Metagenomics is a sequencing approach of the entire genetic pool directly retrieved from an environmental sample. Similarly, targeted metagenomics is based on a targeted genetic pool, for example a sub-community of the sample. Targeted metagenomics increases the sequencing coverage and resolution of detection, circumventing common problems of traditional metagenomics studies.
The first targeting method was based on a molecular marker for endospore-forming bacteria, the global transcription regulator of sporulation (spo0A). After an optimized DNA extraction method for endospores in sediment, where biomass was separated from the sediment particles (indirect DNA extraction), the spo0A gene fragment was amplified and sequenced to determine the diversity of the endospore-forming bacteria (vegetative cells and endospores) in sediments. The second targeting method consisted of a treatment to separate the endospores from vegetative cells, prior to DNA extraction and sequencing. The goal of the treatment was to destroy vegetative cells that are generally more fragile, while leaving the more resistant endospores intact. With this method, the diversity of only the endospores in sediment was detected. The treatment to separate endospores was successful, as shown by an enrichment of endospore-forming bacteria from 10% abundance in the global approach to over 90% abundance in the targeted metagenome. Also the resolution was improved to up to 10-fold increase in detected endospore-forming taxa. The better resolution led to the detection of 34 genera unique to the targeted metagenome, including some supposedly asporogenic groups like Ethanoligenens and Trichococcus and high numbers of sequences that could be classied to a species level such as Bacillus longiquaesitum or Clostridium bowmanii.
The application of targeted metagenomics to a sediment core retrieved from Lake Geneva spanning a time period from 1921 to 2010, revealed substantial diversity of endospore-forming bacteria in sediments. The diversity fluctuated significantly in the last 100 years, reflecting the eutrophication period from 1960 to 1990 as well as sulfate metabolism, input of terrestrial organic matter, and specic climate events. The shift in the community composition during eutrophication was linked to a dominance of anaerobic Clostridia-like members, that reflect anoxic sediment conditions during this time.
The advantage of the treatment is that the communities in vegetative cell state could be differentiated from the communities present as dormant endospores. Using this differentiation
we reported activity of selected endospore-forming bacteria in sediment, for example members from genus Clostridium and Heliobacterium at the sediment surface. In contrast, a small fraction of dormant endospores present at high diversity represent the microbial seed bank. This group of bacteria is inactive for long periods of time but selected members can propagate and become dominant if the environmental conditions change to their favour, as was observed in this study for Desulfotomaculum, Sporomusa or Brevibacillus. The novel targeted metagenomics approaches developed in this work provided a signicant experimental improvement to explore the diversity of endospore-forming bacteria at high resolution. The data provided knowledge on the role of endospore-forming bacteria in freshwater sediment and on freshwater sediment bacteria in general. It is also the first report of metagenomics to reveal the diversity of endospores in sediment and the use of endospores as paleolimnological proxies.