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Molecular Geomicrobiology is the molecular level understanding of microbial activities both in past and present ecosystems. I combine molecular microbiology & organic biogeochemistry techniques to determine:
- Biological sources of lipid biomarkers
- Evolutionary acquisition of lipid biomarkers
- Regulation of microbial lipid synthesis
- Abundance, activity & distribution of key players of carbon, nitrogen and sulfur cycles in marine systems
Education & research experience
11/2013-present: Senior Research Scientist (tenured) at the Department of Marine Microbiology and Biogeochemistry, NIOZ.
Topic: Molecular evolution of lipid synthetic pathways. Anaerobic microorganisms involved in carbon, nitrogen and sulfur cycles. Metagenomics and lipidomics.
10/2009-11/2013: Tenure-track Research Scientist (Geomicrobiology) at the Department of Marine Organic Biogeochemistry, NIOZ.
Topic: Microbial ecology of microorganisms involved in the nitrogen cycle. Lipid biomarkers marine Thaumarchaeota.
2007-2009: Postdoctoral fellow at the Center for Systems Biology at Harvard University (MA, USA).
Topic: Evolution of bacteriophage-host specificity.
2006-2007: Postdoctoral fellow at the Department of Microbiology in the University of Massachusetts (Amherst, MA, USA).
Topic: Anaerobic culturing and gene expression in Desulfovibrio
1/2002–12/2005: PhD in Microbial Ecology in the Department of Microbiology, Faculty of Biology, University of Barcelona (Spain).
Title: Ecophysiological and molecular characterization of estuarine microbial mats. Diploma of European Mention.
Lipid biosynthetic pathways
My research is focused on lipid biomarkers of certain organisms either because they are markers of the presence of a specific group (e.g. ladderane lipids of anammox bacteria), physiological condition (e.g. ornithine lipids, thought to be formed under phosphate limitation), or mostly because they have been seen to correlate to growth temperature and thus used to estimate paleotemperature (e.g. long chain alkenones, GDGTs, and long chain diols involved in the organic paleotemperature proxies UK37, TEX86 and LDI).
In order to improve the predictive nature of lipid biomarkers used for microbial ecology and in paleotemperature proxies it is essential to determine the following:
•Their biological source/s, as well as seasonality and spatial distribution of the source/s.
•How changes in physicochemical conditions influence the abundance and distribution of these biomarkers
•How and when these biomarkers have been acquired through evolution and how these capacity has been spread among different biological taxa
For doing so, I combine lipid analysis with molecular techniques based on:
•Analyzing lipid synthetic pathways: evolution and prediction of gene function
•Targeting phylogenetic, metabolic and lipid biosynthetic genes as markers for the presence of lipid biomarker producers.
•Estimating which physicochemical conditions that induce changes in the synthesis of lipid biomarkers.
Thaumarchaeota diversity and ecophysiology
Members of the Thaumarchaeota phylum have been found to be ubiquitous in marine, freshwater, soils (and others) environments. So far it has been assumed that all thaumarchaeota are chemolithoautotrophs and ammonia oxidizers based on the presence of a unique carbon fixation pathway and the gene coding for ammonia monooxygenase (amoA gene). These physiological characteristics, as well as the relative high abundance of this group in some environments, suggest an important role of Thaumarchaeota in the carbon and nitrogen cycles. In addition, it has been observed that all cultured representatives of the Thaumarchaeota uniquely synthesize the glycerol dialkyl glycerol tetraether (GDGT) crenarchaeol (with 4 cyclopentane and a cyclohexane moiety), which is considered as a biomarker for the presence of this group. The relative abundance of thaumarchaeotal membrane lipids (GDGTs with zero to 4 cyclopentane moieties, GDGT-0 to GDGT-4, and crenarchaeol) has been shown to be correlated with the temperature at which these organisms are growing. Based on this the TEX86 (TetraEther indeX of tetraethers consisting of 86 carbon atoms) paleotemperature proxy was developed and further tested to reconstruct the temperature in past environments.
Anaerobic bacteria involved in Nitrogen and Methane cycles
The re-mineralization of organic matter in anoxic sediments is mainly driven by fermentative microorganisms, sulfate reducers, and methanogens. However, there is a general lack of knowledge on the diversity, abundance and activity of the anaerobic microorganisms involved (directly or indirectly) in organic matter recycling in anoxic sediments.
Methanogens (strictly anaerobic archaea) biologically produce methane, a trace greenhouse gas in the earth’s atmosphere the concentration of which has doubled since industrialization. On its way to the atmosphere, methane travels through anaerobic sediments, passing through zones dominated by different regimes of anaerobic respiration before reaching the aerobic sediment or oxic water column. Along this route methane can be oxidized, which significantly decreases/mitigates the effective emission of this greenhouse gas to the atmosphere. However, it is unclear how ecosystems to different physicochemical conditions with respect to methane production, consumption and thus ultimately emissions to the atmosphere.
Our aim is to improve our understanding of the microbial players involved in anaerobic organic matter remineralization and also specifically focus on those involved in the methane cycle. We also want to assess their individual niches, metabolic pathways, environmental significance, interactions, and their response to environmental changes. Ultimately this information will be key to explore their potential use in biotechnology and to design mitigation strategies for greenhouse gas emission.
This research is conducted in the framework of the Soehngen Institute for Anaerobic Microbiology SIAM (Gravitation grant- Zwaartekracht, from the Dutch Ministry of Education, Culture and Science, read more here) in which the Radboud University, Wageningen University, Delft University of Technology, and NIOZ Royal Netherlands Institute for Sea Research participate.
Phone: +31 0222-369-428
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