Royal Netherlands Institute for Sea Research

Dr. Laura Villanueva

Senior Scientist
Phone number
+31 (0)222 369 428
Location
Texel
Function
Senior Scientist

Expertise

  • Geomicrobiology
  • Organic geochemistry
  • Microbial ecology
  • Molecular evolution
  • Lipid biosynthesis
See more about me @NIOZ here

 

Research interests

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.

 

Research interests

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.
 

Contact me!

Phone: +31 0222-369-428

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Learn more about my research in my blog

 

Linked blogs

Wednesday 29 March 2017
NIOZ@Sea: Black Sea cruise
This edition of NIOZ@Sea is a series of blogs from the Black Sea cruise of our scientists on board research vessel Pelagia. The Black Sea is the largest permanently stratified sea in the world. This is ideal to study the structure of microbial…

NIOZ publications

  • 2017
    Balzano, S.; Villanueva, L.; de Bar, M.; Sinninghe Damsté, J.S.; Schouten, S. (2017). Impact of culturing conditions on the abundance and composition of long chain alkyl diols in species of the genus Nannochloropsis. Org. Geochem. 108: 9-17. https://dx.doi.org/10.1016/j.orggeochem.2017.02.006
    Lipsewers, Y.A.; Vasquez Cardenas, D.; Seitaj, D.; Schauer, R.; Hidalgo-Martinez, S.; Sinninghe Damsté, J.S.; Meysman, F.J.R.; Villanueva, L.; Boschker, H.T.S. (2017). Impact of seasonal hypoxia on activity and community structure of chemolithoautotrophic bacteria in a coastal sediment. Appl. Environ. Microbiol. 83(10): e03517-16. https://dx.doi.org/10.1128/aem.03517-16
    Sinninghe Damsté, J.S.; Rijpstra, W.I.C.; Dedysh, S.N.; Foesel, B.U.; Villanueva, L. (2017). Pheno- and Genotyping of Hopanoid Production in Acidobacteria. Front. Microbiol. 8: 968. https://dx.doi.org/10.3389/fmicb.2017.00968
  • 2016
    Heinzelmann, S.M.; Bale, N.J.; Villanueva, L.; Sinke-Schoen, D.; Philippart, C.J.M.; Sinninghe Damsté, J.S.; Schouten, S.; Van der Meer, M.T.J. (2016). Seasonal changes in the D  /  H ratio of fatty acids of pelagic microorganisms in the coastal North Sea. Biogeosciences 13: 5527-5539. dx.doi.org/10.5194/bg-13-5527-2016
    Kim, J.-H.; Villanueva, L.; Zell, C.; Sinninghe Damsté, J.S. (2016). Biological source and provenance of deep-water derived isoprenoid tetraether lipids along the Portuguese continental margin. Geochim. Cosmochim. Acta 172: 177–204. dx.doi.org/10.1016/j.gca.2015.09.010
    Lipsewers, Y.A.; Hopmans, E.C.; Meysman, F.J.R.; Sinninghe Damsté, J.S.; Villanueva, L. (2016). Abundance and Diversity of Denitrifying and Anammox Bacteria in Seasonally Hypoxic and Sulfidic Sediments of the Saline Lake Grevelingen. Front. Microbiol. 7: 1661. dx.doi.org/10.3389/fmicb.2016.01661
    Lüke, C.; Speth, D.R.; Kox, M.A.R.; Villanueva, L.; Jetten, M.S.M. (2016). Metagenomic analysis of nitrogen and methane cycling in the Arabian Sea oxygen minimum zone. PeerJ 4: e1924. dx.doi.org/10.7717/peerj.1924
    Moore, E.K.; Hopmans, E.C.; Rijpstra, W.I.C.; Villanueva, L.; Sinninghe Damsté, J.S. (2016). Elucidation and identification of amino acid containing membrane lipids using liquid chromatography/high-resolution mass spectrometry. Rapid Comm. Mass Spectrom. 30(6): 739–750. dx.doi.org/10.1002/rcm.7503
    Villanueva, L.; Schouten, S.; Sinninghe Damsté, J.S. (2017). Phylogenomic analysis of lipid biosynthetic genes of Archaea shed light on the ‘lipid divide’. Environ. Microbiol. 19(1): 54-69. dx.doi.org/10.1111/1462-2920.13361
  • 2015
    Heinzelmann, S.M.; Chivall, D.; M'boule, D.; Sinke-Schoen, D.; Villanueva, L.; Sinninghe Damsté, J.S.; Schouten, S.; van der Meer, M.T.J. (2015). Comparison of the effect of salinity on the D/H ratio of fatty acids of heterotrophic and photoautotrophic microorganisms. FEMS Microbiol. Lett. 362(10). dx.doi.org/10.1093/femsle/fnv065
    Heinzelmann, S.M.; Villanueva, L. ; Sinke-Schoen, D.; Sinninghe Damsté, J.S.; Schouten, S.; Van der Meer, M.T.J. (2015). Impact of metabolism and growth phase on the hydrogen isotopic composition of microbial fatty acids. Front. Microbiol. 6: 408. dx.doi.org/10.3389/fmicb.2015.00408
    Moore, E.K.; Hopmans, E.C.; Rijpstra, W.I.C.; Sánchez-Andrea, I.; Villanueva, L.; Wienk, H.; Schoutsen, F; Stams, A.J.M.; Sinninghe Damsté, J.S. (2015). Lysine and novel hydroxylysine lipids in soil bacteria: amino acid membrane lipid response to temperature and pH in Pseudopedobacter saltans. Front. Microbiol. 6: 637. dx.doi.org/10.3389/fmicb.2015.00637
    Moore, E.K.; Villanueva, L.; Hopmans, E.C.; Rijpstra, W.I.C.; Mets, A.; Dedysh, S.N.; Sinninghe Damsté, J.S. (2015). Abundant Trimethylornithine Lipids and Specific Gene Sequences Are Indicative of Planctomycete Importance at the Oxic/Anoxic Interface in Sphagnum-Dominated Northern Wetlands. Appl. Environ. Microbiol. 81(18): 6333-6344. dx.doi.org/10.1128/AEM.00324-15
    Villanueva, L. ; Schouten, S.; Sinninghe Damsté, J.S. (2015). Depth-related distribution of a key gene of the tetraether lipid biosynthetic pathway in marine Thaumarchaeota. Environ. Microbiol. 17(10): 3527–3539. dx.doi.org/10.1111/1462-2920.12508
  • 2014
    Bale, N.; Villanueva, L.; Fan, H.; Hopmans, E.C.; Schouten, S.; Sinninghe Damsté, J.S.; Stal, L.J. (2014). Occurrence and activity of anammox bacteria in surface sediments of the southern North Sea. FEMS Microbiol. Ecol. 89(1): 99–110. hdl.handle.net/10.1111/1574-6941.12338
    Lipsewers, Y.A.; Bale, N.J.; Hopmans, E.C.; Schouten, S.; Sinninghe Damsté, J.S.; Villanueva, L. (2014). Seasonality and depth distribution of the abundance and activity of ammonia oxidizing microorganisms in marine coastal sediments (North Sea). Front. Microbiol. 5: 471 1-12. dx.doi.org/10.3389/fmicb.2014.00472
    Schouten, S.; Villanueva, L.; Hopmans, E.C.; van der Meer, M.T.J.; Sinninghe Damsté, J.S. (2014). Are Marine Group II Euryarchaeota significant contributors to tetraether lipids in the ocean? Proc. Natl. Acad. Sci. U.S.A. 111(41): e4285. dx.doi.org/10.1073/pnas.1416176111
    Villanueva, L.; Besseling, M.; Rodrigo-Gamiz, M.; Rampen, S.; Verschuren, D.; Sinninghe Damsté, J.S. (2014). Potential biological sources of long chain alkyl diols in a lacustrine system. Org. Geochem. 68: 27-30. dx.doi.org/10.1016/j.orggeochem.2014.01.001
    Villanueva, L.; Hopmans, E.C.; Bale, N.; Schouten, S.; Sinninghe Damsté, J.S. (2014). Diversity and distribution of a key sulpholipid biosynthetic gene in marine microbial assemblages. Environ. Microbiol. 16(3): 774-787. dx.doi.org/10.1111/1462-2920.12202
    Villanueva, L.; Rijpstra, W.I.C.; Schouten, S.; Sinninghe Damsté, J.S. (2014). Genetic biomarkers of the sterol-biosynthetic pathway in microalgae. Environmental Microbiology Reports 6(1): 35-44. dx.doi.org/10.1111/1758-2229.12106
    Villanueva, L.; Sinninghe Damsté, J.S.; Schouten, S. (2014). A re-evaluation of the archaeal membrane lipid biosynthetic pathway. Nat. Rev., Microbiol. 12(6): 438-448. dx.doi.org/10.1038/nrmicro3260
    Villanueva, L.; Speth, D.R.; van Alen, T.; Hoischen, A.; Jetten, M.S.M. (2014). Shotgun metagenomic data reveals significant abundance but low diversity of "Candidatus Scalindua" marine anammox bacteria in the Arabian Sea oxygen minimum zone. Front. Microbiol. 5: 31, 1-9. dx.doi.org/10.3389/fmicb.2014.00031
  • 2013
    Buckles, L.K.; Villanueva, L.; Weijers, J.W.H.; Verschuren, D.; Sinninghe Damsté, J.S. (2013). Linking isoprenoidal GDGT membrane lipid distributions with gene abundances of ammonia-oxidizing Thaumarchaeota and uncultured crenarchaeotal groups in the water column of a tropical lake (Lake Challa, East Africa). Environ. Microbiol. 15(9): 2445-2462. dx.doi.org/10.1111/1462-2920.12118
    Moore, E.K.; Hopmans, E.C.; Rijpstra, W.I.C.; Villanueva, L.; Dedysh, S.N.; Wienk, H.; Schoutsen, F; Sinninghe Damsté, J.S. (2013). Novel Mono-, Di-, and Trimethylornithine Membrane Lipids in Northern Wetland Planctomycetes. Appl. Environ. Microbiol. 79(22): 6874-6884. hdl.handle.net/10.1128/AEM.02169-13
  • 2012
    Schouten, S.; Pitcher, A.; Hopmans, E.C.; Villanueva, L.; van Bleijswijk, J.; Sinninghe Damsté, J.S. (2012). Intact polar and core glycerol dibiphytanyl glycerol tetraether lipids in the Arabian Sea oxygen minimum zone: I. Selective preservation and degradation in the water column and consequences for the TEX86. Geochim. Cosmochim. Acta 98: 228-243. https://dx.doi.org/10.1016/j.gca.2012.05.002
  • 2011
    Pitcher, A.; Villanueva, L.; Hopmans, E.C.; Schouten, S.; Reichart, G.J.; Sinninghe Damsté, J.S. (2011). Niche segregation of ammonia-oxidizing archaea and anammox bacteria in the Arabian Sea oxygen minimum zone. ISME J. 5(12): 1896-1904. dx.doi.org/10.1038/ismej.2011.60

Linked projects

SIAM
Funder
Ministerie van OCW
Project duration
1 Jan 2014 - 31 Dec 2023
Microbial lipids: Exploring the natural variability of an unique set of cell constituents
Funder
European Community - European Research Council
Project duration
1 Sep 2016 - 30 Sep 2021
Tracing chemoautotrophic microbes in present and past sedimentary environments
Supervisor
Laura Villanueva
Funder
Netherlands Organization for Scientific Research - Darwin Center
Project duration
1 Jan 2011 - 31 Dec 2014
Biological sources and genetic controls of the paleotemperature proxy TEX86
Supervisor
Laura Villanueva
Funder
Netherlands Organization for Scientific Research
Project duration
1 Nov 2017 - 30 Oct 2021